scicrunch registry exported ontology
type: Ontology
alternative label: screxp
comment: Turtle export of the SciCrunch Registry
version info: 2026-06-22
was generated by: L291

Institution
type: Class

Government granting agency
type: Class

University
type: Class

Institute
type: Class

Resource
type: Class

Organization
type: Class

Commercial Organization
type: Class
subclass of: Organization

TransGenic
type: Organization
type: NamedIndividual
has db xref: nlx_152482
synonym: TransGenic Inc
synonym: Transgenic Inc
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A commercial antibody supplier and knockout mice producer.

monarch-ontologies
type: Resource
type: NamedIndividual
has db xref: nlx_152901
synonym: monarch.owl
abbrev: Monarch Ontologies
IAO_0000115: The set of ontologies used within the Monarch Initiative. MONARCH members are free to add new imports.

Sarah Cannon Research Institute; Tennessee; USA
type: NamedIndividual
has db xref: nlx_158000
synonym: Sarah Cannon Research Institute
abbrev: SCRI
IAO_0000115: A global cancer institute of the Hospital Corporation of America which offers integrated cancer services with access to current therapies.

GE Healthcare
type: Organization
type: NamedIndividual
has db xref: nlx_152368
synonym: Amersham Biosciences
synonym: GE Healthcare Life Sciences
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 10,2024. A commercial antibody supplier and provider of various services., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Neuroshare - Open data specifications and software for neurophysiology
type: Resource
type: NamedIndividual
has db xref: nif-0000-00023
synonym: Neuroshare.org
IAO_0000115: Neuroshare aims to develop a standard for accessing neurophysiological data from any vendor's acquisition device or software. An API is defined, and vendors and communities are encouraged to provide implementations of a library of functions that can read data files collected with that vendor's instrument or software. The neuroshare.org website is a collaborative, vendor-neutral area dedicated to public domain standards and software for neurophysiology.This website is part of an SBIR program funded by the National Institute for Neural Disorders and Stroke and it is currently being administered by Bionic Technologies, LLC. The goals of the SBIR program are to (Phase I) create open library and format standards for neurophysiological experiment data and (Phase II) create a set of free, open-source software tools for low-level handling and processing of neurophysiological data. Upon completion of Phase I and II, neuroshare.org will be maintained by a yet to be determined consortium of government, academic and industry partners. The SBIR was awarded in the fall of 2001 and Phase I officially began in Dec, 2001. The detailed goals of the program are summarized below:Phase I goals :(1) Establish a working group to develop and define the API library of functions.(2) A vendor-neutral web site to facilitate the development of the standards and software and publish the completed products. This site has been dubbed Neuroshare. The home page can be found at neuroshare.sourceforge.net.(3) An open, standardized API library definition for accessing neurophysiology data files. This will allow developers to produce analysis programs that can access a variety of proprietary data formats through libraries supplied by the data format owners. The manner of support will be completely determined by the research groups and vendors that supply the libraries. The Phase I standard was created by a working group consisting of international members from industry and academia. Draft standards were…

University of Algarve; Faro; Portugal
type: NamedIndividual
has db xref: nlx_157657
synonym: Universidade Algarve
synonym: Universidade do Algarve
synonym: University of Algarve
synonym: University of the Algarve
abbrev: UAlg
IAO_0000115: A young state university located in the southern part of Portugal.

G Biosciences
type: Organization
type: NamedIndividual
has db xref: nlx_152367
IAO_0000115: Commercial antibody supplier that provides research materials for projects such as: protein purification, protein analysis, protein estimation assays, DNA purification, plasmid DNA isolation and transformation, protein quantification assays, and coupled assays for methylation. This supplier also provides buffers, reagents, education programs, and training programs.

University at Albany SUNY Labs and Facilities
type: Resource
type: NamedIndividual
has db xref: SciEx_4303
synonym: UAlbany Labs and Facilities
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31, 2025. Facility that conducts wide variety of research programs ranging from cell biology to community-based participatory research. Research is conducted through four academic departments including: the Cancer Research Center, the Prevention Research Center, the Public Health Preparedness Center, the Cardiac Quality improvement initiative and the Center for Health Workforce Studies. This facility also hosts research projects and faculty scholarships to aid Master's and Doctoral students in course work, laboratory rotations and internships.

ncdfFlow
type: Resource
type: NamedIndividual
has db xref: OMICS_05617
synonym: ncdfFlow: A package that provides ncdf based storage for flow cytometry data
IAO_0000115: Software package that provides netCDF storage based methods and functions for manipulation of flow cytometry data.

Computational Neuroscience on the Web
type: Resource
type: NamedIndividual
has db xref: nif-0000-00107
IAO_0000115: Annotated index for computational neurobiology, focusing on compartmental modeling and realistic simulations of biological neural systems. Has resources to find modeling software and software for computational morphology, phase plane and spike train analysis, and web based neuroinformatics. Provides links to major laboratories, researchers, conferences, education and funding for theoretical neurobiology.

Leica | DMRE Fluorescence Microscope
type: Resource
type: NamedIndividual
has db xref: SciRes_000155
synonym: Fluorescence Leica DMRE microscope
abbrev: Leica DMRE microscope
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Microscope that enables bright field and fluorescence imaging options.

Offline Sorter
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_158484
abbrev: OFS
IAO_0000115: Offline spike sorting software. This software tool for viewing and classifying action potential waveforms (spikes) previously collected from single electrodes, stereotrodes and tetrodes accepts file types from many data acquisition companies and software programs.

BSmooth-align
type: Resource
type: NamedIndividual
has db xref: OMICS_01846
IAO_0000115: Software statistics and alignment pipeline that performs the alignment of bisulfite sequence reads and tabulates read-level methylation measurements.

University of Pittsburgh Conte Center for the Neuroscience of Mental Disorders
type: Resource
type: NamedIndividual
has db xref: nlx_144496
synonym: Conte Center for the Neuroscience of Mental Disorders
abbrev: Conte Center
abbrev: Pitt CCNMD
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Conte Center for the Neuroscience of Mental Disorders (CCNMD) at the University of Pittsburgh offers a highly interactive scientific environment for the study of the neurobiology of schizophrenia. Integrates the laboratory and clinical research activities of investigators from the University of Pittsburgh Schools of Medicine and Arts and Sciences and the adjacent Carnegie Mellon University.

4Peaks
type: Resource
type: NamedIndividual
has db xref: OMICS_01015
IAO_0000115: Software application for viewing and editing sequence trace files.

CSDeconv
type: Resource
type: NamedIndividual
has db xref: biotools:csdeconv
has db xref: OMICS_00436
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software application that maps transcription factor binding sites from ChIP-seq data to high resolution using a blind deconvolution approach.

Tablet
type: Resource
type: NamedIndividual
has db xref: OMICS_00896
synonym: Tablet - Next Generation Sequence Assembly Visualization
IAO_0000115: A lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments.

Midwest Transplant Network
type: Organization
type: NamedIndividual
has db xref: nlx_87553
abbrev: MTN
IAO_0000115: An organization that specifically operates in Kansas and the the western half of Missouri, and provides help with connecting the community to organ and tissue procurement, as well as generates general public awareness. This organization is a federally certified non-profit Organ Procurement Organization (OPO) that is meant to help in several facets of transplant and procurement services.

NeuroTribes
type: Resource
type: NamedIndividual
has db xref: nlx_91543
IAO_0000115: Steve Silberman's personal blog highlighting science, culture, politics and neurodiversity. Steve is an investigative reporter for Wired and other national magazines.

Ludwig Boltzmann Cluster Translationale Onkologie
type: Resource
type: NamedIndividual
has db xref: nlx_143958
abbrev: Ludwig Boltzmann Cluster Translational Oncology
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. The projected cluster includes the LBIs for Applied Cancer Research, Clinical Oncology and Photodynamic Therapy, Gynecology and Gynecologic Oncology, Stem Cell Transplantation and Surgical Oncology. The aim of the projected cluster Translational Oncology is the cooperative investigation of genetic and molecular biological characteristics of the tumor cells involved in minimal residual disease (MRD) in vitro and translation of the experimental and diagnostic results into the clinical practice involving therapeutic modalities with the newest generation of antitumoral drugs. Minimal residual disease is the designation for the occurrence of a low number of tumor cells remaining clinically undetected following curative therapy that give rise to tumor relapses. MRD is a central question in cancer therapy, since a major subpopulation of patients which underwent curative resection and therapy ultimately relapse and would have received more aggressive adjuvant therapy, provided that residual disease had been clearly proven. Otherwise low-risk patients would have not been treated aggressively in an adjuvant setting. MRD can be detected by methods in bone marrow or by extremely sensitive PCR (polymerase-chain-reaction)-based methods in peripheral blood. PCR-based methods allow for the characterization of tumor-specific gene expression in circulating tumor cells and thereby provide additional information in regard to malignity of cells and prognosis. The different participating institutions have extensive experience in patient care, organization of clinical studies and laboratory investigation. In particular, expert knowledge in stem cell transplantation and histological detection of MRD, multicentric clinical testing of new anticancer drugs, specialized treatment of various selected tumor entities such as neuroendocrine tumors, gene expression analysis of circulating tumor cells and tumor signatures, and in vit…

MNI Podcasts
type: Resource
type: NamedIndividual
has db xref: nlx_91897
synonym: Montreal Neurological Institute Podcasts
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Collection of podcasts which features experts of the Montreal Neurological Institute and Hospital talking about their research, along with important issues and current events regarding it.

PAMGO
type: Resource
type: NamedIndividual
has db xref: nlx_92278
synonym: PAMGO - Plant-Associated Microbe Gene Ontology
synonym: Plant Associated Microbe Gene Ontology
synonym: Plant-Associated Microbe Gene Ontology
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 10, 2016. A consortium that created universal descriptors to describe functionally similar gene products and their attributes across all organisms. In 2004, the PAMGO interest group joined the GO consortium to extend the GO to include terms describing various processes related to microbe-host interactions. The organization uses a controlled vocabulary to set a process in place to describe plant associated microbes and their interactions with their plant-hosts. These higher order terms can describe gene products of all types of symbionts (e.g. parasites, commensals, and mutualists), including prokaryotes and eukaryotes that associate with plant or animal hosts. This initiative is a multi-institutional collaborative effort to pool information and research in: the bacteria Dickeya dadantii, Pseudomonas syringae pv tomato and Agrobacterium tumefaciens, the fungus Magnaporthe grisea, the oomycetes Phytophthora sojae and Phytophthora ramorum, and the nematode Meloidogyne hapla.

EM-DECODER
type: Resource
type: NamedIndividual
has db xref: nlx_154297
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A haplotype inference program.

Cleveland Clinic Lerner Research Institute Labs and Facilities
type: Resource
type: NamedIndividual
has db xref: SciEx_4372
synonym: Cleveland Clinic Lerner Research Institute Labs & Facilities
synonym: Cleveland Clinic LRI Labs & Facilities
synonym: Cleveland Clinic LRI Labs and Facilities
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023.Offers services in peptide synthesis, peptide modification, purification and quality analysis, N-terminal protein sequencing by Edman degradation, biomolecular interaction analysis and equilibrium and kinetic measurements.

GenomicRanges
type: Resource
type: NamedIndividual
has db xref: OMICS_01161
has db xref: SCR_018096
synonym: GenomicRanges - Representation and manipulation of genomic intervals
IAO_0000115: Software package that defines general purpose containers for storing genomic intervals as well as more specialized containers for storing alignments against a reference genome.

Epilepsy Foundation
type: Resource
type: NamedIndividual
has db xref: nif-0000-10220
synonym: Epilepsy
IAO_0000115: The Epilepsy Foundation of America is the national voluntary agency dedicated solely to the welfare of the almost 3 million people with epilepsy in the U.S. and their families. The organization works to ensure that people with seizures are able to participate in all life experiences; to improve how people with epilepsy are perceived, accepted and valued in society; and to promote research for a cure. :Typical of the Foundations national programs are its Jeanne A. Carpenter Epilepsy Legal Defense Fund, the H.O.P.E. (Helping Other People with Epilepsy) Mentoring Program, a Public Policy Institute, Seniors and Womens Health Initiatives, the Kids Speak Up advocacy program, a school personnel training program, outreach to youth and to the Hispanic community, employment programs and a research grants program. Services commonly provided in local communities are information and referral, counseling, patient and family advocacy, school and community education, support groups and camps for children. Its Web site offers the most comprehensive, medically approved consumer information about epilepsy and seizures on the Internet and is the trusted source for millions of people who seek reliable information about epilepsy. : Each year the Foundation also invites research investigators to apply for grants and fellowships to test new ideas and follow new research leads. The applications, more than a hundred in an average year, are ranked according to merit by a blue ribbon panel of research scientists, and funded according to available resources. Additionally, the Epilepsy Foundation offers a series of training fellowships in basic, clinical and behavioral science to scientists at the start of their careers. These fellowships, awarded to young people at the nation's leading research institutes, have in many cases been the first steps on a lifetime commitment to solving the medical and scientific puzzle of why epilepsy develops and how it can be treated or prevented. Specifically, th…

Multiple Sclerosis Discovery Forum
type: Resource
type: NamedIndividual
has db xref: nlx_156702
synonym: MS Discovery Forum
abbrev: MSDF
IAO_0000115: Portal that aims to inspire connections, clinical advances and accelerate progress toward multiple sclerosis cures. MSDF updates its site with news and information about topics relevant to multiple sclerosis and hosts discussions about controversial subjects with the goal of spreading information and enabling collaboration between researchers. MSDF provides access to drug development pipelines, tissue repositories, the MS gene, animal models, and clinical trials.

SNPSVM
type: Resource
type: NamedIndividual
has db xref: OMICS_03838
IAO_0000115: A support vector machine for calling variants from next-gen sequencing data. It takes as input a BAM-formatted alignment of sequencing reads, and emits a VCF formatted file describing where all the SNPs (single nucleotide polymorphisms) are.

Dipy
type: Resource
type: NamedIndividual
has db xref: nlx_155745
synonym: Diffusion Imaging In Python
synonym: NIPY Diffusion Imaging Analysis
abbrev: DIPY
IAO_0000115: Software Python package for analyzing diffusion data. Software library for analysis of diffusion MRI data.

ReadqPCR
type: Resource
type: NamedIndividual
has db xref: biotools:readqpcr
has db xref: OMICS_03936
synonym: ReadqPCR - Read qPCR data
IAO_0000115: A software package that provides functions to read raw RT-qPCR data of different platforms.

SP-Designer
type: Resource
type: NamedIndividual
has db xref: OMICS_03932
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An open source software program for the design of specific PCR primer pairs from a DNA sequence alignment containing sequences from various taxa.

BlackOPs
type: Resource
type: NamedIndividual
has db xref: OMICS_01229
synonym: BlackOPs: RNA-Seq Variant Blacklist Tool
IAO_0000115: Open source software tool that simulates experimental RNA-seq and DNA whole exome sequences derived from reference genome, aligns these sequences by custom parameters, detects variants and outputs blacklist of positions and alleles caused by mismapping. Used to characterize mappability of RNA-Seq reads and create blacklist of genomic positions of mismapped reads. This blacklist is used to filter potential false positives from variant or RNA editing calls.

Mouse Single Nucleotide Polymorphism Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-20984
synonym: Mouse Single Nucleotide Polymorphism
abbrev: Mouse SNP
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. This website contains a database of the mouse SNP. DNA sequencing was performed along with genotyping. There is information on genotyping, mouse strain, and haplotype map.

Patchmaster
type: Resource
type: NamedIndividual
has db xref: SciRes_000168
synonym: PATCHMASTER
IAO_0000115: Multi-channel data acquisition software. Multi-channel stimulation/acquisition software with programmable experiment control and automation, software Lock-in amplifier and Photometry/Imaging extension. PATCHMASTER supports all HEKA amplifiers and data acquisition hardware.

RCSB PDB Software Tools
type: Resource
type: NamedIndividual
has db xref: nif-0000-31399
synonym: RCSB Software Tools
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Information Portal to Biological Macromolecular Structures provides variety of software tools made available through the RCSB. These tools include: data extraction and deposition preparation tools, data format conversion and validation tools, data parsing tools, dictionary and data management tools, visualization tools that support PDBx/mmCIF, and other PDBx/mmCIF software library tools.

R Manuals
type: Resource
type: NamedIndividual
has db xref: OMICS_01764
synonym: The R Manuals
IAO_0000115: Manuals for R created on Debian Linux that can be downloaded as PDF files, EPUB files (for R-devel and R-patched), or directly browsed as HTML. They may differ from the manuals for Mac or Windows on platform-specific pages, but most parts will be identical for all platforms.

TADS - Treatment for Adolescents with Depression Study
type: Resource
type: NamedIndividual
has db xref: nlx_146236
synonym: Treatment for Adolescents with Depression Study
synonym: Treatment for Adolescents with Depression Study (TADS)
abbrev: TADS
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Multi-site clinical research study examining the short- and long-term effectiveness of an antidepressant medication and psychotherapy alone and in combination for treating depression in adolescents ages 12 to 17. For teens treated in TADS, the trial is designed to provide best-practice practical care for depression.

University of Tennessee Genome Science and Technology Graduate Program
type: Resource
type: NamedIndividual
has db xref: nlx_149162
synonym: Graduate School of Genome Science and Technology
synonym: University of Tennessee Genome Science & Technology
synonym: University of Tennessee Genome Science Technology
synonym: UT Genome Science & Technology
synonym: UT-ORNL Graduate School of Genome Science and Technology
synonym: UTK Genome Science & Technology
abbrev: UT Knoxville GST
abbrev: UTK GST
IAO_0000115: Graduate School of Genome Science and Technology (GST) is a Life Science graduate program founded on two premises. First, whole-genome sequences and related large-scale datasets have transformed how we perform biological research, a trend that is gathering momentum and is anticipated to frame the way the biology research is accomplished for many years to come. Second, advances in technology, whether at the level of instrumentation, computation, or wet lab reagents, have long been a powerful driving force in biology. The GST program is home to faculty mentors from many walks of life. The virulence factors of pathogenic fungi and the engineering of photosynthetic reaction complexes for bioenergy harvesting are just two examples from the cornucopia of research projects being pursued in GST.

Institute for Magnetic Resonance Safety, Education and Research
type: Organization
type: NamedIndividual
has db xref: nif-0000-10678
synonym: IMRSER
IAO_0000115: The Institute for Magnetic Resonance Safety, Education, and Research (IMRSER) was formed in response to the growing need for information and research on matters pertaining to magnetic resonance (MR) safety. The IMRSER is the first independent, multidisciplinary, professional organization devoted to promoting awareness, understanding, and communication of MR safety issues through education and research. Mission Statement To promote awareness and understanding of MR safety, To disseminate information regarding current and emerging MR safety issues, To develop and provide materials and resources to facilitate MR safety-related education and training, To respond to critical MR safety issues with a sense of urgency, and To advance the field of MR safety through support of scientific research. Functions and activities of the IMRSER include development of up-to-date MR safety materials and dissemination of this information to the MR community. This is accomplished predominantly through the efforts of the Advisory Boards. Members of the Advisory Boards of the Institute for Magnetic Resonance Safety, Education, and Research (IMRSER) are charged with creating recommendations, guidelines, position papers, and educational materials pertaining to existing or emerging MR safety issues. This is achieved by utilizing the pertinent peer-reviewed literature and by relying on each members extensive clinical, research, or other appropriate experience. Notably, documents developed by the IMRSER incorporate MR safety guidelines and recommendations created by the International Society for Magnetic Resonance in Medicine (ISMRM), the American College of Radiology (ACR), the Food and Drug Administration (FDA), the National Electrical Manufacturers Association (NEMA), the Medical Devices Agency (MDA), the International Electrotechnical Commission (IEC), and other similar organizations. The IMRSERs rigorous development and review process for MR safety documents ensures that authoritative and r…

GUARDD
type: Resource
type: NamedIndividual
has db xref: biotools:guardd
has db xref: OMICS_04020
synonym: Graphical User-friendly Analysis of Relaxation Dispersion Data
IAO_0000115: MATLAB software designed to organize, automate, and enhance the analytical procedures which operate on CPMG RD NMR data.

MTOPS Prostate Samples Analysis Consortium
type: Resource
type: NamedIndividual
has db xref: nlx_152864
synonym: MTOPS Prostate Samples Analysis (MPSA) Consortium
abbrev: MPSA Consortium
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Cross-disciplinary, multi-institutional network with wide range of experts to analyze serum and tissue samples collected in the Medical Therapy of Prostatic Symptoms (MTOPS) trial. Consortium aims to discover and validate biomarkers for the detection, risk assessment, and disease progression assessment of benign prostatic hyperplasia (BPH).

APSampler
type: Resource
type: NamedIndividual
has db xref: OMICS_04023
IAO_0000115: A software tool that allows multi-locus and multi-level association analysis of genotypic and phenotypic data.

3DMeshMetric
type: Resource
type: NamedIndividual
has db xref: nlx_155578
IAO_0000115: Software visualization tool based on the VTK library. Its main feature is to measure and display surface-to-surface distance between two triangle meshes using user-specified uniform sampling. Offers all the basic tools to visualize meshes such as color, opacity, smoothing, down sampling or type of representation.

Cbrowse
type: Resource
type: NamedIndividual
has db xref: OMICS_04048
IAO_0000115: Software providing an AJAX-based web browser for visualizing and analyzing transcriptome assemblies and contigs.

UTR
type: Resource
type: NamedIndividual
has db xref: OMICS_04052
IAO_0000115: Software application that uses change point model for detecting 3-prime UTR changes by RNA-Seq.

flowCL
type: Resource
type: NamedIndividual
has db xref: OMICS_05594
synonym: flowCL - Semantic labelling of flow cytometric cell populations
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for semantic labelling of flow cytometric cell populations.

CG-Pipeline
type: Resource
type: NamedIndividual
has db xref: OMICS_04062
IAO_0000115: A software tool for assembling genome sequence data and running feature prediction and annotation tools on the assembly.

Batman-Seq
type: Resource
type: NamedIndividual
has db xref: OMICS_00651
synonym: Basic Alignment Tool for MAny Nucleotides
IAO_0000115: A fast BWT-based short reads mapping tools which uses additional statistical method to model error profile of the sequencing experiment.

iMethy
type: Resource
type: NamedIndividual
has db xref: OMICS_00628
IAO_0000115: Software for investigation and visualization of DNA methylation by high-throughput bisulfite sequencing.

dprimer
type: Resource
type: NamedIndividual
has db xref: OMICS_02342
IAO_0000115: A command line software utility for designing degenerate PCR primers against multiple, aligned sequences. Its primary use case is searching for a family of related pathogens in a host tissue sample.

flowBin
type: Resource
type: NamedIndividual
has db xref: OMICS_05593
synonym: flowBin - Combining multitube flow cytometry data by binning
IAO_0000115: A software package to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them. It establishes common bins across tubes in terms of the common markers, then determines expression within each tube for each bin in terms of the tube-specific markers.

eSLDB - eukaryotic Subcellular Localization database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02815
synonym: eukaryotic Subcellular Localization database
abbrev: eSLDB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 22,2022. database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions.

CorMut
type: Resource
type: NamedIndividual
has db xref: biotools:cormut
has db xref: OMICS_03636
synonym: CorMut - Detect the correlated mutations based on selection pressure
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software package for computing correlated mutations based on selection pressure. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network.

ChIPmeta
type: Resource
type: NamedIndividual
has db xref: OMICS_02172
synonym: ChIPmeta with HHM
IAO_0000115: Software using a Hierarchical hidden Markov model for jointly analyzing ChIP-chip and ChIP-seq datasets.

FACS
type: Resource
type: NamedIndividual
has db xref: biotools:facs
has db xref: OMICS_02147
synonym: Fast and Accurate Classification of Sequences
IAO_0000115: Software for classification of Sequences using Bloom filters that can accurately and rapidly align sequences to a reference sequence.

metaSeq
type: Resource
type: NamedIndividual
has db xref: OMICS_02123
IAO_0000115: Software package for meta-analysis of RNA-Seq count data in multiple studies. The probabilities by one-sided NOISeq are combined by Fisher's method or Stouffer's method.

Scholarly Ontologies Project
type: Resource
type: NamedIndividual
has db xref: nlx_149632
synonym: Scholarly Ontologies
synonym: ScholOnto Project
abbrev: ScholOnto
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 25,2022. Project (2001-2004) to build and deploy a prototype infrastructure for making scholarly claims about the significance of research documents. "Claims" are made by making connections between ideas. Any claim is open to counterarguments. The connections are grounded in a discourse/argumentation ontology, which makes possible innovative services for navigating, visualizing and analyzing the network as it grows. They have evolved a suite of prototype tools for modelling conceptual networks of ideas and arguments, publishing them for reuse and argumentation, and navigating, searching and filtering this repository as it grows. Some of these are freely available to play with, but WARNING! they are no longer able to support them. The system they have built is called ClaiMaker. Others include ClaimSpotter, ClaiMapper, ClaimFinder, ClaimBlogger and ClaiMaker Microsoft Word plug-in. Additionally, the ScholOnto RDF Schema is available, http://projects.kmi.open.ac.uk/scholonto/resources/Scholonto2.rdfs User Communities: They envisage such a tool as having potential not only in scholarly publishing, but for corporate knowledge analysis, and in education. Complementary work: ScholOnto's focus on net-centric representations of research is complemented by work on augmenting more conventional textual documents, with threaded commentary and debate. An open source web publishing tool is available called D3E (Digital Document Discourse Environment). Many applications are illustrated on the site, including the award-winning Journal of Interactive Media in Education.We are no longer able to support tools, so are not able to assist if you have problems or lose data.

Dissect
type: Resource
type: NamedIndividual
has db xref: biotools:dissect
has db xref: OMICS_01346
synonym: DIScovery of Structural Events Containing Transcripts
synonym: Dissect: DIScovery of Structural Events Containing Transcripts
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions.

Fusion Analyser
type: Resource
type: NamedIndividual
has db xref: biotools:fusionanalyser
has db xref: OMICS_01347
synonym: FusionAnalyser
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16, 2023. Software used to detect gene fusions from paired-end RNA-Seq data.

FusionCatcher
type: Resource
type: NamedIndividual
has db xref: biotools:fusioncatcher
has db xref: OMICS_01348
IAO_0000115: Software that searches for novel/known fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples.

GASV
type: Resource
type: NamedIndividual
has db xref: biotools:gasv
has db xref: OMICS_01352
synonym: Geometric Analysis of Structural Variants
IAO_0000115: Software tool for identifying structural variants (SVs) from paired-end sequencing data.GASV distribution includes three components that are typically run in succession: the BAM file of unique paired-read mappings is processed; structural variants are identified by clustering discordant fragments; and a probabilistic algorithm improves the specificity of GASV predictions.

GHOSTM
type: Resource
type: NamedIndividual
has db xref: OMICS_02563
synonym: ghostm: GPU-based HOmology Search Tool for Metagenomics
synonym: GPU-based HOmology Search Tool for Metagenomics
IAO_0000115: Software homology search tool for huge short reads generated by next-generation sequencers.Can detect remote homologs like BLAST and is about 40 times more efficient than BLAST by using a GPU-computing technique.

Colorado College Department of Psychology
type: Organization
type: NamedIndividual
has db xref: nif-0000-00391
abbrev: CCDPy
IAO_0000115: A department within Colorado College that is dedicated to providing academic programs for undergraduate education. Students are educated in a variety of research techniques, statistics and design experiments.

Cross Collaboration Initiatives at the NIH
type: Resource
type: NamedIndividual
has db xref: nif-0000-00402
synonym: National Institutes of Health Division of Program Coordination Planning and Strategic Initiatives
synonym: NIH Division of Program Coordination Planning and Strategic Initiatives
abbrev: DPCPSI
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. NIH Division of Program Coordination Planning and Strategic Initiatives.

MPScope
type: Resource
type: NamedIndividual
has db xref: nlx_155796
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Software suite for custom-built multiphoton microscopes available as freeware for the Wintel platform. The MPScope package features the acquisition software MPScan, analysis program MPView and several software utilities.

nFuse
type: Resource
type: NamedIndividual
has db xref: OMICS_01353
synonym: nFuse: Discovery of Complex Genomic Rearrangements in Cancer
IAO_0000115: Software that predicts fusion transcripts and associated CGRs from matched RNA-seq and Whole Genome Shotgun Sequencing (WGSS).

Image Registration Toolkit
type: Resource
type: NamedIndividual
has db xref: nlx_155983
synonym: Medical Image Registration ToolKit
abbrev: IRTK
abbrev: MIRTK
IAO_0000115: Software image processing toolkit. Provides collection of libraries and command-line tools to assist in processing and analyzing imaging data. Used for adult and neonatal brain MR image registration, including rigid, affine, and non-rigid transformations, as well as reconstruction of cortical surface meshes.

PD5
type: Resource
type: NamedIndividual
has db xref: OMICS_02366
synonym: PD5: A Software Library for the Development of Primer Design Applications
IAO_0000115: An open-source C++ software library of classes for the design and analysis of primers suitable for a wide range of PCR applications.

GeneTex
type: Organization
type: NamedIndividual
has db xref: nlx_152372
IAO_0000115: An antibody supplier for the purposes of life science and biomedical research. This company has a wide variety of immunological reagents that focus on areas of research such as cancer, cell biology, epigenetics, immunology and infectious diseases.

Genemed
type: Organization
type: NamedIndividual
has db xref: nlx_152371
IAO_0000115: A supplier of cancer and infectious disease diagnostic reagents. The company also provides services such as tissue-based and molecular diagnostics to their partners to accelerate their in vitro diagnostic device (IVD) product development and commercialization.

National Laboratory for Scientific Computing; Rio de Janeiro; Brazil
type: Organization
type: NamedIndividual
has db xref: nlx_155570
synonym: Laboratorio Nacional de Computacao Cientifica
synonym: Laboratório Nacional de Computação Científica
synonym: National Laboratory for Scientific Computing
abbrev: LNCC
IAO_0000115: Brazilian laboratory dedicated to conducting research, developing and training of human resources for scientific computing with special emphasis on construction and application of mathematical and computational models for solving scientific and technological problems.

Patchwork
type: Resource
type: NamedIndividual
has db xref: biotools:patchwork
has db xref: OMICS_02118
IAO_0000115: Software tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, ~4x, low tumor cell content or are aneuploid. Patchwork takes BAM files as input whereas PatchworkCG takes input from CompleteGenomics files. TAPS performs the same analysis as Patchwork but for microarray data.

QuadGT
type: Resource
type: NamedIndividual
has db xref: OMICS_02108
IAO_0000115: Software package for calling single-nucleotide variants in four sequenced genomes comprising a normal-tumor pair and the two parents. Genotypes are inferred using a joint model of parental variant frequencies, de novo germline mutations, and somatic mutations. The model quantifies the descent-by-modification relationships between the unknown genotypes by using a set of parameters in a Bayesian inference setting. Note that you can use it on any subset of the four related genomes, including parent-offspring trios, and normal-tumor pairs without parental samples.

VariantAnnotation
type: Resource
type: NamedIndividual
has db xref: OMICS_02073
synonym: VariantAnnotation - Annotation of Genetic Variants
IAO_0000115: Software package to annotate variants, compute amino acid coding changes, and predict coding outcomes.

ReQON
type: Resource
type: NamedIndividual
has db xref: OMICS_02033
synonym: Recalibrating Quality Of Nucleotides
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format.

SnowsShoes-FTD
type: Resource
type: NamedIndividual
has db xref: OMICS_01356
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023. A free bioinformatics software tool to help identify fusion transcripts from paired-end transcriptome sequencing data. The source codes of SnowShoes-FTD are provided in two formats: one configured to run on the Sun Grid Engine for parallelization with shorter run time, and the other formatted to run on a single LINUX node.

timecourse
type: Resource
type: NamedIndividual
has db xref: biotools:timecourse
has db xref: OMICS_01980
synonym: timecourse - Statistical Analysis for Developmental Microarray Time Course Data
IAO_0000115: Software functions for data analysis and graphical displays for developmental microarray time course data.

SOAPfuse
type: Resource
type: NamedIndividual
has db xref: OMICS_01357
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE.Documented on August 23,2022. An open source tool developed for genome-wide detection of fusion transcripts from human being paired-end RNA-Seq data. This tool is a part of a larger set of tools to efficiently align oligonucleotides onto reference sequences .

SOAPfusion
type: Resource
type: NamedIndividual
has db xref: biotools:soapfusion
has db xref: OMICS_01358
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 22,2022. An open source software tool for fusion discovery with paired-end RNA-Seq reads. The tool follows a different strategy by finding fusions directly and verifying them, differentiating it from all other existing tools by finding the candidate regions and searching for the fusions afterwards.

Academia.edu
type: Resource
type: NamedIndividual
has db xref: nlx_152526
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Social networking site for academic researchers that allows researchers to share papers, find people working in a field and see analytics on papers etc

StratML
type: Resource
type: NamedIndividual
has db xref: nlx_152542
synonym: Strategy Markup Language
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. XML vocabulary and schema for strategic plans, designed to create a world wide web of intentions, stakeholders and results.

VectorValuedHistogramNormalizer
type: Resource
type: NamedIndividual
has db xref: nlx_156014
IAO_0000115: Software tool for MRI intensity standardization by aligning histograms of higher dimensions. The methods defined in http://www5.informatik.uni-erlangen.de/Forschung/Publikationen/2006/Jaeger06-ANM.pdf are implemented as and ITK filter.

Adaptively Sampled Particle Fluids
type: Resource
type: NamedIndividual
has db xref: nif-0000-23328
abbrev: ASPF
IAO_0000115: Scalable particle fluid simulation code for Lagrangian particle-based fluid simulation. This adaptive sampling strategy allows using smaller (and thus more) particles in geometrically complex regions, while less particles are used for thick flat fluid volumes. Additionally, a novel distance-based particle surface definition is implemented which hides the particle granularity and allows dynamic resampling near the fluid-air interface. The code is implemented in C++ and should compile on Linux.

pFind Studio: pLink
type: Resource
type: NamedIndividual
has db xref: biotools:pLink-2
has db xref: OMICS_02404
synonym: pLink
synonym: pLink2
synonym: pLink (pFind Studio)
IAO_0000115: Software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Spotfinder
type: Resource
type: NamedIndividual
has db xref: OMICS_00848
synonym: TIGR Spotfinder
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software designed for the rapid, reproducible and computer-aided analysis of microarray images and the quantification of gene expression.

RNA STRAND-The RNA secondary STRucture and statistical ANalysis Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-03415
synonym: RNA secondary STRucture and statistical ANalysis Database
abbrev: RNA STRAND
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A scientific community-crowdsourced database containing the RNA secondary structures of known types and organisms. It is meant to provide a simple and powerful way to analyze, search and update a shared repository of information.

rSNP Guide
type: Resource
type: NamedIndividual
has db xref: biotools:rsnp_guide
has db xref: nif-0000-03428
IAO_0000115: A system of databases which stores information on the influence of mutations in regulatory gene regions . This tool helps recognize protein binding sites that are being altered by mutation. It has four cross-linked sub databases that focus on specific aspects including: (1) the effect of single nucleotide mutations in regulatory gene regions and their interaction with nuclear proteins; (2) references to original publications on the subject; (3) the experimental details of these publications; and (4) the protocols of these experiments. This resource is aimed at providing information to further research on the influence of specific sequence alterations on disease susceptibility, drug resistance and healthcare.

GOALIE
type: Resource
type: NamedIndividual
has db xref: nlx_149255
synonym: Generalized Ontological Algorithmic Logical Invariants Extractor
synonym: Generalized Ontological Algorithmic Logical Invariants Extractor (GOALIE)
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Generalized Ontological Algorithmic Logical Invariants Extractor (GOALIE) is a tool for the construction of time-course dependent enrichments. Requires an ODBC connection to an instance of the GO database. Platform: Windows compatible, Mac OS X compatible, Linux compatible

Danish Multiple Sclerosis Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_143736
synonym: Danish Multiple Sclerosis Center Genetics in MS
synonym: Danish Multiple Sclerosis Center: Genetics in MS
synonym: DMSC Genetics in MS
synonym: DMSC Genetics in Multiple Sclerosis
synonym: DMSC: Genetics in MS
abbrev: Danish MS Biobank
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. We have collected DNA for more than 15 years, and today we have DNA from more than 1,800 Danish MS patients and 1,200 controls, all kept in the Danish Multiple Sclerosis Biobank in DMSC. In order to increase the sample size for genetic testing, we have participated in the Nordic MS Genetic Network since 1994, and today the Nordic material consists of more than 6,000 MS cases and 6,000 controls. The research in DMSC is focused on the candidate gene approaches and the genetic influence on the differences in treatment response. We are part of the IMSGC (International Multiple Sclerosis Genetic Consortium) and the Wellcome Trust Case Control Consortium (WTCCC), where 23 research groups from 15 countries are performing the largest set of MS genome-wide association study (GWAS), genotyping 11,000 cases and 11,000 controls using 500,000 SNP chip. Primary results have elucidated associations to more than 100 gene variations (SNPs). Following this collaboration we are joining the Immunochip Consortium, where 1,000 Danish cases and 1,000 Danish controls participate in a large scale genetic analysis, investigating best genes/regions/SNPs in MS together with other international MS research groups and 9 other autoimmune diseases research groups, looking for shared autoimmune genes. The risk of MS has been increasing over the last 50 years, especially among women older than 40 years. On this background we have initiated a project looking at aspects of gender differences, including different treatment responses. Furthermore, we have initiated a large-scale vitamin D project, investigating gene variations within the vitamin D pathway, and the importance of vitamin D in clinical and immunological disease activity. In addition, we have collected more than 800 questionnaires from MS patients dealing in detail with lifestyle and environmental exposure for a project studying gene-environmental interactions.

AbMining ToolBox
type: Resource
type: NamedIndividual
has db xref: OMICS_04063
IAO_0000115: Python scripts to analyze antibody libraries sequenced by next generation sequencing methods (454, Ion Torrent, MiSeq).

SNAVI
type: Resource
type: NamedIndividual
has db xref: biotools:snavi
has db xref: OMICS_04122
synonym: Signaling Networks Analysis and Visualization
IAO_0000115: Desktop application for analysis and visualization of large-scale cell signaling networks.

MetAssign
type: Resource
type: NamedIndividual
has db xref: OMICS_04679
IAO_0000115: Software that combines information from the mass-to-charge ratio, retention time and intensity of each peak, together with a model of the inter-peak dependency structure, to increase the accuracy of peak annotation. The software has been implemented as part of the mzMatch metabolomics analysis pipeline, which is available for download.

EPIGEN
type: Resource
type: NamedIndividual
has db xref: nlx_143740
synonym: EPIGEN Consortium
synonym: EPIGEN: An international consortium dedicated to tackling epilepsy through genetics
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Group of clinical care and epilepsy research centers who are committed to improving the lives of people with epilepsy through an understanding of the genetics of epilepsy. The consoritum was in an effort to speed discovery to epilepsy genetics by pooling the resources of several research centres., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Neuron Registry Curator Interface
type: Resource
type: NamedIndividual
has db xref: nif-0000-00540
synonym: INCF Neuron Registry
abbrev: NRCI
IAO_0000115: Repository of neuron types characterized by machine-readable part-relation-value triple-based neuron properties. A Curator Interface facilitates the direct knowledge transfer of information from the participating neuroscientist for entry into the Neuron Registry.

JChemPaint
type: Resource
type: NamedIndividual
has db xref: OMICS_04959
abbrev: JCP
IAO_0000115: Chemical 2D structure editor and viewer application/applet based on the Chemistry Development Kit (CDK).

siRNArules
type: Resource
type: NamedIndividual
has db xref: OMICS_04742
IAO_0000115: An open-source JAVA program that is surprisingly efficient at predicting active siRNAs.

AutoPrime
type: Resource
type: NamedIndividual
has db xref: OMICS_02333
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Server to rapidly design primers for real-time PCR measurement of eukaryotic expression.

Cognitorium
type: Resource
type: NamedIndividual
has db xref: nlx_152561
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented October 28, 2015. Interactive, informative and educational community platform dedicated to cognitive science or the multidisciplinary exploration of the mind. This online platform, will help gather and link information providing a thorough and reliable source of information for students and professionals in the field, as well as help bridge the gap between academia and the society. Due to the multidisciplinary nature of cognitive science, the work is becoming increasingly specialized. Therefore to keep an eye on the bigger picture, it seems necessary to bring the discoveries of various disciplines together in one place, look at their similarities and differences and discuss them for future directions.

BMSR Workshops
type: Resource
type: NamedIndividual
has db xref: nlx_152568
synonym: Biomedical Simulations Resource Workshops
IAO_0000115: Forum for the dissemination of leading-edge methodologies for modeling and simulation in biomedicine, they serve to foster substantive interactions among Workshop attendees.

BMSR Short Courses
type: Resource
type: NamedIndividual
has db xref: nlx_152569
synonym: Biomedical Simulations Resource Short Courses
IAO_0000115: Short courses to train the broader biomedical research community in the modeling and simulation methodologies developed by Resource Scientists and others.

RmiR.Hs.miRNA
type: Resource
type: NamedIndividual
has db xref: OMICS_05797
synonym: RmiR.Hs.miRNA: Various databases of microRNA Targets
IAO_0000115: Software package for various databases of microRNA Targets.

MysiRNA-designer
type: Resource
type: NamedIndividual
has db xref: OMICS_04748
IAO_0000115: Software that integrates several factors in an automated work-flow considering mRNA transcripts variations, siRNA and mRNA target accessibility, and both near-perfect and partial off-target matches.

Tissue Engineering Resource Center
type: Resource
type: NamedIndividual
has db xref: nlx_152637
synonym: TERC: Tissue Engineering Resource Center
abbrev: TERC
IAO_0000115: Biomedical technology research center designed to advance basis and clinical aspects of tissue engineering, to provide training for investigators and dissemination of scientific findings and new techniques. Expertise and facilities are focused on research, problem solving and training for biomedical community through integrated systems approach to challenges in tissue engineering. Mission for TERC is to engineer human tissues for medical impact. Includes Functional human tissue grafts: human tissues for application in regenerative medicine;Human disease models in vitro: in vitro models of human disease to provide new experimental tools to understand progression of disease, effects and mechanisms of drug action; Biological materials research: bioengineering tools for cell biology studies in context of tissue development, regeneration and disease.

National MS Society
type: Resource
type: NamedIndividual
has db xref: nlx_143693
synonym: National Multiple Sclerosis Society
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Society helps people affected by Multiple Sclerosis by funding cutting-edge research, driving change through advocacy, facilitating professional education, and providing programs and services that help people with MS and their families move their lives forward.

University of California at San Diego Cognitive Science Graduate Student Fellowship Opportunities
type: Resource
type: NamedIndividual
has db xref: nif-0000-10500
synonym: UCSD Cognitive Science Fellowships
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. This resource is a frequently updated listing of graduate student in cognitive science fellowship opportunities. For current opportunities, please see the PDF document.

Laser Biomedical Research Center
type: Resource
type: NamedIndividual
has db xref: nlx_152645
synonym: Laser Biomedical Research Center (LBRC)
synonym: MIT Laser Biomedical Research Center
abbrev: LBRC
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Biomedical technology research center that develops basic scientific understanding and new techniques required for advancing clinical applications of lasers and spectroscopy. LBRC merges optical spectroscopy, imaging, scattering, and interferometry techniques to study biophysics and biochemistry of healthy and diseased biological structures from subcellular to entire-organ scale.

TACOA
type: Resource
type: NamedIndividual
has db xref: OMICS_01467
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software that can accurately predict the taxonomic origin of genomic fragments from metagenomic data sets by combining the advantages of the k -NN approach with a smoothing kernel function.

Brain Trauma Foundation
type: Organization
type: NamedIndividual
has db xref: grid.417506.1
has db xref: ISNI: 0000 0001 2172 2553
has db xref: nlx_143730
has db xref: Wikidata: Q4955793
abbrev: BTF
IAO_0000115: The Brain Trauma Foundation (BTF) is a national non-profit organization dedicated to improving the outcome of traumatic brain injury (TBI) patients worldwide by developing best practices guidelines, quality improvement programs, conducting clinical research, and educating medical professionals and consumers. Our efforts also focus on public education aimed at increasing awareness and understanding of the symptoms of a concussion. Our goal is to better educate coaches, nurses, athletes, parents and all citizens about the importance of recognizing concussions and taking the appropriate steps to ensure people receive appropriate care. Also by educating healthcare professionals on the immediate care for coma patients, we estimate that thousands of lives could be saved each year in the U.S., millions worldwide, and more would be spared life-long disabilities. Research has proven that all brain damage does not occur at the moment of impact but rather evolves over the ensuing hours and days after the initial injury, due to brain swelling and inadequate oxygen and blood flow to the injured brain. In most cases, this secondary damage can be controlled by applying scientific, evidence-based diagnostic and treatment Guidelines, which BTF has developed with medical organizations and physicians with expertise in TBI. BTF offers updated continuing education activities for all levels of health care professionals caring for TBI patients. The online activities include recorded presentations, live web-based lectures, and interactive learning modules based on the latest scientific-evidence. Also available on the BTF Learning Portal is an online version of the EMS course developed in coordination with National Highway Traffic Safety Administration. The Brain Trauma Foundation leads the way in cutting-edge clinical research on Traumatic Brain Injury (TBI). Improving diagnosis and treatment of TBI requires a focus on clinical research. Our mission is to improve the outcome of TBI patient…

Treephyler
type: Resource
type: NamedIndividual
has db xref: OMICS_01469
synonym: Treephyler: fast taxonomic profiling of metagenomes
IAO_0000115: A software tool for fast taxonomic profiling of metagenomes.

MeGO
type: Resource
type: NamedIndividual
has db xref: nlx_156939
synonym: Mobile Genetic Element Ontology
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Gene Ontology dedicated to the functions of mobile genetic elements. The terms defined are used to annotate phage and plasmid protein families in ACLAME. Note: The phage ontology PhiGO has now been incorporated in MeGO and can thus be accessed in MeGO version 1.0 and up.

MedGen
type: Resource
type: NamedIndividual
has db xref: nlx_156941
has db xref: OMICS_01549
IAO_0000115: A database of organized information related to human medical genetics, such as attributes of conditions with a genetic contribution.

Google Sites
type: Resource
type: NamedIndividual
has db xref: nlx_157257
abbrev: Sites
IAO_0000115: A free online service to easily create and share webpages.

BrainTechSci.
type: Resource
type: NamedIndividual
has db xref: nlx_51508
synonym: BrainTechSci
IAO_0000115: Blog about brain technology and science news that covers topics such as high-resolution brain imaging, brain maps API and whole-brain atlases.

NeuroScholar
type: Resource
type: NamedIndividual
has db xref: nif-0000-00067
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software package for knowledge management of neuroscientific literature. Used for creating knowledge models that answer specific questions with direct links to the literature.

D-Tailor
type: Resource
type: NamedIndividual
has db xref: OMICS_04768
synonym: DNA-Tailor
IAO_0000115: A fully extendable software framework, for property-based design of synthetic DNA sequences.

Neural Circuit Tracer
type: Resource
type: NamedIndividual
has db xref: nlx_152603
abbrev: NCTracer
IAO_0000115: Open source software for automated and manual tracing of neurites from light microscopy stacks of images. NCTracer 2.0 is developed for the Windows 7, 64-bit operating system and requires a minimum of 4 GB of RAM. This version does not run on 32-bit computers, Mac or Linux OS.

BioLemmatizer
type: Resource
type: NamedIndividual
has db xref: OMICS_04827
IAO_0000115: A domain-specific lemmatization software tool for the morphological analysis of biomedical literature.

AffyRNADegradation
type: Resource
type: NamedIndividual
has db xref: biotools:affyrnadegradation
has db xref: OMICS_01975
IAO_0000115: Software package that helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.

Orphelia
type: Resource
type: NamedIndividual
has db xref: OMICS_01492
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23,2022. A metagenomic open reading frame (ORF) finding tool for the prediction of protein coding genes in short, environmental DNA sequences with unknown phylogenetic origin. The resource is based on a two-stage machine learning approach that uses linear discriminants to extract features from the ORFs. An artificial neural network then combines the features and computes a gene probability for each ORF fragment.

ArrayExpress (R)
type: Resource
type: NamedIndividual
has db xref: OMICS_01974
IAO_0000115: Software to access the ArrayExpress Repository at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet

Parallel-META
type: Resource
type: NamedIndividual
has db xref: OMICS_01519
synonym: Parallel META
synonym: Parallel Meta
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Open source pipeline for metagenomic data analysis, which enables efficient and parallel analysis of multiple metagenomic datasets and visualization of results for multiple samples. Can perform rapid data mining among microbial community data for comparative taxonomic and functional analysis.

Body Mass Index Calculator
type: Resource
type: NamedIndividual
has db xref: nlx_152731
synonym: Calculate Your Body Mass Index
abbrev: BMI Calculator
IAO_0000115: Body Mass Index (BMI) for adults can be calculated using only height and weight. Body mass index (BMI) is a measure of body fat based on height and weight that applies to adult men and women.

ENTROPY BLOCKER
type: Resource
type: NamedIndividual
has db xref: nlx_154300
has db xref: nlx_154581
has db xref: SCR_007247
synonym: R/ENTROPY BLOCKER
synonym: R/ENTROPY_BLOCKER
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software application aiming at identifying haplotype blocks. The likelihood of the data is calculated minus the model complexity. The resulting blocks have very low diversity and the linkage disequilibrium with SNP's outside the blocks is low. (entry from Genetic Analysis Software)

Faceted Search Based Ontology Visualizer
type: Resource
type: NamedIndividual
has db xref: nlx_155874
abbrev: ontologyviz
IAO_0000115: Software that allows user to do faceted search on an ontology and enables visualization of the search results on the 3D digital atlas. Currently supports faceted search of functional neuroanatomy.

BWH Partners Tissue and Blood Repository
type: Resource
type: NamedIndividual
has db xref: nlx_156143
synonym: Brigham and Women's Hospital Partners Tissue and Blood Repository
synonym: Brigham and Women's Hospital PartnersTissue and Blood Repository Core
synonym: Partners Tissue and Blood Repository Core
IAO_0000115: A repository which provides specimen acquisition, processing and storage services, and access to archived frozen tissue specimens to the BWH/MGH/DFCI research community.

CovalentDock Cloud
type: Resource
type: NamedIndividual
has db xref: covalentdock_cloud
has db xref: OMICS_01597
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Web service that is used by researchers and scientists to perform protein-ligand covalent docking. This form allows for the formation of covalent linkages between the ligand and the receptor.

Symptom Score for Benign Prostatic Hyperplasia
type: Resource
type: NamedIndividual
has db xref: nlx_152737
synonym: American Urological Association's Symptom Score for Benign Prostatic Hyperplasia
synonym: AUA Symptom Score for BPH
abbrev: AUA BPH
abbrev: AUABPH
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Adapted from the American Urology Association Symptom Score for Benign Prostatic Hyperplasia, this chart will assist physicians, researchers, and patients in assessing the severity of the problem.

DOCK
type: Resource
type: NamedIndividual
has db xref: OMICS_01598
synonym: UCSF DOCK
IAO_0000115: An algorithm used to predict and analyse binding modes of docking molecules. Users can search ligand databases for compounds that inhibit enzymatic activity and bind to particular molecules and nucleic acid targets. Molecular docking is used to predict a predominant binding mode(s) of a ligand in three-dimensional structure. This method can be used for molecular biology and computer-assisted drug design.

exomeSuite
type: Resource
type: NamedIndividual
has db xref: OMICS_04839
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software application designed to analyze variant call files from next generation sequencing data to identify variants causing disease.

Neuroscience Link List
type: Resource
type: NamedIndividual
has db xref: nif-0000-00083
synonym: The World-Wide Web Virtual Library:Neurosciences
synonym: World-Wide Web Virtual Library:Neuroscience
synonym: World-Wide Web Virtual Library:Neuroscience (Biosciences)
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A website that provides links to many neuroscience resources on the web as well as links to university neuroscience and neurobiology program home-pages.

SPAdes
type: Resource
type: NamedIndividual
has db xref: OMICS_01502
synonym: SPAdes Genome Assembler
IAO_0000115: Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Sequence Read Format
type: Resource
type: NamedIndividual
has db xref: OMICS_05130
synonym: Sequence Read Format (SRF)
abbrev: SRF
IAO_0000115: A generic format for DNA sequence data. The primary motivation for creating SRF has been to enable a single format capable of storing data generated by any DNA sequencing technology.

Genetics of Kidneys in Diabetes
type: Resource
type: NamedIndividual
has db xref: nlx_152764
synonym: Genetics of Kidneys in Diabetes (GoKinD) Study
synonym: Genetics of Kidneys in Diabetes Study
abbrev: Go KinD
abbrev: GoKinD
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Collect, store, and distribute genetic samples from cases and controls of type 1 diabetes and diabetic nephropathy for investigator-driven research into the genetic basis of diabetic nephropathy. As the risk of kidney complications in type 1 diabetes appears to have a considerable genetic component, this study assembled a large data resource for researchers attempting to identify causative genetic variants. The types of data collected allowed traditional case-control testing, a rapid and often powerful approach, and family-based analysis, a robust approach that is not influenced by population substructure.

Porifera Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157558
abbrev: PORO
IAO_0000115: An ontology covering the anatomy of Porifera (sponges).

International Union of Basic and Clinical Pharmacology
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100009703
has db xref: grid.479924.5
has db xref: nlx_47304
synonym: International Union of Pharmacology
abbrev: IUPHAR
IAO_0000115: Voluntary, non-governmental, non-profit pharmacologist association promoting international cooperation, sponsoring international and regional activities, encouraging free exchange of scientists and ideas, developing public awareness, establishing advisory committees. Has official relations with the World Health Organization (WHO). Helps pharmacologists to participate with other branches of science in international activities, either directly or under ICSU, WHO and UNESCO. Member of the International Council for Science (ICSU) and participates in the work of its scientific committees. Has its own publishing program. Pharmacology International, is published every June and December. Member Directory is maintained continually, as an online resource. Provides IUPHAR Receptor Database, major on-line repository of characterization data for receptors and drugs, and the IUPHAR Ion Channels Database. Official Reports from The IUPHAR Committee on Receptor Nomenclature and Drug Classification are published in Pharmacological Reviews. IUPHAR World Congresses of Pharmacology are held every few years.

Project Halo
type: Resource
type: NamedIndividual
has db xref: nlx_144483
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Project Halo is a staged, long-range research effort by Vulcan Inc. towards the development of a Digital Aristotlea reasoning system capable of answering novel questions and solving advanced problems in a broad range of scientific disciplines and related human affairs. The project focuses on creating two primary functions: a tutor capable of instructing and assessing students in those subjects, and a research assistant with broad, interdisciplinary skills to help scientists and others in their work. Vulcan began work towards this ambitious vision in 2003 with the Halo Pilot a six-month effort to investigate the feasibility of creating a scientific knowledge base capable of answering novel questions from the AP (1st year college level) chemistry test. Three teams SRI International, Cycorp, and Ontoprise developed knowledge bases, for a limited section of an AP-chemistry syllabus, that were able to correctly answer 40 to 50 percent of the associated questions from the AP test. Since 2004, Project Halo has worked to improve these systems, with an emphasis on enabling knowledge entry by domain experts, instead of specialists in artificial intelligence software. In 2004, Vulcan began the development of Automated User-Centered Reasoning and Acquisition System (AURA), by SRI, that enables domain experts (graduate students in Biology, Chemistry, and Physics) to enter knowledge from introductory science textbooks. In 2006, an evaluation of AURA showed that students could create AURA knowledge bases that correctly answered 40 percent of the questions on a limited AP exam. In 2008, the next evaluation demonstrated an improvement of that score to 70 percent correct. In parallel, Project Halo has sponsored Ontoprise to develop semantic extensions to MediaWiki, the software that Wikipedia runs on. Ontoprise has developed a set of Semantic MediaWiki (SMW)+ extensions to MediaWiki that provide a community-based envi…

Archaezyme Ltd.
type: Organization
type: NamedIndividual
has db xref: SciEx_10649
synonym: Archaezyme
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An enzyme developer and provider of biochemical and consultancy services. Its consultancy services include organizing proof of concepts and planning startup companies, laboratories, and analytical methods. The company also offers writing and editing services for scientific and grant proposals, as well as technology assessments. The company is located in central Israel; however, all of their services are offered worldwide.

Core Life Sciences
type: Commercial Organization
type: NamedIndividual
has db xref: SciEx_10652
synonym: Core Life Sciences Inc.
IAO_0000115: A commercial organization that supplies researchers with life science instruments, reagents and consumables, and lab services.

CommonMind Consortium
type: Resource
type: NamedIndividual
has db xref: nlx_144615
abbrev: CommonMind
IAO_0000115: Sage Bionetworks, Mount Sinai School of Medicine (MSSM), University of Pennsylvania (Penn), the National Institute of Mental Health (NIMH), and Takeda Pharmaceuticals Company Limited (TAKEDA) have launched a Public-Private Pre-Competitive Consortium, the CommonMind Consortium, to generate and analyze large-scale genomic data from human subjects with neuropsychiatric disease and to make this data and the associated analytical results broadly available to the public. This collaboration brings together disease area expertise, large scale and well curated brain sample collections, and data management and analysis expertise from the respective institutions. As many as 450 million people worldwide are believed to be living with a mental or behavioral disorder: schizophrenia and bipolar disorder are two of the top six leading causes of years lived with disability according to the World Health Organization. The burden on the individual as well as on society is significant with estimates for the health care costs for these individuals as high as four percent GNP. This highlights a grave need for new therapies to alleviate this suffering. Researchers from MSSM including Dr. Pamela Sklar, Dr. Joseph Buxbaum and Dr. Eric Schadt will join with Dr. Raquel Gur and Dr. Chang-Gyu Hahn from Penn to combine their extensive brain bank collections for the generation of whole genome scale RNA and DNA sequence data. Dr.Pamela Sklar, Professor of Psychiatry and Neuroscience at MSSM commented this is an exciting opportunity for us to use the newest genomic methods to really expand our understanding of the molecular underpinnings of neuropsychiatric disease, while Dr Raquel Gur, Professor of Psychiatry from Penn observed this will be a great complement to some of the large-scale genetic analyses that have been carried out to date because it will give a more complete mechanistic picture. The CommonMind Consortium is committed to generating an open resource for the community and invites others…

LC Sciences
type: Organization
type: NamedIndividual
has db xref: SciEx_4449
synonym: LC Sciences LLC
IAO_0000115: A genomics and proteomics company that offers customizable oligonucleotide and peptide microarray products for nucleic acid and protein-profiling, biomarker-screening, drug screening, and development of diagnostic-devices.

FastQ Screen
type: Resource
type: NamedIndividual
has db xref: OMICS_01042
IAO_0000115: Software that allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

Nifti-Importer for WEKA
type: Resource
type: NamedIndividual
has db xref: nlx_152806
synonym: Weka Nifti-Importer
IAO_0000115: Java-based software platform designed for the implementation, distribution and application of classifiers and methods for regression analyses for all kinds of data. Unfortunately, technical issues and some pecularities of fMRI data prevented the import and classification of neuroimaging data in this software. A tool for the integration of fMRI data in WEKA is presented, and thereby provide a way to access a broad collection of recent analysis tools for data classification.

University of Maryland Labs and Facilities
type: Resource
type: NamedIndividual
has db xref: SciEx_4469
synonym: UMD Labs & Facilities
synonym: UMD Labs and Facilities
synonym: University of Maryland Labs & Facilities
IAO_0000115: A collection of laboratories hosted through the University of Maryland. These laboratories include: the BioAnalytical Service Laboratory, Biotechnology Research and Education Program, and the Sequencing Core.

University of Texas Medical Branch at Galveston
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100008013
has db xref: grid.176731.5
has db xref: ISNI: 0000 0001 1547 9964
has db xref: nlx_69430
has db xref: Wikidata: Q921264
synonym: University of Texas Medical Branch
synonym: UT Medical Branch
synonym: UT Medical Branch at Galveston
abbrev: UTMB
IAO_0000115: A division of the University of Texas that is dedicated to medical education.

University of Florida; Florida; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100007698
has db xref: grid.15276.37
has db xref: ISNI:0000 0004 1936 8091
has db xref: nlx_80063
has db xref: Wikidata:Q501758
synonym: UFlorida
synonym: University of Florida
synonym: University of Florida (UF)
abbrev: UF
IAO_0000115: Public research university in Gainesville, Florida, United States. Member of state university system of Florida with undergraduate and graduate programs in arts and sciences.

GEOquery
type: Resource
type: NamedIndividual
has db xref: biotools:geoquery
has db xref: OMICS_01972
synonym: GEOquery - Get data from NCBI Gene Expression Omnibus (GEO)
IAO_0000115: Software that establishes a bridge between GEO and BioConductor.

GenNav
type: Resource
type: NamedIndividual
has db xref: nlx_149123
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. GenNav searches GO terms and annotated gene products, and provides a graphical display of a term's position in the GO DAG.

Bovine Genome Database
type: Resource
type: NamedIndividual
has db xref: OMICS_04529
synonym: BovineGenome.org
synonym: The Bovine Genome Database
abbrev: BGD
IAO_0000115: Database and integrated tools to improve annotation of the bovine genome and to integrate the genome sequence with other genomics data.

UW Department of Biochemistry
type: Organization
type: NamedIndividual
has db xref: nlx_149153
synonym: University of Washington Department of Biochemistry
IAO_0000115: A department within the University of Washington which focuses on both undergraduate and postgraduate education in biochemistry.

Louisiana State University Health Sciences Center New Orleans; Louisiana; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100010519
has db xref: grid.279863.1
has db xref: ISNI:0000 0000 8954 1233
has db xref: nlx_152028
has db xref: Wikidata:Q6460011
synonym: Louisiana State University Health Sciences Center - New Orleans
synonym: Louisiana State University Health Sciences Center New Orleans
synonym: LSU Health New Orleans
synonym: LSU Health Sciences
synonym: LSU Health Sciences Center - New Orleans
synonym: LSU Health Sciences Center New Orleans
abbrev: LSUHSC-NO
IAO_0000115: A Louisiana-based university with programs in dentistry, medicine, public health, patient care and allied health professions. This university Includes a graduate program in fields including neuroscience, pharmacology, and genetics.

GISTIC
type: Resource
type: NamedIndividual
has db xref: OMICS_02296
synonym: GISTIC2.0
synonym: GISTIC 2
synonym: GISTIC 2.0
IAO_0000115: Software to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth. By separating SCNA profiles into underlying arm-level and focal alterations, they improve the estimation of background rates for each category.

University of Florida College of Medicine; Florida; USA
type: Organization
type: NamedIndividual
has db xref: nlx_80125
synonym: UF College of Medicine
synonym: University of Florida College of Medicine
abbrev: UF COM
IAO_0000115: A medical school which offers degrees in medicine, in addition to medical science, biomedical engineering, physician assistant studies and an interdisciplinary program in biomedical sciences.

University of Stuttgart; Stuttgart; Germany
type: Organization
type: NamedIndividual
has db xref: nlx_71546
IAO_0000115: A public research university with 10 programs in disciplines of science, social science and humanities. The institution has technical programs in civil, mechanical, industrial and electrical engineering.

DESeq
type: Resource
type: NamedIndividual
has db xref: biotools:deseq
has db xref: OMICS_01306
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Software for differential gene expression analysis based on the negative binomial distribution. It estimates variance-mean dependence in count data from high-throughput sequencing assays and tests for differential expression.

Morphometry BIRN
type: Resource
type: NamedIndividual
has db xref: nif-0000-00069
synonym: Brain Morphometry Testbed
synonym: mbirn calibration
synonym: mBIRN_calib
synonym: Morphometry BIRN Multi-site Multi-session Structural MRI Data
synonym: Morphometry Testbed
abbrev: MBIRN
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 4th,2023. Calibration data set of spoiled gradient-recalled echo magnetic resonance imaging data from five healthy volunteers (four males and one female) scanned twice at four sites having 1.5T systems from different vendors (Siemens, GE, Marconi Medical Systems) pooled by the Morphometry Testbed's (MBIRN). Some subjects were also scanned a single time at another site. One subject was only scanned twice at three sites (subject 73213384) and once at another site. For each subject, four Fast Low-Angle Shot (FLASH) scans with flip angles of 3, 5, 20, and 30 degrees were obtained in a single scan session, from which tissue proton density and T1 maps can be derived. These data were acquired to investigate various metrics of within-site and across-site reproducibility. The images have been defaced so that no facial features can be reconstructed from these data. The Morphometry Testbed (MBIRN) of the Biomedical Informatics Research Network (BIRN) focused on pooling and analyzing of neuroimaging data acquired at multiple sites. Specific applications include potential relationships between anatomical differences and specific memory dysfunctions, such as Alzheimer's disease. With the completion of the initial BIRN testbed phase, each of the original BIRN testbeds have now been retired in order to focus on new users in other biomedical domains.

Postgwas
type: Resource
type: NamedIndividual
has db xref: OMICS_04393
IAO_0000115: A comprehensive software toolkit for post-processing, visualization and advanced analysis of GWAS results.

SynaptomeDB
type: Resource
type: NamedIndividual
has db xref: nlx_157656
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Ontology-based knowledgebase for synaptic genes. These genes encode components of the synapse including neurotransmitters and their receptors, adhesion / cytoskeletal proteins, scaffold proteins, transporters, and others. It integrates various and complex data sources for synaptic genes and proteins., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

INCF Dataspace
type: Resource
type: NamedIndividual
has db xref: nlx_157665
abbrev: DataSpace
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 21, 2017. Repository for sharing of neuroscience data, text, images, sounds, movies, models and simulations.

South African Medical Research Council
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100001322
has db xref: grid.415021.3
has db xref: ISNI: 0000 0000 9155 0024
has db xref: nlx_152007
has db xref: Wikidata: Q7565733
synonym: Medical Research Council South Africa
synonym: MRC South Africa
synonym: SA Medical Research Council
abbrev: SA MRC
abbrev: SAMRC
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Organization which focuses on the promotion of health and increased quality of life for South Africans through research, development and technology. This organization conducts basic laboratory investigations, clinical research and public health studies, and its research focuses around the study of TB, HIV, chronic diseases, alcohol and drug abuse, and women's health.

Colin 3T/7T High-resolution Atlas
type: Resource
type: NamedIndividual
has db xref: nlx_157729
synonym: Colin 3T / 7T High-resolution Atlas
IAO_0000115: High-field extension of the Colin27 single-subject atlas with additional high-resolution, quantitative, averaged scans at both 3T and 7T.

cov-est
type: Resource
type: NamedIndividual
has db xref: nlx_157740
IAO_0000115: Covariance estimation library used in Improved Estimation and Interpretation of Correlations in Neural Circuits.

BLASTPLOT
type: Resource
type: NamedIndividual
has db xref: OMICS_01433
IAO_0000115: A PERL module that can quickly plot the BLAST results from short sequences (primers, probes, reads) against reference targets. This software generates PNG graphs for all of the reference sequences associated with a BLAST result set.

miRanalyzer
type: Resource
type: NamedIndividual
has db xref: OMICS_00361
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. A microRNA detection and analysis tool for next-generation sequencing experiments. The program uses a minimum match length of 17bp starting at the first base of the read. The maximum read length is set to 28bp. Reads with more than 5 matches to the genome are discarded, and if a read matches to more than 5 transcripts or Rfam entries it will be removed.

Magnolya
type: Resource
type: NamedIndividual
has db xref: OMICS_00347
IAO_0000115: A software which enables copy number variation (CNV) detections without using a reference genome. Magnolya directly compares the two next-generation sequences datasets.

GMATo
type: Resource
type: NamedIndividual
has db xref: OMICS_00106
synonym: Genome Microsatellite Analyzing Tool
synonym: Genome-wide Microsatellite Analyzing Tool
synonym: Genome-wide Microsatellite Analyzing Tool (GMATo)
IAO_0000115: A software tool used for simple sequence repeats (SSR) or microsatellite characterization. It also facilitates SSR marker design on a genomic scale, microsatellite mining at any length, and comprehensive statistical analysis for DNA sequences in any genome at any size. Analysis parameters are customizable.

NIH Toolbox Picture Vocabulary Test
type: Resource
type: NamedIndividual
has db xref: nlx_157773
abbrev: Picture Vocabulary Test
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A measure of receptive vocabulary that is administered in a computerized adaptive format. The respondent is presented with an audio recording of a word and four photographic images on the computer screen and is asked to select the picture that most closely matches the meaning of the word. This test takes approximately 4 minutes to administer and is recommended for ages 3-85.

GemSIM
type: Resource
type: NamedIndividual
has db xref: biotools:GemSIM
has db xref: OMICS_01507
IAO_0000115: A software package for generating realistic simulated next-generation genome sequencing reads with quality score values. The software is written in Python with a command-line user interface.

Grinder
type: Resource
type: NamedIndividual
has db xref: OMICS_01508
IAO_0000115: An open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms. The tool is available through multiple interfaces like GUI, CLI and API. It is useful for simulating clinical or environmental microbial communities and complements the use of in vitro mock communities.

Educational Resources in Neuroscience
type: Resource
type: NamedIndividual
has db xref: nlx_143786
synonym: ERIN Resources
synonym: ERIN: Educational Resources In Neuroscience
abbrev: ERIN
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23,2022. A database that lists, reviews, and rates resources for teaching neuroscience at the graduate and undergraduate level.

Mind Hacks
type: Resource
type: NamedIndividual
has db xref: nlx_48997
IAO_0000115: Mind Hacks: Neuroscience and psychology tricks to find out what's going on inside your brain. Mind Hacks is also a book by Tom Stafford and Matt Webb.

CMFreg
type: Resource
type: NamedIndividual
has db xref: nlx_155534
IAO_0000115: A sequence of fully automated voxel-wise rigid registration that utilizes stable structures of reference for assessment of craniofacial changes overtime.The major strengths of this method are that registration does not depend on the precision of the 3D surface models and that a stable structure of reference can be used without the simple best fit of all surfaces.

Wavelet Analysis of Image Registration
type: Resource
type: NamedIndividual
has db xref: nif-0000-00357
abbrev: WAIR
IAO_0000115: A software tool for the quantitative analysis of various n-dimensional (n-D) image registration techniques. The series of 'C' subroutines which comprise the WAIR library can be easily incorporated into the user's site specific programs and adapted to their particular needs. Wavelet-space triangle analysis is applicable for studying a family of warps on single or multiple n-D data sets. For each data set the WAIR routine assigns a positive real number to every warp alignment in the family, and the best warp for the given data will be the one with the smallest value. It uses the original data prior to warping and the target of the warp in determining warp ranking in reduced wavelet space. Cluster group classification (CGC) is applicable for analyzing the overall performance of a family of warps of a group of data sets. A single number is assigned to each registration alignment, based on its group-clustering characteristics. Spread group classification (SGC) gives preference to registration techniques that spread apart baseline versus activation functional signal for group data.

High-Throughput GoMiner
type: Resource
type: NamedIndividual
has db xref: nlx_149300
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A web program that organizes lists of genes of interest (for example, under- and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology and automates the analysis of multiple microarrays then integrates the results across all of them in exportable output files and visualizations. High-Throughput GoMiner is an enhancement of GoMiner and is implemented with both a command line interface and a web interface. The program can also: efficiently perform automated batch processing of an arbitrary number of microarrays; produce a human- or computer-readable report that rank-orders the multiple microarray results according to the number of significant GO categories; integrate the multiple microarray results by providing organized, global clustered image map visualizations of the relationships of significant GO categories; provide a fast form of false discovery rate multiple comparisons calculation; and provide annotations and visualizations for relating transcription factor binding sites to genes and GO categories.

NIH Toolbox Words-in Noise Test
type: Resource
type: NamedIndividual
has db xref: nlx_157784
synonym: NIH Toolbox Words-in Noise (WIN) Test
abbrev: WIN Test
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Assessment test that measures how much difficulty a person might have hearing in a noisy environment. A recorded voice instructs the participant to listen to and then repeat words. The task becomes increasingly difficult as the background noise gets louder. This test was developed to measure a person's ability to recognize single words presented amid varying levels of background noise. Recommended for participants ages 6-85 and takes approximately six minutes to administer.

Dissociation Experiences Scale
type: Resource
type: NamedIndividual
has db xref: nlx_157837
abbrev: DES
IAO_0000115: Assessment scale that is a 28 question self test used to screen patients for dissociative identity disorder (formerly called Multiple Personality Disorder). The 28 questions ask the patient about their experiences and their daily life and how often certain events happen.

University of Vermont Labs and Facilities; Center of Biomedical Research Excellence (COBRE) in Neuroscience
type: Resource
type: NamedIndividual
has db xref: SciEx_2000
synonym: University of Vermont Labs & Facilities
abbrev: UVM Labs & Facilities
abbrev: UVM Labs and Facilities
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. A university-based lab facility for research in biomedicine and neuroscience. The center was created to expand neuroscience research and training, develop shared core facilities and provide funding for research by neuroscience faculty. There is an emphasis on interdisciplinary neuroscience research and dialogue between basic and clinical neuroscientists.

Buss-Perry Aggression Questionnaire
type: Resource
type: NamedIndividual
has db xref: nlx_157852
synonym: Aggression Questionnaire
synonym: Buss Perry Aggression Questionnaire
abbrev: AGQ
IAO_0000115: A 29 item aggression assessment where participants rank certain statements along a 5 point continuum from "extremely uncharacteristic of me"to "extremely characteristic of me". The scores are normalized on a scale of 0 to 1, with 1 being the highest level of aggression. The questionnaire returns scores for 4 dimensions of aggression: Physical Aggression, Verbal Aggression, Anger, Hostility.

Illuminate
type: Resource
type: NamedIndividual
has db xref: OMICS_02102
synonym: Illuminate - Analytics toolkit for Illumina sequencer metrics
IAO_0000115: Python module and utilities to parse the metrics binaries output by Illumina sequencers, and provides usable data in the form of python dictionaries and dataframes. Intended to emulate the output of Illumina SAV, it allows you to print sequencing run metrics to the command line as well as work with the data programmatically.

RNAcontext
type: Resource
type: NamedIndividual
has db xref: biotools:rnacontext
has db xref: OMICS_02253
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Motif finding software suited for using large-scale RNA-binding affinity datasets to determine the relative binding preferences of RNA-binding proteins (RBPs) for a wide range of RNA sequences and structures. The tool is also implemented in a website.

University of Washington Nath Research Group
type: Resource
type: NamedIndividual
has db xref: SciEx_2024
synonym: University of Washington Labs & Facilities
abbrev: UW Labs & Facilities
abbrev: UW Labs and Facilities
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. University of Washington - affiliated research lab focused on understanding the roles of protein dynamics in health and human disease. They focus on developing methods to characterize and control protein dynamics through utilizing methods like single-molecule fluorescence, computational modeling, and protein engineering. There is an emphasis on proteins involved in degenerative disorders such as Alzheimer's disease, stress responses and drug metabolism.

UNAVCO Geodetic Web Services
type: Resource
type: NamedIndividual
has db xref: SciRes_000177
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Web services to access UNAVCO data collection. Adding /gps, /met, /pore, /tilt, and /strain gives the sensor JSON description.

EnvO
type: Resource
type: NamedIndividual
has db xref: nlx_153832
synonym: Environment Ontology
IAO_0000115: Community ontology for the concise, controlled description of environmental features and habitats. It provides a structured vocabulary that is designed to support the annotation of any organism or biological sample with environment descriptors. EnvO contains terms for biomes, environmental features, and environmental material.

EdgeBio
type: Organization
type: NamedIndividual
has db xref: SciEx_203
synonym: Edge Bio
synonym: EdgeBio.com
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A contract research organization that provides genomics services such as sequencing, bioinformatics, NGS data analysis and whole exome sequencing. EdgeBio is a CLIA-approved service provider.

MIMOSA
type: Resource
type: NamedIndividual
has db xref: biotools:mimosa
has db xref: OMICS_05642
synonym: MIMOSA - Mixture Models for Single-Cell Assays
synonym: MIMOSA: Mixture Models For Single Cell Assays
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for modeling count data using Dirichlet-multinomial and beta-binomial mixtures with applications to single-cell assays.

F2DockClient
type: Resource
type: NamedIndividual
has db xref: OMICS_01599
IAO_0000115: A collection of user interfaces packaged into TexMol that allows a user to interactively submit protein-protein docking jobs to a remote computing cluster, monitor the status of the jobs and retrieve and visually display/compare the results.

FlexX
type: Resource
type: NamedIndividual
has db xref: OMICS_01600
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software with two main applications: predicting the binding mode of three-dimensional proteins and virtual high-throughput screening (vHTS) which allows screening of compounds at rapid speeds.

Glide
type: Resource
type: NamedIndividual
has db xref: OMICS_01601
IAO_0000115: Software package which approximates a complete search of the conformational, orientational, and positional space of the ligand in a given receptor. Used in drug development for predicting protein ligand binding modes and ranking ligands via high throughput virtual screening.

GOLD
type: Resource
type: NamedIndividual
has db xref: OMICS_01602
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software for virtual screening and identifying the binding mode of active molecules. It is comprehensively validated, widely used, and allows for high database enrichments. The software utilizes a novel methodology which avoids computationally expensive sequential docking of ligands into multiple protein structures.

Google Tech Talks - YouTube
type: Resource
type: NamedIndividual
has db xref: nlx_149374
abbrev: Google Tech Talks
IAO_0000115: Google Tech Talks is a grass-roots program at Google for sharing information of interest to the technical community. At its best, it's part of an ongoing discussion about our world featuring top experts in diverse fields. Presentations range from the broadest of perspective overviews to the most technical of deep dives, on topics well-established to wildly speculative.

Molegro Virtual Docker
type: Resource
type: NamedIndividual
has db xref: OMICS_01603
IAO_0000115: An integrated platform for predicting protein-ligand interactions, the visualization of new ideas and analyzing protein targets.

Sanjeevini
type: Resource
type: NamedIndividual
has db xref: OMICS_01605
IAO_0000115: A complete drug designing software suite with an accessible web-server for targeted directed lead molecule discovery.

Acquisition and Analysis for Electron Tomography
type: Resource
type: NamedIndividual
has db xref: nif-0000-10145
synonym: TOM software toolbox
abbrev: TOM Toolbox
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software platform for low dose electron tomography (ET) for all processing steps: acquisition, alignment, reconstruction, and analysis. Requires: Matlab R2008a and Image Processing Toolbox (V6.1)

SODOCK
type: Resource
type: NamedIndividual
has db xref: biotools:sodock
has db xref: OMICS_01606
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An optimization algorithm based on particle swarm optimization (PSO) for solving flexible protein-ligand docking problems.

HEM
type: Resource
type: NamedIndividual
has db xref: OMICS_01970
synonym: HEM - Heterogeneous error model for identification of differentially expressed genes under multiple conditions
IAO_0000115: Software package that fits heterogeneous error models for analysis of microarray data

brainhack.org
type: Resource
type: NamedIndividual
has db xref: nlx_149390
synonym: BrainHack
IAO_0000115: Forum for collaborative projects in the field of brain science. Everyone is invited to submit projects, either existing ones that you want to see featured or new ones that you want launch and work on in a collaborative, open way.

Surflex-Dock
type: Resource
type: NamedIndividual
has db xref: OMICS_01607
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software program that screens large libraries of compounds including ligands, and their docking.

Cascleave
type: Resource
type: NamedIndividual
has db xref: OMICS_01670
synonym: Cascleave 2.0
synonym: Cascleave 2.0 - Caspase substrate cleavage site prediction
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A novel tool developed using Java program for the high-throughput in silico identification of substrate cleavage sites for various caspases from the amino acid sequences of the substrates.

Evernote
type: Resource
type: NamedIndividual
has db xref: nlx_149450
IAO_0000115: A note taking software that synchronizes information such as notes, web clips, audio files, photos and video collected across multiple devices. It allows for easy sharing and collaboration on projects.

MetaDE
type: Resource
type: NamedIndividual
has db xref: OMICS_04033
synonym: MetaDE: Microarray meta-analysis for differentially expressed gene detection
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30, 2022. Software package that implements 12 major meta-analysis methods for differential expression analysis.Package was removed from the CRAN repository.Formerly available versions can be obtained from the archive.Archived on 2018-01-23 as check problems were not corrected in time.

Cell Death Proteomics Database
type: Resource
type: NamedIndividual
has db xref: OMICS_01672
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A database of resources on cancer processes such as cell death. It is a subset of a larger database on cancer proteomics that focuses on anti-cancer drugs and cancer types in addition to cancer processes. It utilizes scientific articles from PubMed, UniProt and other resources along with information such as author information, sample types and useful hyperlinks.

NPG publishing format
type: Resource
type: NamedIndividual
has db xref: nlx_151382
synonym: Next-Generation Paper digital format
synonym: Next-Generation Paper format
synonym: NGP Publishing Framework
abbrev: NGP Format
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A standard next-generation paper (NGP) digital format for reading and digitally archiving scientific research papers to offer better imaging, data sharing and an improved reading experience. The NGP format is designed to retain traditional elements (i.e. Abstract, Introduction, etc.). Papers are viewed using any web browser running on any computing platform, including mobile devices. A button menu system provides navigation between pages. The format provides a more streamlined reading experience by providing as much information to the reader inline as possible, without requiring the user to skip between pages. To accomplish this, pop-up figure and reference details provide additional information without disrupting the flow of the paper. Clicking on standard figure data reveals full-resolution images, and live web links can be optionally followed from pop-up citations or inline links for additional information. Multimedia, such as hi-definition video or audio clips, is easily embedded within the new NGP format. The reader may also customize their reading experience by selecting alternative text and background color themes. The NGP format was created using non-proprietary open-source software including HTML and Javascript, and can be packaged to run offline independent of a live Internet connection. Data are fully captured and communicated utilizing the latest technologies available. The SCORE Imaging (Petzold et al.) paper was submitted to the publisher using this format to take advantage of its superior technical capabilities (http://zfishbook.org/NGP/).

GPS-Calpain Cleavage Detector
type: Resource
type: NamedIndividual
has db xref: OMICS_01673
synonym: Calpain Cleavage Detector
abbrev: GPS-CCD
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software package for the prediction of calpain cleavage sites.

Type 1 Diabetes - Rapid Access to Intervention Development
type: Resource
type: NamedIndividual
has db xref: nlx_152742
synonym: Type 1 Diabetes - Rapid Access to Intervention Development (T1D-RAID)
abbrev: T1D-RAID
IAO_0000115: NOTE: The T1D-RAID program is not currently accepting applications. Cooperative program that makes available, on a competitive basis, NCI resources for the pre-clinical development of drugs, natural products, and biologics to facilitate translation to the clinic of novel, scientifically meritorious therapeutic interventions for type 1 diabetes and its complications. A partial listing of those services includes: high-throughput screening, studies in animal models, formulation, pharmacology and toxicology studies, and bulk substances acquisition. Requests to T1D-RAID are brief (20 pages or less), and should clearly outline the resources required to ready the proposed therapeutic agent for clinical trials. T1D-RAID should enable entry into the clinic of promising molecules that are not otherwise likely to receive an adequate and timely clinical test. T1D-RAID is designed to accomplish the tasks that are rate-limiting in bringing discoveries from the laboratory to the clinic. Once a project has been approved, NIDDKstaff interact directly with the Principal Investigator (PI). NCI contractors perform the T1D-RAID-approved tasks under the direction of NIDDKand NCI staff. The required tasks will vary from project to project. In some cases T1D-RAID will support only one or two key missing steps necessary to bring a compound to the clinic; in other cases it may be necessary to supply the entire portfolio of development requirements needed to file an IND. Examples of tasks that can be supported by T1D-RAID include, but are not limited to: * Definition or optimization of dose and schedule for in vivo activity * Development of pharmacology assays * Conduct of pharmacology studies with a pre-determined assay * Acquisition of bulk substance (GMP and non-GMP) * Scale-up production from lab-scale to clinical-trials lot scale * Development of suitable formulations * Development of analytical methods for bulk substances * Production of dosage forms * Stability assurance of dosage form…

Fiduswriter
type: Resource
type: NamedIndividual
has db xref: nlx_156046
synonym: Fidus Writer
IAO_0000115: An online collaborative editor for academics that use citations and/or formulas. The editor focuses on the content rather than the layout, so that with the same text, it can be published in multiple ways: On a website, as a printed book, or as an ebook.

GraBCas
type: Resource
type: NamedIndividual
has db xref: biotools:grabcas
has db xref: OMICS_01674
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software tool for predicting granzyme B and caspase cleavage sites.

Coalition For Accelerating Standards and Therapies
type: Resource
type: NamedIndividual
has db xref: nlx_157879
synonym: Coalition For Accelerating Standards and Therapies (CFAST)
abbrev: CFAST
IAO_0000115: Consortium establishing data standards, tools and methods for conducting research in therapeutic areas important to public health including Alzheimer's disease, Parkinson's disease, multiple sclerosis, polycystic kidney disease, and tuberculosis.CDISC and C-Path have agreed to discontinue using separate CFAST brand, but they both remain committed to this mission and continue to partner to develop and publish therapeutic area data standards.

Multiple Myeloma Research Foundation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100001253
has db xref: grid.429426.f
has db xref: ISNI: 0000 0000 9350 5788
has db xref: nlx_157895
has db xref: Wikidata: Q6934894
abbrev: MMRF
IAO_0000115: Research foundation that funds research to develop new treatments for multiple myeloma, an incurable blood cancer.

Queensland Cyber Infrastructure Foundation Ltd
type: Organization
type: NamedIndividual
has db xref: SciEx_4541
synonym: qcif
synonym: Queensland Parallel Supercomputing Foundation
synonym: the Queensland Cyber Infrastructure Foundation
abbrev: QCIF
IAO_0000115: Provides digital infrastructure capabilities for research and innovation across Queensland and Australia. Provides services, infrastructure and support for computation and data driven collaborative research and its application in industry. Members are six Queensland universities – The University of Queensland, Queensland University of Technology, Griffith University, James Cook University, CQUniversity, and the University of Southern Queensland. The University of the Sunshine Coast is an associate member. Member employees provide support and development services.

PKD Foundation
type: Organization
type: NamedIndividual
has db xref: nlx_157910
synonym: Polycystic Kidney Disease Foundation
IAO_0000115: Organization and funder of polycystic kidney disease research to find treatments. The organization also raises awareness for the disease through education, advocacy and support.

Washington University School of Medicine Knight Alzheimers Disease Research Center
type: Resource
type: NamedIndividual
has db xref: nif-0000-11285
has db xref: nlx_144153
has db xref: SCR_008779
synonym: ADRC
synonym: Charles F. and Joanne Knight Alzheimer's Disease Research Center
synonym: Knight ADRC
synonym: Knight Alzheimer's Disease Research Center
synonym: Knight Alzheimers Disease Research Center
synonym: Washington University School of Medicine in St. Louis Knight ADRC
synonym: WU Knight ADRC
synonym: WUADRC
IAO_0000115: The Charles F. and Joanne Knight Alzheimer Disease Research Center (Knight ADRC) supports researchers and our surrounding community in their pursuit of answers that will lead to improved diagnosis and care for persons with Alzheimer disease (AD). The Center is committed to the long-term goal of finding a way to effectively treat and prevent AD. The Knight ADRC facilitates advanced research on the clinical, genetic, neuropathological, neuroanatomical, biomedical, psychosocial, and neuropsychological aspects of Alzheimer disease, as well as other related brain disorders.

Images of the Drosophila Nervous System
type: Resource
type: NamedIndividual
has db xref: nif-0000-12508
synonym: IDNS
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Drosophila neurobiology with 3D images, enhancer traps, Golgi impregnations and protocols. This data contains a schematic view onto the brain of an adult fly is a clickable imagemap. The set of links overlaps with those of the 3D-clickable version, but is not identical.

c3net
type: Resource
type: NamedIndividual
has db xref: OMICS_01681
IAO_0000115: Software package that allows inferring gene regulatory networks with direct physical interactions from microarray expression data using C3NET.

ANU Centre for Advanced Microscopy Core Facility
type: Resource
type: NamedIndividual
has db xref: nlx_157284
synonym: ANU Center for Advanced Microscopy
synonym: ANU Centre for Advanced Microscopy
synonym: Australian National University Centre for Advanced Microscopy
abbrev: ANU CAM
IAO_0000115: Centre for Advanced Microscopy provides open access, state-of-the art microscopy and microanalysis equipment and expertise to national and international researchers, students and industry partners in the materials and life sciences. Offers services to support experimental design, data acquisition and analysis, train users in the use of instruments and help with sample preparation, provide research collaboration.

Council for Scientific and Industrial Research; Gauteng; South Africa
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100001332
has db xref: grid.7327.1
has db xref: ISNI: 0000 0004 0607 1766
has db xref: nlx_158309
has db xref: Wikidata: Q849145
synonym: Council for Scientific and Industrial Research
synonym: CSIR South Africa
abbrev: CSIR
IAO_0000115: A leading scientific and technology research, development and implementation organization in Africa that undertakes directed research and development for socio-economic growth and improving the quality of life of South African citizens.

Full Moon BioSystems
type: Organization
type: NamedIndividual
has db xref: nlx_152366
IAO_0000115: An antibody supplier based out of the Silicon Valley which has a focus on products used for proteomic research. The company supplies products such as ELISA based antibody arrays, DNA and protein microarray substrates and imaging system calibration and validation tools.

Context Likelihood of Relatedness
type: Resource
type: NamedIndividual
has db xref: OMICS_01682
abbrev: CLR
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software that infers regulatory interactions between transcription factors and their targets using a compendium of gene expression profiles.

GENIE3
type: Resource
type: NamedIndividual
has db xref: biotools:genie3
has db xref: OMICS_01683
IAO_0000115: An algorithm for the inference of gene regulatory networks from expression data.

Inferelator
type: Resource
type: NamedIndividual
has db xref: OMICS_01684
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Algorithm for learning parsimonious regulatory networks from systems biology data sets de novo. Software that utilizes inference algorithm to model genetic regulatory networks.Inferelator 2.0 is scalable framework for reconstruction of dynamic regulatory network models., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Clinical Data Interchange Standards Consortium
type: Organization
type: NamedIndividual
has db xref: nlx_157914
abbrev: CDISC
IAO_0000115: A global, open, multidisciplinary, non-profit organization that has established standards to support the acquisition, exchange, submission and archive of clinical research data and metadata. Its mission is to develop and support global, platform-independent data standards that enable information system interoperability to improve medical research and related areas of healthcare. CDISC standards are vendor-neutral, platform-independent and freely available via the CDISC website.

MODENT - A Tool For Reconstructing Gene Regulatory Networks
type: Resource
type: NamedIndividual
has db xref: biotools:modent
has db xref: OMICS_01685
abbrev: ModEnt
IAO_0000115: A computational tool that reconstructs gene regulatory networks from high throughput experimental data.

CRASH
type: Resource
type: NamedIndividual
has db xref: nif-0000-30274
IAO_0000115: Portal for placebo controlled trial of the effects of 48-hour infusion of corticosteroids on death and on neurological disability, among adults with head injury and some impairment of consciousness. The outcomes will be measured by rates of death and neurological disability. Patients are recruited (or entered by their doctors when informed consent is not obtainable due to impaired cognitive functioning) on a case-by-case basis as head injured patients come through emergency departments. Randomization is done via a 24-hour telephone line that will denote which pack of medication (either the corticosteroids or saline solution as control) to give.

Miller Lab at the Penn State Center for Comparative Genomics and Bioinformatics
type: Resource
type: NamedIndividual
has db xref: nif-0000-30237
IAO_0000115: A portal for the Miller Lab at Penn State that does research in comparative genomics and bioinformatics. The website has resources such as web-based applications for genetic databases, software for genomic analysis and publications from the lab.

AusBiotech: Australia's Biotechnology Organization
type: Resource
type: NamedIndividual
has db xref: nif-0000-30134
synonym: AusBiotech
IAO_0000115: A portal to Australia's biotechnology industry organization and national network that represents members from sectors including but not limited to human health, agriculture and the environment. The organization provides representation and support to their member companies.

Zhejiang University; Zhejiang; China
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100004835
has db xref: grid.13402.34
has db xref: ISNI:0000 0004 1759 700X
has db xref: nlx_149178
has db xref: Wikidata:Q197543
synonym: Zhejiang University
abbrev: ZJU
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A public research university with twelve main academic disciplines that include science, engineering, agriculture and medicine. The university has campuses across China in locations such as Yuquan, Zhijiang and Zhoushan. It has studies available in undergraduate, graduate and post-doctorate degrees.

MRNet
type: Resource
type: NamedIndividual
has db xref: OMICS_01686
synonym: MRNet: A Multicast/Reduction Network
IAO_0000115: A software-based network that provides efficient multicast and reduction communications for parallel and distributed tools and systems. Some key features of this resource include scalable data aggregation, multiple concurrent data channels and high-bandwidth communication.

UnSplicer
type: Resource
type: NamedIndividual
has db xref: OMICS_01806
IAO_0000115: An RNA-seq alignment program that provides alignment of short reads to a reference genome. The program requires two inputs that are provided by the output of GeneMark-ES: HMM model parameters and ab initio gene predictions. UnSplicer is a sister pipeline to TrueSight.

MSU Subzero Science and Engineering Research Core Facility
type: Resource
type: NamedIndividual
has db xref: nlx_156416
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A suite of laboratories that study the effect of the cold on projects across several scientific disciplines. These facilities have the ability to simulate other environmental conditions such as solar radiation and humidity in addition to subzero temperatures.

OHSU MRI Support Core Laboratory
type: Resource
type: NamedIndividual
has db xref: nlx_156452
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 6,2022. Core facility that provides the following services: MRI examination of sedated non-human primate subjects. The magnetic resonance imaging (MRI) core provides ONPRC investigators with equipment and assistance to perform MRI exams of sedated NHP subjects.

ChromasPro
type: Resource
type: NamedIndividual
has db xref: OMICS_01808
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31,2023. Software which is able to assemble data from 454 and Illumina next-generation sequencers, with up to 100,000 sequences if 2 Gb RAM is available.

Brigham and Women's Hospital Labs and Facilities
type: Organization
type: NamedIndividual
has db xref: SciEx_4604
synonym: Brigham and Womens Hospital Labs & Facilities
abbrev: BWH Labs & Facilities
abbrev: BWH Labs and Facilities
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A service-providing lab facility based in the Brigham and Women's Hospital. Services include imaging and access to a specimen bank.

Duplicate reads removal
type: Commercial Organization
type: NamedIndividual
has db xref: OMICS_02101
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Plug-in tool to filter out duplicate reads that is specifically well-suited to handle those coming from PCR amplification errors which can have a negative effect because a certain sequence is represented in artificially high numbers.

AETIONOMY
type: NamedIndividual
has db xref: biotools:AETIONOMY
has db xref: nlx_157972
IAO_0000115: Consortium founded to establish mechanism-based taxonomies for Alzheimer's and Parkinson's disease and other neurodegenerative disorders (NDD), with the goal of facilitating development of more effective and targeted treatments. To do this, the consortium collects and analyzes data to: * Create new ways to combine underutilized data currently available in the literature, public databases, and from private companies * Determine how to dynamically organize and structure different types of knowledge about NDD * Determine how to apply this knowledge to construct new patient group classification * Identify correlations between disease features at molecular, tissue or organ-specific, and clinical levels * Identify sub-groups of patients based on the molecular cause of their disease, as opposed to the nature and location of their symptoms * Deliver data, tools, and recommendations for the biomedical community in the treatment of NDD A mechanism-based taxonomy is hoped to advance the: # Description and organization of the indication-specific data # Linking of data to disease models, based on causal and correlative relationships The expected outcome of AETIONOMY is a new NDD taxonomy system that distinguishes mixed pathologies, allowing for new features or classes to be added into the taxonomy, all with the goal of aiding drug and biomarker discovery.

SimToolDB
type: Resource
type: NamedIndividual
has db xref: nlx_153905
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Provides accessible location for storing and efficiently retrieving tools which aid simulations of neuronal and network compartmental models. Simulation tools can be coded in any language for any environment. Simulation tools code can be viewed before downloading or auto-launching.

Queen Mary University of London Labs and Facilities
type: Resource
type: NamedIndividual
has db xref: SciEx_4628
synonym: Queen Mary University of London Labs & Facilities
abbrev: QMUL Labs & Facilities
abbrev: QMUL Labs and Facilities
IAO_0000115: A collection of laboratory and research facilities in London that cover several domains including but not limited to: biological and chemical sciences, cancer research, condensed matter and material physics, computational research and clinical trials.

PEpiD
type: Resource
type: NamedIndividual
has db xref: OMICS_01845
synonym: Prostate Epigenetic Database
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A database to store the curated epigenetic data from studies of prostate cancer retrieved by literature mining. The Prostate Epigenetic Database (PEpiD) is meant as a resource for finding previous studies of prostate cancer in humans, mice and rats. Searches can be targeted through the categories of DNA methylation, histone modification, and microRNA.

Neurotic Physiology
type: Resource
type: NamedIndividual
has db xref: nlx_153934
synonym: Scicurious
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Blog by Bethany Brookshire on all that is good, bad, and weird in physiology and neuroscience. Scicurious is the pen name of Bethany Brookshire who has a PhD in Physiology from the Wake Forest University School of Medicine. She has a Bachelor of Arts in Philosophy and a Bachelor of Science in Biology from the College of William and Mary. She is currently finishing up a post-doc in psychiatry at the University of Pennsylvania. Her professional interests are in neurophysiology, specifically the interactions of neurotransmitter systems. Having obtained her PhD, she wishes to further her career in science writing, education, and research. You can also find her writing at SciAm blogs.

TAPIR: target prediction for plant microRNAs
type: Resource
type: NamedIndividual
has db xref: biotools:tapir
has db xref: OMICS_04004
abbrev: TAPIR
IAO_0000115: Web server designed for prediction of plant microRNA targets.

BAMS Nested Regions
type: Resource
type: NamedIndividual
has db xref: nif-0000-10175
synonym: Brain Architecture Management System Nested Regions
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 7th, 2019. BAMS is an online resource for information about neural circuitry. The BAMS Nested Regions view focuses on the major brain regions and their relationships.

iOMICS
type: Resource
type: NamedIndividual
has db xref: OMICS_02159
IAO_0000115: A genomics data analysis platform which generates decision models for healthcare organizations and medical research. This service is meant to utilize data through machine learning methods.

Megraft
type: Resource
type: NamedIndividual
has db xref: biotools:megraft
has db xref: OMICS_02161
IAO_0000115: A software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes.

VARiD
type: Resource
type: NamedIndividual
has db xref: biotools:varid
has db xref: OMICS_02163
IAO_0000115: Software using a Hidden Markov Model for SNP (single nucleotide polymorphism) and indel identification with AB-SOLiD color-space as well as regular letter-space reads.

Cistrome
type: Resource
type: NamedIndividual
has db xref: biotools:cistrome
has db xref: OMICS_02173
has db xref: SCR_017663
synonym: Galaxy Cistrome
IAO_0000115: Web based integrative platform for transcriptional regulation studies.

PSGInfer
type: Resource
type: NamedIndividual
has db xref: OMICS_01967
synonym: PSGInfer: Inference of alternative splicing from RNA-Seq data with probabilistic splice graphs
IAO_0000115: Software for inference of alternative splicing from RNA-Seq data with probabilistic splice graphs.

Pharmaceuticals and Medical Devices Agency
type: Organization
type: NamedIndividual
has db xref: grid.490702.8
has db xref: ISNI: 417639556
has db xref: nlx_157922
has db xref: Wikidata: Q932661
synonym: Japanese Pharmaceuticals and Medical Devices Agency
synonym: Pharmaceuticals and Medical Devices Agency - Japan
synonym: Pharmaceuticals and Medical Devices Agency Japan
abbrev: PMDA
IAO_0000115: A Japanese regulatory government agency which regulates the safety, efficacy and quality of pharmaceuticals and medical devices in order to protect the public health of the people. The agency plays three main roles: drug and medical device testing, post-marketing drug safety, and victim compensation for those affected by adverse drug reactions from pharmaceuticals or other biological products. It is an incorporated administrative agency with non-civil service status.

Philipps-University Marburg; Marburg; Germany
type: Organization
type: NamedIndividual
has db xref: nlx_89596
synonym: Philipps-University
synonym: Philipps-University Marburg
synonym: Philipps-Universität
synonym: Philipps-Universität Marburg
synonym: University of Marburg
IAO_0000115: A public university in Germany which has a heavy emphasis on research. The institution has programs in a wide range of fields, most notably life sciences, nano sciences, material sciences and medicine.

Sorbonne University; Paris; France
type: Organization
type: NamedIndividual
has db xref: Crossref Funder ID: 501100019125
has db xref: GRID: grid.462844.8
has db xref: ISNI: 0000 0001 2308 1657
has db xref: nlx_17035
has db xref: Wikidata: Q41497113
synonym: Paris; Universite Pierre et Marie Curie
synonym: Pierre and Marie Curie University
synonym: Sorbonne Université; Pierre and Marie Curie University
synonym: University Pierre and Marie Curie
synonym: University Pierre et Marie Curie
abbrev: UPMC
IAO_0000115: A public research university in France that emphasizes medical and scientific research centered on four themes: life and health, the living earth and environment, matter and new materials and modeling and engineering. It is a member of the Sorbonne Universities alliance.

Pohang University of Science and Technology; Pohang; South Korea
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100002541
has db xref: grid.49100.3c
has db xref: ISNI:0000 0001 0742 4007
has db xref: nlx_156801
has db xref: Wikidata:Q40018
synonym: Pohang University of Science and Technology
abbrev: POSTECH
IAO_0000115: A private university in Pohang, South Korea which has an emphasis on the education and research at both the undergraduate and graduate levels. This institution is home to four government-funded research centers in basic sciences such as the National Institute for Nanomaterials Technology. They have the highest educational investment and the most per-student scholarship support in Korea.

Polish Academy of Sciences Poznan; Poznan; Poland
type: Organization
type: NamedIndividual
has db xref: nlx_11309
synonym: PAN
IAO_0000115: An academy of sciences that is based in Poland. The academy is an important institution for the development of science research in Poland, in addition to being part of a larger network of research institutes.

CoGenT++
type: Resource
type: NamedIndividual
has db xref: nif-0000-02674
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 26, 2016. A data environment for computational research in comparative and functional genomics, designed to address issues of consistency, reproducibility, scalability and accessibility., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Polish Academy of Sciences Warsaw; Warsaw; Poland
type: Organization
type: NamedIndividual
has db xref: nlx_22116
synonym: Polish Academy of Science
synonym: Polska Akademia Nauk
synonym: Warsaw Scientific Society
synonym: Warsaw Society of Friends of Learning
abbrev: PAN
abbrev: PAS
IAO_0000115: Polish state sponsored institution of higher learning. Headquartered in Warsaw, it is responsible for spearheading development of science across country by society of distinguished scholars and network of research institutes. Polish research institution comprised of smaller institutes with goal to support development of science and establishing standards of research quality and ethics.

Polish Ministry of Science and Higher Education
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100004569
has db xref: grid.425823.a
has db xref: ISNI: 0000 0001 0684 6072
has db xref: nlx_149369
has db xref: Wikidata: Q4294468
synonym: Ministry of Science and Higher Education (Poland)
synonym: Ministry of Science and Higher Education - Republic of Poland
synonym: Polish Ministry of Science Higher Education
IAO_0000115: Polish governmental agency that administers governmental activities in science and higher education. Funding is provided by the state for scientific research.

Polytechnic University of Catalonia; Barcelona; Spain
type: Organization
type: NamedIndividual
has db xref: nlx_158613
synonym: BarcelonaTech
synonym: Polytechnic University of Catalonia
synonym: Universitat Politecnica de Catalunya
synonym: Universitat Politecnica de Catalunya BarcelonaTech
synonym: Universitat Politècnica de Catalunya
synonym: Universitat Politècnica de Catalunya BarcelonaTech
synonym: UPC BarcelonaTech
abbrev: UPC
IAO_0000115: A public research university in Spain which specializes in the fields of architecture, engineering and technology at the undergraduate, graduate and postdoctoral level. UPC focuses heavily on internationalization, this is demonstrated through their large population of international PhD and master's degree students. They are a member of the Top Industrial Managers for Europe network and several university federations, including the Conference of European Schools for Advanced Engineering Education and Research (CESAER).

Polytechnic University of Madrid; Madrid; Spain
type: Organization
type: NamedIndividual
has db xref: nlx_35130
synonym: Polytechnic University of Madrid
synonym: Technical University of Madrid
synonym: Universidad Politecnica de Madrid
synonym: Universidad Politécnica de Madrid
abbrev: UPM
IAO_0000115: A public technical university in Madrid with progams at the undergraduate, graduate and postdoctorate level in fields such as architecture and mining in addition to engineering in areas including forestry, agriculture, computer science and aeronautics.

Polytechnic University of Milan; Milan; Italy
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100006690
has db xref: grid.4643.5
has db xref: ISNI:0000 0004 1937 0327
has db xref: nlx_155545
has db xref: Wikidata:Q392904
synonym: Politecnico di Milano
synonym: Politecnico di Milano; Milan; Italy
synonym: Polytechnic University of Milan
IAO_0000115: A technical university in Italy that offers programs in engineering, architecture and design at the undergraduate, graduate and postdoctoral level. The university has two main campuses in the city of Milan where teaching and research occur; there are several satellite campuses scattered across five different cities.

Polytechnic University of Valencia; Valencia; Spain
type: Organization
type: NamedIndividual
has db xref: nlx_157969
synonym: Polytechnic University of Valencia
synonym: Technical University of Valencia
synonym: Universidad Politécnica de Valencia
synonym: Universitat Politecnica de Valencia
synonym: Universitat Politècnica de València
abbrev: UPV
IAO_0000115: A technical university in Spain which offers degree programs in 14 different faculties, including business administration, computer science and industrial engineering at the undergraduate, graduate and postdoctoral level. The school has five different campuses.

Pompeu Fabra University; Barcelona; Spain
type: Organization
type: NamedIndividual
has db xref: grid.5612.0
has db xref: ISNI:0000 0001 2172 2676
has db xref: nlx_52215
has db xref: Wikidata:Q24543
synonym: Pompeu Fabra University
synonym: Universitat Pompeu Fabra
synonym: UPF Barcelona
abbrev: UPF
IAO_0000115: Public university in Spain that offers programs in social sciences and humanities, health and life sciences, international training in communication and communication sciences. Has colleges based on topics such as law, translation and interpretation, and engineering. Research is organized into economics and business, experimental sciences and health, law.

Ponce School of Medicine and Health Sciences; Puerto Rico; USA
type: Organization
type: NamedIndividual
has db xref: nlx_156112
synonym: Ponce School of Medicine
synonym: Ponce School of Medicine & Health Sciences
synonym: Ponce School of Medicine and Health Sciences
IAO_0000115: A private university in Puerto Rico which offers graduate degrees in medicine, clinical psychology, biomedical sciences, medical sciences and public health. The Ponce Research Institute, housed at the university, does research in basic, behavioral, public health and clinical sciences, focusing on areas such as non-communicable diseases, health disparities, and community health and outreach.

Pondicherry University; Puducherry; India
type: Organization
type: NamedIndividual
has db xref: grid.412517.4
has db xref: ISNI:0000 0001 2152 9956
has db xref: nlx_158603
has db xref: Wikidata:Q283032
synonym: Pondicherry University
abbrev: PU
IAO_0000115: A public university in India that has several schools focused on different areas of study, including but not limited to: management, technology, physical and chemical sciences, social sciences and international studies. The university houses a Central Instrumentation Facility that provides three services: the Mechanical Shop, the Glass blowing Shop and the Electrical Shop, all of which provide support in the repair and servicing of scientific equipment as well as the fabrication of components for experimental setups.

MochiView
type: Resource
type: NamedIndividual
has db xref: OMICS_02174
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2022. Java software that integrates browsing of genomic sequences, features, and data with DNA motif visualization and analysis.

University of Wollongong Labs and Facilities
type: Resource
type: NamedIndividual
has db xref: SciEx_4870
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Molecular Horizons members are supported by laboratories and facilities. These include Laser Chemistry Laboratory, NMR Facility, Mass Spectrometry Facility, X-Ray Laboratory, Spectroscopy facilities. Other Major Equipment and facilities are available at Illawarra Health and Medical Research Institute.

Trinity College Dublin; Dublin; Ireland
type: Organization
type: NamedIndividual
has db xref: nlx_87233
synonym: College of the Holy and Undivided Trinity of Queen Elizabeth near Dublin
synonym: Trinity
synonym: Trinity College
synonym: Trinity College Dublin
synonym: Trinity College Dublin - University of Dublin
synonym: University of Dublin
abbrev: TCD
IAO_0000115: A public university, which is a part of the University of Dublin, and contains three main academic disciplines: Arts, Humanities and Social Sciences; Engineering, Mathematics and Sciences; and Health Sciences. The institution offers degrees at the undergraduate and graduate level.

RSEM
type: Resource
type: NamedIndividual
has db xref: biotools:rsem
has db xref: OMICS_01287
has db xref: OMICS_01966
synonym: RNA-Seq by Expectation-Maximization
synonym: RSEM-v1.3.0
IAO_0000115: Software package for quantifying gene and isoform abundances from single end or paired end RNA Seq data. Accurate transcript quantification from RNA Seq data with or without reference genome. Used for accurate quantification of gene and isoform expression from RNA-Seq data.

RNAmotifs
type: Resource
type: NamedIndividual
has db xref: OMICS_02287
synonym: rna motifs
synonym: rna_motifs
IAO_0000115: Software that evaluates the sequence around differentially regulated alternative exons to identify clusters of short and degenerate sequences, referred to as multivalent RNA motifs.

Pontifical Catholic University of Argentina School of Medical Sciences; Buenos Aires; Argentina
type: Organization
type: NamedIndividual
has db xref: nlx_143793
synonym: Pontifical Catholic University of Argentina School of Medical Sciences
synonym: Pontificia Universidad Cat�lica Argentina Facultad de Ciencias M�dicas
synonym: UCA Facultad de Ciencias M�dicas
synonym: UCA School of Medical Sciences
abbrev: School of Medical Sciences - UCA
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10th,2023. Private medical school in Buenos Aires that offers degree programs in the medical sciences. Resource is in Spanish.

M(at)CBETH
type: Resource
type: NamedIndividual
has db xref: OMICS_02292
synonym: MicroArray Classification BEnchmarking Tool on Host server
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2023. Web service for performing microarray classification. It aims at finding the best prediction among different classification methods by using randomizations of the benchmarking dataset.

MS-Spectre
type: Resource
type: NamedIndividual
has db xref: OMICS_02496
synonym: Mass Spectrometry Analysis Software
IAO_0000115: Software that provides (Quantitiave) analysis of multiple ls-ms(ms) runs, using mzXML import of raw data coming from spectrometers.

Quant
type: Resource
type: NamedIndividual
has db xref: biotools:quant
has db xref: OMICS_02504
IAO_0000115: A software tool for the proteomics community that may help improving analysis of proteomic experimental data.

Simulation Experiment Description Markup Language
type: Resource
type: NamedIndividual
has db xref: nlx_158098
abbrev: SED-ML
IAO_0000115: An XML-based format for encoding simulation experiments. SED-ML allows to define the models to use, the experimental tasks to run and which results to produce.

Kymata Atlas
type: Resource
type: NamedIndividual
has db xref: nlx_158115
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An online atlas of neural function, maintained by Cambridge University and the MRC Cognition and Brain Sciences Unit (CBSU).

RNASeqReadSimulator
type: Resource
type: NamedIndividual
has db xref: OMICS_01964
IAO_0000115: A software tool to generate simulated single-end or paired-end RNA-Seq reads. # It allows users to randomly assign expression levels of transcripts and generate simulated single-end or paired-end RNA-Seq reads. # It is able to generate RNA-Seq reads that have a specified positional bias profile. # It is able to simulate random read errors from sequencing platforms. # The simulator consists of a few simple Python scripts. All scripts are command line driven, allowing users to invoke and design more functions.

iFad
type: Resource
type: NamedIndividual
has db xref: OMICS_01959
IAO_0000115: An R software package implementing a bayesian sparse factor model for the joint analysis of paired datasets, the gene expression and drug sensitivity profiles, measured across the same panel of samples, e.g. cell lines.

GramCluster
type: Resource
type: NamedIndividual
has db xref: OMICS_01956
IAO_0000115: Software implementing a fast and accurate progressive clustering algorithm that relies on a grammar-based sequence distance and is particularly useful in clustering large datasets.

GProX
type: Resource
type: NamedIndividual
has db xref: OMICS_02506
synonym: Graphical Proteomics Data Explorer
IAO_0000115: A freely available complete software platform for comprehensive and integrated analysis and visualization of large proteomics datasets.

PeptideProphet
type: Resource
type: NamedIndividual
has db xref: biotools:peptideprophet
has db xref: OMICS_02520
IAO_0000115: Software that automatically validates peptide assignments to MS/MS spectra made by database search programs such as SEQUEST.

Home Dialyzors United
type: Resource
type: NamedIndividual
has db xref: nlx_158394
abbrev: HDU
IAO_0000115: A non-profit patient organization dedicated to educate, support and advocate for home dialysis. Their main focus is advocating and supporting those on home hemodialysis and peritoneal dialysis modalities. Membership is free and inclusive of dialyzors, care partners, nurses, nephrologists, renal professionals and others.

Progress and Health Foundation; Seville; Spain
type: Resource
type: NamedIndividual
has db xref: nlx_158210
synonym: Fundacion Progreso y Salud
synonym: Fundacion Publica Andaluza Progreso y Salud
synonym: Fundación Progreso y Salud
synonym: Progress and Health Foundation
abbrev: FPS
IAO_0000115: An organization that supports the public health system in Andalusia, Spain through three main activities: research and innovation in health, technologies line information and communication, and training and evaluation of professional skills. It also provides management support to the Health Quality Agency of Andalusia, which is the driving entity of the Andalusian Quality Model. Resource is in Spanish.

Pusan National University; Busan; South Korea
type: Organization
type: NamedIndividual
has db xref: nlx_156774
synonym: Busan National University
synonym: Pusan National University
abbrev: BNU
abbrev: PNU
IAO_0000115: A national public university in Busan, South Korea which offers degree programs in a wide variety of disciplines such as nursing, education, nano technologies and the creative arts at both the undergraduate and graduate level.

Queens University; Ontario; Canada
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100003321
has db xref: grid.410356.5
has db xref: ISNI:0000 0004 1936 8331
has db xref: nlx_63241
has db xref: Wikidata:Q1420038
synonym: Queen's College at Kingston
synonym: Queens University; Kingston; Canada
IAO_0000115: Public university in Ontario, Canada that offers degree programs in the social sciences and engineering at both the undergraduate, graduate, postdoctorate and professional level. The university operates six research centers that focus on disciplines such as neuroscience, computing, human mobility and Southern African research.

Queens University Belfast; Ireland; United Kingdom
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100000873
has db xref: grid.4777.3
has db xref: ISNI:0000 0004 0374 7521
has db xref: nlx_143527
has db xref: Wikidata:Q877925
synonym: Queen's University Belfast
abbrev: Queen's
IAO_0000115: A public research university in Belfast, Ireland that offers degree programs in a wide variety of disciplines at the undergraduate, graduate and postgraduate level.

University of Illinois College of Pharmacy
type: NamedIndividual
has db xref: nlx_63570
synonym: UICCP
IAO_0000115: A public pharmacy school, part of the University of Illinois. It offers a four-year professional degree program that leads to the PharmD, the highest level of professional education in pharmacy. The college also offers programs leading to six master's degrees and four doctorate degrees, covering a spectrum of research areas within the pharmaceutical sciences.

CNTools
type: Resource
type: NamedIndividual
has db xref: OMICS_02061
synonym: CNTools - Convert segment data into a region by sample matrix to allow for other high level computational analyses
IAO_0000115: Software package that provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data.

GEArray Expression Analysis Suite 2.0
type: Resource
type: NamedIndividual
has db xref: nif-0000-30602
synonym: GEArray
IAO_0000115: THIS RESOURCE HAS BEEN DISCONTINUED, documented April 15, 2016. New GEArray Expression Analysis Suite 2.0 was released at Dec 21, 2006, please read Release Notices for details. SABiosciences' GEArray Analysis Suite uses advanced Java functionality. In order to experience full functionality of this Portal, the following free programs and upgrades for PC and Macs should be properly installed. PC Environment Downloads Browser compatibility is not an issue on Windows systems, so all operating systems running Windows 98 and above and either Internet explorer or Netscape should be fine. Java 1.4.1 or above is required--this should download automatically upon the first entry into the Portal. If this does not happen, Java 1.5 is available for download from the following URL: Java 1.5 Mac Environment Downloads Browser compatibility is an issue, and Mac Operating Systems prior to Panther are not able to fully take advantage of this Portal's functionality. These programs need to be downloaded and installed in a specific order as follows: Panther 10.3.5 (Operating System), Safari 1.2 (Compatible Internet Browser) and Java 1.4.2 (Java environment). Abstract. INTRODUCTION: Toll-like receptors (TLR) comprehend an emerging family of receptors that recognize pathogen-associated molecular patterns and promote the activation of leukocytes. Surgical trauma and ischemia-reperfusion injury are likely to provide exposure to endogenous ligands for TLR in virtually all kidney transplant recipients. METHODS: Macroarray (GEArray OHS-018.2 Series-Superarray) analyses of 128 genes involved in TLR signaling pathway were performed in nephrectomy samples of patients with chronic allograft nephropathy (CAN) and acute rejection (AR, vascular and non vascular). The analysis of each membrane was performed by GEArray Expression Analysis Suite 2.0. RESULTS: Macroarray profile identified a gene expression signature that could discriminate CAN and AR. Three genes were significantly expressed between CAN a…

Lasergene's SeqMan Pro
type: Resource
type: NamedIndividual
has db xref: OMICS_01810
synonym: DANSEUR Lasergenes SeqMan Pro
synonym: Lasergenes SeqMan Pro
synonym: SeqMan Pro
synonym: SeqMan Pro - Software for Contig Assembly and Analysis Including SNP Discovery Coverage Evaluation and Project Annotation
IAO_0000115: Software for analysis and DNA sequence assembly of Sanger data. It also provides visualizations and analysis of next-gen projects assembled by SeqMan NGen.

National University of Singapore, Computational Bioengineering Laboratory
type: Resource
type: NamedIndividual
has db xref: nif-0000-10369
synonym: NUS CompBioLab
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Computational Bioengineering Laboratory in the Division of Bioengineering at the National University of Singapore has expertise in mathematical modeling, software and algorithm development, numerical techniques such as finite element analysis, computer simulation and visualization, signal and image processing plus an understanding of the biological systems that drive our efforts. The following are the main themes underlying the Computational Bioengineering Laboratory projects: - Computational Biology - Computational Physiology - Biosignal & Bioimage Processing - Integrated Physiology & the Physiome Project

Proteomics and Human Proteome: From Bench to Bedside
type: Resource
type: NamedIndividual
has db xref: nif-0000-10402
synonym: Proteomics Meeting
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. This website contains lecture videos from the events and discussions of the SEProt congress meeting, the theme of which is Human proteome. From Bench to Bedside. Sponsors: These videos are supported by the University of Navarra.

ProteinProphet
type: Resource
type: NamedIndividual
has db xref: biotools:proteinprophet
has db xref: OMICS_02521
IAO_0000115: Software that automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST.

OMSSAPercolator
type: Resource
type: NamedIndividual
has db xref: OMICS_02524
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software tool which interfaces OMSSA with Percolator, a post search machine learning method for rescoring database search results.

Flicker
type: Resource
type: NamedIndividual
has db xref: biotools:nci_flicker
has db xref: OMICS_02538
IAO_0000115: An open-source stand-alone computer program for visually comparing 2D gel images.

cn.FARMS
type: Resource
type: NamedIndividual
has db xref: biotools:cn.farms
has db xref: OMICS_02060
synonym: cn.farms - factor analysis for copy number estimation
IAO_0000115: Software R package for copy number variation analysis that allows analysis of the most common Affymetrix (250K-SNP6.0) array types and supports high-performance computing using snow and ff.

LIPAGE
type: Resource
type: NamedIndividual
has db xref: OMICS_02553
synonym: LIMS for proteomics
IAO_0000115: Laboratory information management system for proteomics. The software works with 2DPAGE-based proteomics workflow.

DNASTAR: Lasergene Core Suite
type: Commercial
type: NamedIndividual
has db xref: OMICS_01811
synonym: DNASTAR's Lasergene Core Suite software
synonym: Lasergene Core Suite
synonym: Lasergene Molecular Biology Suite
synonym: Sanger Sequence Assembly Software
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software suite for the assembly and analysis of Sanger sequencing data within the SeqMan Pro application. The software's functions include: assembling reads into groups based on sequence names, trimming vector and poor quality data, restoration of sequence ends and designing of sequence primers.

Indeed
type: Resource
type: NamedIndividual
has db xref: nlx_144165
synonym: Indeed.com
synonym: indeed: one search. all jobs
IAO_0000115: A database of job listings

Clonality
type: Resource
type: NamedIndividual
has db xref: OMICS_02059
synonym: Clonality - Clonality testing
IAO_0000115: Software package for clonality testing providing statistical tests for clonality versus independence of tumors from the same patient based on their loss of heterozygosity (LOH) or genomewide copy number profiles.

oneClickCGH
type: Resource
type: NamedIndividual
has db xref: OMICS_02050
IAO_0000115: Platform-independent array copy number analysis software that provides straightforward yet comprehensive detection and reporting of copy number changes.

CGH Fusion
type: Commercial Organization
type: NamedIndividual
has db xref: OMICS_02049
IAO_0000115: Software for DNA Copy Number and loss of heterozygosity (LOH) analysis designed with high-throughput diagnostic laboratories in mind.

Kravitz Dataset 2
type: Resource
type: NamedIndividual
has db xref: nlx_151410
IAO_0000115: Dataset of the spike and laser timestamps from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings." The code will analyze spike trains around laser pulses to determine if a cell is significantly activated by the laser, and therefore expresses an excitatory opsin, such as channelrhodopsin-2. It returns an excel sheet that simply identifies the activated cells.

Screensaver
type: Resource
type: NamedIndividual
has db xref: OMICS_02556
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software for a Lab Information Management System (LIMS) for high-throughput screening of small molecule and RNAi biological assays.

Zebrafish Neuroscience Research Consortium
type: Organization
type: NamedIndividual
has db xref: nlx_151974
synonym: Zebrafish Neuroscience Research Consortium (ZNRC)
abbrev: ZNRC
IAO_0000115: A group of scientists who collaborate and promote zebrafish neuroscience research. The consortium has opportunities for networking, scholarly publications and zebrafish-related symposia and conferences. The consortium is a supporter of the Zebrafish Neurophenome Project (ZNP), an initiative for a database of zebrafish behavioral and physiological data in an online, open source format.

fqzcomp
type: Resource
type: NamedIndividual
has db xref: OMICS_00957
IAO_0000115: A basic fastq compressor, designed primarily for high performance.

Penn Cell and Developmental Biology Zebrafish Core
type: Resource
type: NamedIndividual
has db xref: nlx_156471
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Core facility that provides the following services: Maintenance of transgenic or mutant zebrafish lines, Zebrafish research training, Zebrafish embryo supply service. The CDB Zebrafish Core facility provides services and training to Penn faculty interested in using the zebrafish model system as part of their research program.

Penn Clinical Research Computing Unit
type: Resource
type: NamedIndividual
has db xref: nlx_156474
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Core facility that provides the following services: Clinical data management, Project operations and compliance support, Custom database application development, Research technology support, Proposal development service. The Clinical Research Computing Unit (CRCU) is a designated core research facility within Penn Medicine, specializing in clinical research informatics (CRI) collaboration and research IT services with a growing number of clinical and translational research investigators at Penn. The CRCU currently supports 58 funded projects, valued at more than $336 M (total costs, all years) to Penn. Although situated within the Center for Clinical Epidemiology and Biostatistics (CCEB), the CRCU supports an increasing volume of its research portfolio led by PIs external to the CCEB. This year the total value of these research programs was $ 243 M, so that the proportion attributable to PIs external to CCEB exceeded 70% ($243 M / $336 M = 72%). Established originally on April 1, 1997, within the Biostatistics Unit of the Center for Clinical Epidemiology and Biostatistics (CCEB) at the University of Pennsylvania School of Medicine, the primary foci were to develop a research computing base for the new program in Biostatistics, as well as to create the capacity and resources to compete successfully for data coordinating centers (DCCs) of federally funded, large-scale, multi center clinical trials, and epidemiological studies. These technology resources also permitted CCEB faculty and staff to provide essential collaborative CRI support for Penn investigators throughout the wide array of basic science and clinical departments, centers, and institutes, thus enhancing their likelihood of funding success. On July 1, 2002, the CRCU restructured its operations and expanded its focus in response to the overall research project growth within the CCEB and the University. The CRCU, as an organizational unit, mo…

BrainFX
type: Resource
type: NamedIndividual
has db xref: nlx_155712
IAO_0000115: A developer tool to provide batch processing capability for pipelines. Users input data into a input table and run analysis with it. It is used to power CamBA and Brainwaver User interfaces.

dinifti
type: Resource
type: NamedIndividual
has db xref: nlx_155843
synonym: NYU CBI DICOM to NIfTI Converter
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software which converts DICOM images to NIfTI format.

Penn Community Outreach Using Health System Informatics Core
type: Resource
type: NamedIndividual
has db xref: nlx_156476
synonym: Penn COHSI
abbrev: COHSI
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Informatics core for the purpose of promoting clinical research by collecting data from the Penn Health System.

PyMOL
type: Resource
type: NamedIndividual
has db xref: nlx_156834
has db xref: OMICS_03802
IAO_0000115: A user-sponsored molecular visualization software system on an open-source foundation. The software has the capabilities to view, render, animate, export, present and develop three dimensional molecular structures.

GraphPad
type: Organization
type: NamedIndividual
has db xref: nlx_156835
IAO_0000115: A commercial graphing software company that offers scientific software for statistical analyses, curve fitting and data analysis. It offers four programs: Prism, InStat, StatMate and QuickCalcs.

MatrixScience
type: Organization
type: NamedIndividual
has db xref: nlx_156837
abbrev: Matrix Science
IAO_0000115: A collection of both commercial and noncommercial software products which includes: Mascot Distiller, Mascot Parser, and Mascot Server. Mascot Distiller is commercial and provides a single interface to process raw data into de-isotoped peak lists. This tool can also be used for the easy distribution of search and quantitative results to colleagues. The non-commercial Mascot Parser software provides an API (Application Programmer Interface) that makes it easier to access search results written in C++, Java, Python and Perl. Mascot Server is non-commercial, and is a collection of peptide mass fingerprints as well as a MS/MS database. A selection of popular sequence databases are available online and include SwissProt, NCBInr, and the EST divisions of EMBL. This server is best used for evaluating and searching for smaller data sets.

Research Network and Patient Registry Inventory Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157575
abbrev: RNPRIO
IAO_0000115: Ontology for Inventories of Clinical Data Research Networks, Patient-Powered Research Networks, and Patient Registries

Semantic DICOM Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157583
abbrev: SEDI
IAO_0000115: An ontology for DICOM as used in the SeDI project.

Time Event Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157610
abbrev: TEO
IAO_0000115: Ontology for representing events, time, and their relationships.

Variation Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157622
abbrev: VARIO
IAO_0000115: An ontology for standardized, systematic description of effects, consequences and mechanisms of variations.

ArrayPlex
type: Resource
type: NamedIndividual
has db xref: OMICS_00745
IAO_0000115: Open source software that integrates various forms of microarray data from diverse annotation and primary data sources. This software provides a programmatic framework (API set) that will be used for collaborative development and deploys an easy to maintain client-server architecture.

Vertebrate Skeletal Anatomy Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157624
abbrev: VSAO
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An anatomy ontology covering the vertebrate skeletal system that integrates terms for skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system.

DB BioTech
type: Organization
type: NamedIndividual
has db xref: nlx_157658
synonym: DB Bio Tech
synonym: DBBiotech
IAO_0000115: Commercial antibody vendor that provides products that utilize in-vitro cloning technology to create rabbit clonal and monospecific clonal antibodies. This company produces antibodies which correspond strictly to the conserved linear epitope of the antigen molecule.

IrfanView
type: Organization
type: NamedIndividual
has db xref: nlx_157659
IAO_0000115: An open source graphic viewer. Some features include batch conversion, paint options, basic editing and several supported file formats. It is compatible with Windows 9x, ME, NT, 2000, XP, 2003 , 2008, Vista, Windows 7, Windows 8, and Windows 10.

MiRdup
type: Resource
type: NamedIndividual
has db xref: OMICS_00404
IAO_0000115: A software used for the validation of pre-miRNAs predictions as well as predict the final structure of mature miRNA.

MeQA
type: Resource
type: NamedIndividual
has db xref: biotools:meqa
has db xref: OMICS_00616
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2022. Software for pre-processing, quality assessment, read distribution and methylation estimation for MeDIP-sequence datasets. It has the ability to quickly analyze sequence data for DNA methylation. This software integrates customized scripting and existing utilities tools that work on both paired end and single end data.

Methyl-Analyzer
type: Resource
type: NamedIndividual
has db xref: OMICS_00617
IAO_0000115: A data analysis pipeline for the Methyl-MAPS method.

Annotare
type: Resource
type: NamedIndividual
has db xref: OMICS_00741
synonym: annotare: a tool for annotating high-throughput biomedical investigations and resulting data
IAO_0000115: A software tool for annotating biomedical investigations and the resulting data, then producing a MAGE-TAB file. This software is a standalone desktop which features: an editor function, an annotation modifier, incorporation of terms from biomedical ontologies, standard templates for common experiment types, a design aid to help create a new document, and a validator that checks for syntactic and semantic violations.

CpGassoc
type: Resource
type: NamedIndividual
has db xref: OMICS_00793
IAO_0000115: Software R package to test association between methylation at CpG sites across genome and phenotype of interest, adjusting for any relevant covariates. Can perform standard analyses of large datasets without need to manually input data. Can handle mixed effects models with chip or batch entering model as random intercept. Includes tools to apply quality control filters, perform permutation tests, and create QQ plots, manhattan plots, and scatterplots for individual CpG sites.

Koadarray
type: Resource
type: NamedIndividual
has db xref: OMICS_00842
IAO_0000115: A fully automatic array image analysis software which can process single or multiple array images. Koadarray automatically finds the spot locations within each image and quantifies the spot intensity data. It can be used in conjunction with radioactive applications, macroarray applications, fluorescent microarray image analysis and fluorescent microplate images.

Alternative Splicing Annotation Project II Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02572
synonym: Alternative Splicing Annotation Project II
synonym: ASAP II Database
abbrev: ASAP II
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on 8/12/13. An expanded version of the Alternative Splicing Annotation Project (ASAP) database with a new interface and integration of comparative features using UCSC BLASTZ multiple alignments. It supports 9 vertebrate species, 4 insects, and nematodes, and provides with extensive alternative splicing analysis and their splicing variants. As for human alternative splicing data, newly added EST libraries were classified and included into previous tissue and cancer classification, and lists of tissue and cancer (normal) specific alternatively spliced genes are re-calculated and updated. They have created a novel orthologous exon and intron databases and their splice variants based on multiple alignment among several species. These orthologous exon and intron database can give more comprehensive homologous gene information than protein similarity based method. Furthermore, splice junction and exon identity among species can be valuable resources to elucidate species-specific genes. ASAP II database can be easily integrated with pygr (unpublished, the Python Graph Database Framework for Bioinformatics) and its powerful features such as graph query, multi-genome alignment query and etc. ASAP II can be searched by several different criteria such as gene symbol, gene name and ID (UniGene, GenBank etc.). The web interface provides 7 different kinds of views: (I) user query, UniGene annotation, orthologous genes and genome browsers; (II) genome alignment; (III) exons and orthologous exons; (IV) introns and orthologous introns; (V) alternative splicing; (IV) isoform and protein sequences; (VII) tissue and cancer vs. normal specificity. ASAP II shows genome alignments of isoforms, exons, and introns in UCSC-like genome browser. All alternative splicing relationships with supporting evidence information, types of alternative splicing patterns, and inclusion rate for skipped exons are listed in separate tables. Users can also se…

Social Phobia/Social Anxiety Association
type: Resource
type: NamedIndividual
has db xref: nif-0000-10430
synonym: SP/SAA
IAO_0000115: This resource provides information on: -- a definition of social anxiety disorder (social phobia) -- practical examples of what life is like for people with social phobia, -- an invitation to join a free moderated mailing list edited specifically for people with social phobia (social anxiety disorder)

RADtools
type: Resource
type: NamedIndividual
has db xref: OMICS_03727
IAO_0000115: Software tools for processing RAD Sequencing Illumina reads. Version 1.0 is a pipeline for transforming Illumina reads into candidate genetic markers.

IGOR Pro
type: Resource
type: NamedIndividual
has db xref: nlx_156887
has db xref: SCR_014216
synonym: Igor Pro - Technical graphing and data analysis
synonym: Igor Software
IAO_0000115: Software used for visualizing and graphing data, image processing, and programming. It is designed for use by scientists and engineers and supports large data sets, evenly spaced data, and various data import formats. The software includes a suite of image processing operations for image filtering, manipulation, and quantification and is completely programmable.

AxoGen
type: Organization
type: NamedIndividual
has db xref: nlx_47454
IAO_0000115: A medical technology company whose research and products revolve around peripheral nerve repair.

Georgia Institute of Technology Labs and Facilities
type: Resource
type: NamedIndividual
has db xref: SciEx_940
abbrev: Georgia Tech Labs & Facilities
abbrev: Georgia Tech Labs and Facilities
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2023. University affiliated laboratory which is composed of two main departments, the Center for Organic Photonics and Electronics (COPE) and the Magnetic Resonance Laboratory. COPE creates flexible organic photonic and electronic materials and devices. The Magnetic Resonance Laboratory performs MRI and magnetic bore.

Bangkok Biomaterial Center
type: Resource
type: NamedIndividual
has db xref: nlx_54103
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented May 9, 2017.

CryoCord Stem Cell Bank
type: Resource
type: NamedIndividual
has db xref: nlx_57364
synonym: CryoCord Premier Stem Cell Bank
synonym: CryoCord Sdn Bhd
IAO_0000115: A stem cell bank in Malaysia which provides and carries out long-term human stem cells and tissue cryopreservation and research. The general public can use their biobanking services for personal use.

Defense Advanced Research Projects Agency
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100000185
has db xref: grid.421816.8
has db xref: ISNI: 0000 0000 9580 5207
has db xref: nlx_152039
has db xref: Wikidata: Q207361
abbrev: DARPA
IAO_0000115: A military affiliated research institute which focuses on funding and approving new and ongoing programs while ensuring a balanced investment portfolio. This organization is mainly concerned with making investments in technologies that can be used for national security.

Malaysian Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_67604
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016.

Dutch Ministry of Education Culture and Science
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100003245
has db xref: grid.425718.d
has db xref: ISNI: 0000 0000 9328 2422
has db xref: nlx_149499
has db xref: nlx_153826
has db xref: Wikidata: Q1049362
IAO_0000115: Dutch Ministry responsible for education, culture, science, research, gender equality and communications.This organization also strives to make a good work environment for teachers, artists and researchers.

National Endowment for the Humanities
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100000103
has db xref: grid.422239.c
has db xref: ISNI: 0000 0001 0281 9499
has db xref: nlx_151503
has db xref: Wikidata: Q478050
abbrev: NEH
IAO_0000115: A federal grant-making agency supporting research, preservation, public programs, and education in the humanities.

Center for Computational Biology at UCLA
type: Resource
type: NamedIndividual
has db xref: nif-0000-10492
synonym: CCB at UCLA
synonym: Center for Computational Biology
abbrev: CCB
abbrev: UCLA CCB
abbrev: USC CCB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2022. Center focused on the development of computational biological atlases of different populations, subjects, modalities, and spatio-temporal scales with 3 types of resources: (1) Stand-alone computational software tools (image and volume processing, analysis, visualization, graphical workflow environments). (2) Infrastructure Resources (Databases, computational Grid, services). (3) Web-services (web-accessible resources for processing, validation and exploration of multimodal/multichannel data including clinical data, imaging data, genetics data and phenotypic data). The CCB develops novel mathematical, computational, and engineering approaches to map biological form and function in health and disease. CCB computational tools integrate neuroimaging, genetic, clinical, and other relevant data to enable the detailed exploration of distinct spatial and temporal biological characteristics. Generalizable mathematical approaches are developed and deployed using Grid computing to create practical biological atlases that describe spatiotemporal change in biological systems. The efforts of CCB make possible discovery-oriented science and the accumulation of new biological knowledge. The Center has been divided into cores organized as follows: - Core 1 is focused on mathematical and computational research. Core 2 is involved in the development of tools to be used by Core 3. Core 3 is composed of the driving biological projects; Mapping Genomic Function, Mapping Biological Structure, and Mapping Brain Phenotype. - Cores 4 - 7 provide the infrastructure for joint structure within the Center as well as the development of new approaches and procedures to augment the research and development of Cores 1-3. These cores are: (4)Infrastructure and Resources, (5) Education and Training, (6) Dissemination, and (7) Administration and Management. The main focus of the CCB is on the brain, and specifically on neuroimaging. …

National Health Research Institutes; Taipei; Taiwan
type: Organization
type: NamedIndividual
has db xref: nlx_152538
abbrev: NHRI-Taipei
IAO_0000115: Nonprofit, government-funded research organization dedicated to the enhancement of medical research and the improvement of health care in Taiwan. Research interests include both aspects of basic biomedical sciences and specific diseases such as cancer, mental disorders and infectious diseases. The institute is meant to provide direction to national science and technology development in health and medical care, educate young scientists and physicians, establish an objective and fair system for research, and promoting domestic and international cooperation.

National Institute for Basic Biology; Okazaki; Japan
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100006324
has db xref: grid.419396.0
has db xref: ISNI: 0000 0004 0618 8593
has db xref: nlx_18219
has db xref: Wikidata: Q11426453
synonym: National Institute for Basic Biology
abbrev: NIBB
IAO_0000115: An organization which promotes studies in biology by conducting research itself as well as in cooperation with other research institutions. This organization covers a wide variety of biological fields, such as cell biology, developmental biology, neurobiology, evolutionary biology and theoretical biology. NIBB also offers graduate education programs through the Graduate University for Advanced Studies (SOKENDAI). This program provides five-year Doctoral courses for university graduates and a three-year senior Doctoral course for those with a Master's degree already.

rtd
type: Resource
type: NamedIndividual
has db xref: OMICS_03723
IAO_0000115: Reference-free ddRADseq analysis software tools. The pipeline script generates reference-sorted, indexed BAM from uniqued reads from radtag sequencing lanes.

PaintShop Pro
type: Commercial Organization
type: NamedIndividual
has db xref: SciRes_000165
IAO_0000115: Photo-editing software including editing features, fast brushes, creative tools and color selection that will help turn snapshots into beautiful, gallery-worthy images.

University of Utah School of Medicine; Utah; USA
type: Organization
type: NamedIndividual
has db xref: nlx_99359
IAO_0000115: An university in Utah which provides opportunities in teaching, research and clinical experience for developing physicians. This organization provides MD degrees, physician training, residency, fellowship specialty training and degrees in public health or research.

University of Vermont; Vermont; USA
type: Organization
type: NamedIndividual
has db xref: grid.59062.38
has db xref: ISNI:0000 0004 1936 7689
has db xref: nlx_15669
has db xref: Wikidata:Q1048898
synonym: University of Vermont
abbrev: UVM
IAO_0000115: An academic organization in Burlington, Vermont. This university provides undergraduate, graduate and medical degrees.

University of Zaragoza; Zaragoza; Spain
type: Organization
type: NamedIndividual
has db xref: nlx_144537
synonym: Universidad de Zaragoza
synonym: University of Zaragoza
abbrev: UZ
IAO_0000115: An undergraduate and postgraduate university which is located in Zaragoza, Spain.

University of Zurich; Zurich; Switzerland
type: Organization
type: NamedIndividual
has db xref: nlx_15354
synonym: Universitat Zurich
synonym: University of Zurich
abbrev: UZH
IAO_0000115: University located in Zürich, Switzerland was founded in 1833. Has faculties in Philosophy, Human Medicine, Economic Sciences, Law, Mathematics and Natural Sciences, Theology and Veterinary Medicine. Offers the widest range of subjects and courses of any Swiss higher education institution. As of October 2018, 23 Nobel laureates and 1 Turing Award winner have been affiliated with University of Zurich as alumni, faculty or researchers.

Washington University in St. Louis; Missouri; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100007268
has db xref: grid.4367.6
has db xref: ISNI:0000 0001 2355 7002
has db xref: nlx_47548
has db xref: Wikidata:Q777403
synonym: Washington University
abbrev: WashU
abbrev: WUSTL
IAO_0000115: Private research university in Greater St. Louis with its main campus mostly in unincorporated St. Louis County, Missouri and Clayton, Missouri.

Yunnan University; Yunnan; China
type: Organization
type: NamedIndividual
has db xref: nlx_157806
IAO_0000115: An university in China which offers undergraduate, master's, and doctorate degrees. This organization has a total of 20 different programs.

ABrowse
type: Resource
type: NamedIndividual
has db xref: OMICS_00899
IAO_0000115: A genome browser framework which gives an open browsing experience, open data access, collaborative work support, and a framework to import annotations. Multiple data access approaches are supported for external platforms to retrieve data from ABrowse. This resource also contains an online user-space in which users can create, store and share comments, annotations and landmarks.

GPViz
type: Resource
type: NamedIndividual
has db xref: OMICS_00915
IAO_0000115: A versatile Java-based software used for dynamic gene-centered visualization of genomic regions and/or variants.

cuteNMR
type: Resource
type: NamedIndividual
has db xref: OMICS_03391
IAO_0000115: A multi-platform NMR processing application.

Jnomics
type: Resource
type: NamedIndividual
has db xref: OMICS_04074
IAO_0000115: A collection of cloud-scale DNA sequence analysis tools.

JMolDraw
type: Resource
type: NamedIndividual
has db xref: OMICS_05000
IAO_0000115: 2-D chemical structure drawing software program.

CGAP-Align
type: Resource
type: NamedIndividual
has db xref: OMICS_05480
IAO_0000115: A time efficient read alignment tool built on the top of BWA.

ARACHNE
type: Resource
type: NamedIndividual
has db xref: biotools:arachne
has db xref: OMICS_01812
synonym: ARACHNE (Unsupported)
synonym: ARACHNE: a whole-genome shotgun assembler
IAO_0000115: A software for genome assembly, and is specifically designed to analyze long Sanger-chemistry reads.

Kinannote
type: Resource
type: NamedIndividual
has db xref: OMICS_05965
IAO_0000115: Software that identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine / threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com.

HudsonAlpha Genomics Services Lab
type: Resource
type: NamedIndividual
has db xref: SciEx_221
synonym: Genomics Services Lab
synonym: HudsonAlpha Institute for Biotechnology Genomics Services Lab
IAO_0000115: A lab that offers genetic research tools such as RNA sequencing and a variety of arrays.

CLC Main Workbench
type: Commercial Organization
type: NamedIndividual
has db xref: OMICS_01813
IAO_0000115: A suite of software for DNA, RNA and protein sequence data analysis. The software allows for the analysis and visualization of Sanger sequencing data as well as gene expression analysis, molecular cloning, primer design, phylogenetic analyses, and sequence data management.

ParseCNV
type: Resource
type: NamedIndividual
has db xref: OMICS_02566
IAO_0000115: Software that takes CNV calls as input and creates SNP based statistics for CNV occurrence in cases and controls then calls CNVRs based on neighboring SNPs of similar significance.

TAPS
type: Resource
type: NamedIndividual
has db xref: OMICS_02571
synonym: Tumor Aberration Prediction Suite
IAO_0000115: A bioinformatic tool for the identification of allele-specific copy numbers in tumor samples using data from Affymetrix SNP arrays.

PyroHMMsnp
type: Resource
type: NamedIndividual
has db xref: OMICS_02617
IAO_0000115: Software using a realignment-based SNP calling method for 454 and Ion Torrent sequencing data.

TransView
type: Resource
type: NamedIndividual
has db xref: OMICS_02048
IAO_0000115: Software package to generate, access and display read densities of sequencing based data sets such as from RNA-Seq and ChIP-Seq.

pvac
type: Resource
type: NamedIndividual
has db xref: biotools:pvac
has db xref: OMICS_02031
synonym: pvac: PCA-based gene filtering for Affymetrix arrays
IAO_0000115: Software package that contains the function for filtering genes by the proportion of variation accounted for by the first principal component (PVAC).

riboPicker
type: Resource
type: NamedIndividual
has db xref: biotools:ribopicker
has db xref: OMICS_02618
IAO_0000115: Software to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets.

Mississippi State University; Mississippi; USA
type: Organization
type: NamedIndividual
has db xref: Crossref Funder ID 100007250
has db xref: GRID grid.260120.7
has db xref: ISNI 0000 0001 0816 8287
has db xref: nlx_23152
has db xref: Wikidata Q1939211
IAO_0000115: Public university in Mississippi with land, sea and space grants that offers degree programs in areas such as agriculture and applied sciences at the undergraduate and graduate levels.

Ohio Northern University; Ohio; USA
type: Organization
type: NamedIndividual
has db xref: grid.261323.7
has db xref: ISNI:0000 0001 2187 1348
has db xref: nlx_143792
has db xref: Wikidata:Q1683585
abbrev: ONU
IAO_0000115: A public university in Ohio with land, sea and space grants that offers degree programs and research at the undergraduate and graduate level.

University of Wroclaw; Wroclaw; Poland
type: Organization
type: NamedIndividual
has db xref: nlx_48592
IAO_0000115: A public research university in Poland. The school offers degree programs in business, humanities, chemistry, global studies and more at the undergraduate, graduate and doctoral level.

UPR Medical Mycology Laboratory
type: Resource
type: NamedIndividual
has db xref: nlx_156608
synonym: University of Puerto Rico Medical Mycology Lab
IAO_0000115: A lab facility associated with the University of Puerto Rico. The lab provides services like air quality analysis as well as instruments like microscopes and spore traps.

Vanderbilt Bradykinin Core Laboratory
type: Resource
type: NamedIndividual
has db xref: nlx_156642
IAO_0000115: A lab facility at Vanderbilt University Medical Center that provides histological sample preparation.

Epoch Clinical Trial Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157400
abbrev: CTONT
IAO_0000115: Ontology of clinical trial terminology.

Creative Diagnostics
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_158541
IAO_0000115: An antibody supplier that also provides diagnostic components, assay reagents and contract biologic RandD and manufacturing services. The company focuses on providing services to help clients develop, manufacture and commercialize their products.

NucleoFinder
type: Resource
type: NamedIndividual
has db xref: biotools:nucleofinder
has db xref: OMICS_00510
IAO_0000115: A software for a statistical approach for the detection of nucleosome positions in a cell population. The software identifies important features of nucleosome organization such as the spacing downstream of active promoters and the enrichment and depletion of GC/AT dinucleotides of in vitro nucleosomes.

Allegheny College; Pennsylvania; USA
type: Organization
type: NamedIndividual
has db xref: nlx_40570
IAO_0000115: A private liberal arts college that offers degrees in social sciences, humanities and natural sciences at the undergraduate level.

London School of Economics and Political Science; London; United Kingdom
type: Organization
type: NamedIndividual
has db xref: nlx_158056
synonym: London School of Economics
synonym: London School of Economics and Political Science
abbrev: LSE
IAO_0000115: A public research university in London with an emphasis in social science degree programs such as law, mathematics, public affairs and international history. The university offers degrees at the undergraduate, graduate and doctoral level.

Tel Aviv University; Ramat Aviv; Israel
type: Organization
type: NamedIndividual
has db xref: nlx_45243
synonym: TAU
IAO_0000115: A public university in Israel with degree programs in areas such as arts, engineering, humanities, the law and medicine at the undergraduate and graduate level. The university has affiliated but independent schools that focus on specific areas such as music, environmental studies, dentistry, social work, education and neuroscience.

Tianjin University; Tianjin; China
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100004517
has db xref: grid.33763.32
has db xref: ISNI:0000 0004 1761 2484
has db xref: nlx_28979
has db xref: Wikidata:Q2031560
synonym: TJU
IAO_0000115: A national university in China with degree programs that include engineering, economics, humanities, law and art at the undergraduate, graduate and doctoral level.

Tuskegee University; Alabama; USA
type: Organization
type: NamedIndividual
has db xref: grid.265253.5
has db xref: ISNI:0000 0001 0707 9354
has db xref: nlx_156108
has db xref: Wikidata:Q1682329
synonym: Tuskegee University
IAO_0000115: A private, historically black university that offers degree programs at the undergraduate, graduate, doctoral and professional levels. The university has programs that include veterinarian studies, allied health, nursing, education

University of Southern Queensland; Queensland; Australia
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100001795
has db xref: grid.1048.d
has db xref: ISNI:0000 0004 0473 0844
has db xref: nlx_46605
has db xref: Wikidata:Q978124
synonym: USQ
IAO_0000115: A public university in Australia that offers degree programs in business, law and education as well as health, engineering and the sciences at the undergraduate level. The university also does research at three research institutes and seven research centers which focus on a wide range of business, agricultural, scientific, environmental, and technological issues.

University of Texas at Dallas; Texas; USA
type: Organization
type: NamedIndividual
has db xref: grid.267323.1
has db xref: ISNI:0000 0001 2151 7939
has db xref: nlx_11355
has db xref: Wikidata:Q1781394
abbrev: UTD
IAO_0000115: A public research university in Texas that offers degree programs in engineering, business, political science and the natural sciences at the undergraduate and graduate levels. The university also houses research that focuses on space science, bioengineering, cybersecurity, nanotechnology, and behavioral and brain sciences.

bzip2
type: Resource
type: NamedIndividual
has db xref: OMICS_00951
IAO_0000115: A data compressor for files. This software is freely available, patent free, and is organized as a library with a programming interface.

Lonza
type: Organization
type: NamedIndividual
has db xref: grid.473847.b
has db xref: ISNI: 0000 0004 4691 9813
has db xref: SciEx_4981
IAO_0000115: A supplier of various biochemical products for research in pharmacy and biotechnology as well as the specialty ingredients market. Examples of products include active pharmaceutical ingredients, stem cell therapies, drinking water sanitizers and agriculture services and products.

GENSENG
type: Resource
type: NamedIndividual
has db xref: OMICS_00345
IAO_0000115: Software for detecting copy number variations from next generation sequencing data. Used to identify regions of discrete copy number changes while simultaneously accounting for effects of multiple confounders.

University of Massachusetts; Massachusetts; USA
type: Organization
type: NamedIndividual
has db xref: GRID grid.266684.8
has db xref: ISNI 0000 0001 2184 9220
has db xref: nlx_18192
has db xref: Wikidata Q1061122
synonym: UMass
synonym: University of Massachusetts
synonym: University of Massachusetts System
IAO_0000115: A five-campus public university system in Massachusetts. The system includes four universities, a medical school, and a satellite campus.

AS-Peak
type: Resource
type: NamedIndividual
has db xref: OMICS_00566
abbrev: ASPeak
IAO_0000115: A software that utilizes a peak detection algorithm to identify RNA-protein binding sites.

University of Sydney; Sydney; Australia
type: NamedIndividual
has db xref: Crossref funder ID:501100001774
has db xref: grid.1013.3
has db xref: ISNI:0000 0004 1936 834X
has db xref: nlx_143763
has db xref: Wikidata:Q487556
synonym: University of Sydney
IAO_0000115: A public research university in Sydney, Australia that offers a wide range of degree programs at the undergraduate and graduate level.

SunnyLab
type: Organization
type: NamedIndividual
has db xref: nlx_152472
IAO_0000115: An antibody supplier that provides a range of human antigens, serum and plasma, and cell culture reagents.

TEDDY
type: Resource
type: NamedIndividual
has db xref: nlx_152857
synonym: TEDDY study
synonym: The Environmental Determinants of Diabetes in the Young
abbrev: TEDDY
IAO_0000115: International consortium of six centers assembled to participate in the development and implementation of studies to identify infectious agents, dietary factors, or other environmental agents, including psychosocial factors, that trigger type 1 diabetes in genetically susceptible people. The coordinating centers recruit and enroll subjects, obtaining informed consent from parents prior to or shortly after birth, genetic and other types of samples from neonates and parents, and prospectively following selected neonates throughout childhood or until development of islet autoimmunity or T1DM. The study tracks child diet, illnesses, allergies and other life experiences. A blood sample is taken from children every 3 months for 4 years. After 4 years, children will be seen every 6 months until the age of 15 years. Children are tested for 3 different autoantibodies. The study will compare the life experiences and blood and stool tests of the children who get autoantibodies and diabetes with some of those children who do not get autoantibodies or diabetes. In this way the study hopes to find the triggers of T1DM in children with higher risk genes.

Trans-Institute Angiogenesis Research Program
type: Resource
type: NamedIndividual
has db xref: nlx_152866
synonym: Trans-Institute Angiogenesis Research Program (TARP)
abbrev: TARP
IAO_0000115: Trans-NIH program encouraging and facilitating the study of the underlying mechanisms controlling blood vessel growth and development. Other aims include: to identify specific targets and to develop therapeutics against pathologic angiogenesis in order to reduce the morbidity due to abnormal blood vessel proliferation in a variety of disease states; to better understand the process of angiogenesis and vascularization to improve states of decreased vascularization; to encourage and facilitate the study of the processes of lymphangiogenesis; and to achieve these goals through a multidisciplinary approach, bringing together investigators with varied backgrounds and varied interests.

LiGraph
type: Resource
type: NamedIndividual
has db xref: nlx_152884
synonym: LiGraph - Convert a sugar graph to ASCII IUPAC sugar nomenclature or as a graph
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31,2023. Web service that generates schematic drawings of oligosaccharides which are often used to display glycan structure.

pdb-data
type: Resource
type: NamedIndividual
has db xref: nlx_152888
synonym: search pdb data
IAO_0000115: Search for carbohydrate containing PDB entries by criteria like species or the compound / classification terms. You can choose predefined, frequent terms from the pull-down-menus or enter your own queries manually.

is-rSNP
type: Resource
type: NamedIndividual
has db xref: OMICS_01930
synonym: In silico regulatory SNP detection
synonym: is-rSNP: in silico regulatory SNP detection
IAO_0000115: Software tool that predicts whether a single nucleotide polymorphism (SNP) is a regulatory SNP (rSNP). For a given SNP, and using a statistical framework, it can successfully predict the set of transcription factors (TFs) for which binding is affected. The algorithm provides the statistical power to scan large numbers of SNPs, making it suitable to use to screen all associated SNPs output by a typical genome-wide association studies (GWAS).

ILLUMINUS
type: Resource
type: NamedIndividual
has db xref: nlx_154408
has db xref: OMICS_00726
synonym: Illuminus: the genotype calling algorithm
abbrev: Illuminus
IAO_0000115: A fast and accurate algorithm for assigning single nucleotide polymorphism (SNP) genotypes to microarray data from the Illumina BeadArray technology.

QUALIFIER
type: Resource
type: NamedIndividual
has db xref: OMICS_05618
synonym: QUALIFIER - Quality Control of Gated Flow Cytometry Experiments
IAO_0000115: Software that provides quality control and quality assessment tools for gated flow cytometry data.

BindingDB
type: Resource
type: NamedIndividual
has db xref: nif-0000-02603
has db xref: r3d100012074
IAO_0000115: Web accessible database of data extracted from scientific literature, focusing on proteins that are drug-targets or candidate drug-targets and for which structural data are present in Protein Data Bank . Website supports query types including searches by chemical structure, substructure and similarity, protein sequence, ligand and protein names, affinity ranges and molecular weight . Data sets generated by BindingDB queries can be downloaded in form of annotated SDfiles for further analysis, or used as basis for virtual screening of compound database uploaded by user. Data are linked to structural data in PDB via PDB IDs and chemical and sequence searches, and to literature in PubMed via PubMed IDs .

World Health Organization: The Global Health Library
type: Resource
type: NamedIndividual
has db xref: nif-0000-10556
synonym: GHL
IAO_0000115: The Global Health Library assembles health data, readable in many languages. The GHL aims to: * point to reliable information collections and systems, in which different users and user groups (ministries of health, policy makers, health workers, information providers, patients and their families, general public) can focus on the knowledge that best meets their health information needs; * act as a facilitator enabling access to information contents produced by numerous key providers - be they commercial companies, government institutions, civil society, not-for-profit organizations, and regional or international bodies; and * strive for universality, with focus on developing countries, and will act as a resource locator for print materials essential to areas that do not have access to electronic content.

WILEY Interdisciplinary Reviews
type: Resource
type: NamedIndividual
has db xref: nif-0000-10668
synonym: Wiley Interdisciplinary Reviews series
abbrev: WIREs
IAO_0000115: Wiley Interdisciplinary Reviews series combines features of encyclopedic reference works and review journals in innovative online format. They are designed to promote cross-disciplinary research ethos while maintaining the highest scientific and presentational standards, but should be viewed first and foremost as evolving online databases of cutting-edge reviews.

FunctSNP
type: Resource
type: NamedIndividual
has db xref: OMICS_01925
synonym: FunctSNP - Linking SNPs to functional knowledge
IAO_0000115: An R package for linking SNPs (Single Nucleotide Polymorphisms) to functional knowledge.

Micro-Analyzer
type: Resource
type: NamedIndividual
has db xref: biotools:microanalyzer
has db xref: OMICS_01919
synonym: microAnalyzer
IAO_0000115: Java tool that performs the preprocessing of Expression and SNPs microarray Affymetrix. The software allows the automatic download and the use of the clustering and visualization software as the Mev 4.0. The tool is equipped by a graphical interface (Swing) that allows to the user to: Create the workspace (files .cel, preferred algorithms , output, libraries to use); Run/save analysis and workspace settings (xml); Efficient download of the libraries (http, ftp, MD5); Customize basic and graphical settings (objects serialization and deserialization). Type of SNPs: Mapping 500k or preceding chips, SNP 5.0, SNP 6.0. Available for 32 or 64 bit systems, and for Windows and Linux Systems.

Molecular Connections NetPro
type: Resource
type: NamedIndividual
has db xref: nif-0000-20877
abbrev: MolCon
abbrev: NetPro
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Comprehensive database of Protein-Protein and Protein-Small molecules interaction, consisting of more than 320,000 interactions captured from more than 1500 abstracts, approximately 1600 published journals and more than 60,000 references. The strength of NetPro lies in the complete manual curation of literature. It covers several entities other than proteins as interacting partners, like RNA, DNA, processes, etc. with well defined, exhaustive interaction terms. NetPro has received several accolades for the quality and quantity of data it contains. It has become an important resource for target identification, validation and pathway research and has subscribers from all over the globe including 3 of the top 5 pharmas.

Ulysses
type: Resource
type: NamedIndividual
has db xref: nif-0000-20895
synonym: Projection of Protein Networks across Species
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2, 2022. System to annotate human genes based on gene interactions in model organisms. Data are transferred from amenable species like yeast, fly, and worm through homology, and functional gene annotation is facilitated through framework of large database. Used to perform interolog analysis by projection of model organism interaction data onto homologous human proteins, and thus serves as an accelerator for analysis of uncharacterized human proteins.

Protein-Protein Interactions Table for Human herpesvirus 1
type: Resource
type: NamedIndividual
has db xref: nif-0000-20905
synonym: HSV1 PPI
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. The scope of the project includes molecular information pertaining to oral pathogens, bacterial and viral. The website contains a table of protein-protein interactions for human herpesvirus 1. It is operated for the U.S. Department of Energy's National Nuclear Security Administration.

Protein-RNA Interaction Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-20906
abbrev: PRID
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2,2022. It is a repository of interactions found by Entangle and compiled into various tables for use by the RNA community. This data does not have a user interface, but data can be accessed in tables. It contains raw Excel/Access Databases and data processed into useful Figures for people who don't want to wade through the primary data. At present it contains informations from 42 PDBs.

flowStats
type: Resource
type: NamedIndividual
has db xref: OMICS_05611
synonym: flowStats - Statistical methods for the analysis of flow cytometry data
IAO_0000115: Software using statistical methods and functionality to analyze flow data that is beyond the basic infrastructure provided by the flowCore package.

dbSTS
type: Resource
type: NamedIndividual
has db xref: biotools:dbsts
has db xref: nif-0000-20939
has db xref: r3d100010649
synonym: Database of Sequence Tagged Sites
synonym: dbSTS: database of Sequence Tagged Sites
synonym: NCBI dbSTS
synonym: NCBI dbSTS: database of Sequence Tagged Sites
synonym: Sequence Tagged Sites Database
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, as of October 1, 2013; however, the site is still accessible. NCBI resource that contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites. STS sequences are incorporated into the STS Division of GenBank. The dbSTS database offers a route for submission of STS sequences to GenBank. It is designed especially for the submission of large batches of STS sequences.

BD Biosciences | FACSCalibur Flow Cytometry System
type: Resource
type: NamedIndividual
has db xref: SciRes_000153
synonym: FACSCalibur flow cytometer
abbrev: BD FACSCalibur system
IAO_0000115: Automated benchtop flow cytometry system. It allows measuring four fluorochrome-conjugates, forward and side scatter., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Polar Geospatial Center
type: Resource
type: NamedIndividual
has db xref: nlx_154743
abbrev: PGC
IAO_0000115: Portal as data resource, map repository, and GIS service provider for federally-funded scientists conducting research in the Arctic and Antarctic. The PGC holds an extensive collection of satellite imagery and aerial photography at varying resolutions.

Academic Seismic Portal at UTIG
type: Resource
type: NamedIndividual
has db xref: nlx_154745
has db xref: r3d100010631
synonym: Academic Seismic Portal (ASP) at UTIG
abbrev: ASP at UTIG
abbrev: ASP_UTIG
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Database of processed seismic reflection / refraction data providing access to metadata, SEG-Y files, navigation files, seismic profile images, processing histories and more. The main features of the web site include a geographic search engine using Google Plugins, a metadata search engine, and metadata pages for the various seismic programs. Metadata are uploaded into mySQL, a public-domain SQL server, and then PHP scripts query the metadata and directories, creating web pages, displaying images, and providing ftp links.

Random findings from the data
type: Resource
type: NamedIndividual
has db xref: nlx_155490
IAO_0000115: Blog about random findings from data written by Leon French.

Opal Research
type: Resource
type: NamedIndividual
has db xref: SciRes_000140
synonym: Omicia Opal
synonym: Omicia Opal Research
synonym: Opal Research Variant Interpretation
IAO_0000115: Software which integrates a comprehensive, automated genome annotation engine with the VAAST and Phevor disease gene prioritization tools to rank gene variants on the severity of their impact on protein function and likelihood to cause disease. Each variant in a gene is analyzed for its impact on protein function, conservation and frequency. Each gene is ranked rather than filtered in order to ensure critical targets are not prematurely removed.

Convert MNI coordinates to or from XYZ
type: Resource
type: NamedIndividual
has db xref: nlx_155600
IAO_0000115: Input either normalized MNI coordinates from a 3D image, or input real world XYZ matrix coordinates, and this code will convert coordinates of one type to the other.

flowPeaks
type: Resource
type: NamedIndividual
has db xref: biotools:flowpeaks
has db xref: OMICS_05604
IAO_0000115: Software for fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.

metaMA
type: Resource
type: NamedIndividual
has db xref: OMICS_03524
synonym: Meta analysis for MicroArrays
synonym: Meta-analysis for MicroArrays
IAO_0000115: Software R package for meta-analysis for microarrays. It combines either p-values or modified effect sizes from different studies to find differentially expressed genes.

rTANDEM
type: Resource
type: NamedIndividual
has db xref: OMICS_03516
synonym: rTANDEM - Interfaces the tandem protein identification algorithm in R
IAO_0000115: An R/Bioconductor package that interfaces the X!Tandem protein identification algorithm.

flowFlowJo
type: Resource
type: NamedIndividual
has db xref: OMICS_05598
synonym: flowFlowJo - Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm
IAO_0000115: A Bioconductor package that can import gates defined by the commercial package FlowJo and work with them in a manner consistent with the other flow packages in Bioconductor. FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the FlowJo Workspace. This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm.

Licensing issues in software and data
type: Resource
type: NamedIndividual
has db xref: nlx_155651
abbrev: NITRC Licensing
IAO_0000115: Discussion forum on licensing issues in software and data. All are invited to participate or join the project and contribute. A listing of software licenses are available.

Local Binary Pattern Analysis Tools for MR Brain Images
type: Resource
type: NamedIndividual
has db xref: nlx_155652
abbrev: LBP Analysis Tools for MR Brain Images
IAO_0000115: The packaged tools perform Local Binary Pattern on Three Orthogonal Planes (LBP-TOP) analysis on MR brain images. One can use them to extract LBP texture features for machine learning applications or other advance analysis. Bash scripts performing simple preprocessing with FSL and AFNI as well as LBP mapping programs written by Java are both including in this package. The output is the histogram describing the brain morphology.

MIView
type: Resource
type: NamedIndividual
has db xref: nlx_155661
IAO_0000115: OpenGL based medical image viewer that contains useful tools such as a DICOM anonymizer and format conversion utility. MIView can read DICOM, Analyze/Nifti, and raster images, and can write Analyze/Nifti and raster images.

TargetCaller
type: Resource
type: NamedIndividual
has db xref: OMICS_01807
IAO_0000115: R software package for transcription factor (TF) target gene prediction based on ChIP-seq data. Version 0.4 contains code to compute FDR-corrected q-values via permutations of the peak-to-gene assignments (ClosestGene only).

uManager
type: Resource
type: NamedIndividual
has db xref: nlx_155812
synonym: Micro Manager
synonym: Micro-Manager
IAO_0000115: Software package for control of automated microscopes. Cross-platform desktop application, to control motorized microscopes, scientific cameras, stages, illuminators, and other microscope accessories.

NICHD Developmental Neuroethology - Laboratory of Comparative Ethology
type: Resource
type: NamedIndividual
has db xref: nif-0000-00398
synonym: Developmental Neuroethology - Laboratory of Comparative Ethology
abbrev: NICHD Laboratory of Comparative Ethology
IAO_0000115: Understanding the mechanisms underlying the expression and perception of auditory communication in nonhuman primates provides important insights for understanding the neural systems that mediate nonverbal auditory communication in humans. Our research is devoted to understanding the changes in vocal behavior that are associated with maturation and social experience under normative conditions, and to investigating neural systems to define their roles in auditory communication. The anterior cingulate gyrus, in the frontal cerebral cortex, is an essential neural system for the expression of the primate isolation call, a structural and functional equivalent of the cry sounds of humans. Bilateral removal of this structure in adult squirrel monkeys resulted in a long-lasting inability to emit isolation calls. Partial recovery, often over many weeks, initially took the form of production of short, faint and uninflected versions of the typical isolation call. Humans suffering infarct damage to this region likewise show an initial recovery in the form of short, faint, monosyllabic sounds, suggesting that the anterior cingulate gyrus of nonhuman primates is the evolutionary precursor of a neural structure involved in human affective expression and speech. Our working model of isolation call production is that the anterior cingulate gyrus is the site where the command to produce this vocalization is initiated. Since the anterior cingulate region also has reciprocal connections with temporal lobe auditory cortex, a presumptive feedback pathway exists for registering commands to initiate vocalization with the temporal lobe cortex, which plays a major role in perceiving and decoding the acoustic details of species-specific vocalizations. At present, we do not know the role of the anterior cingulate gyrus in the production of infant vocalizations. However, we have found that neonatal removal of the amygdala, an important forebrain component of the limbic system, or portions of the…

PSCBS
type: Resource
type: NamedIndividual
has db xref: OMICS_05545
synonym: PSCBS: Analysis of Parent-Specific DNA Copy Numbers
IAO_0000115: Software R package for segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.

Open Colleges
type: Resource
type: NamedIndividual
has db xref: nlx_155866
IAO_0000115: A resource for online accredited courses in a wide variety of areas, including accounting, animal care, beauty, building and construction, business, education, design and writing. This resource is based in Australia.

Grantees Meeting for NITRC
type: Resource
type: NamedIndividual
has db xref: nlx_155875
IAO_0000115: This project is meant for planning the NITRC Grantee meetings. A website for organizing meetings for the Neuroimaging Informatics Tools and Resources Clearinghouse, to facilitate participants meeting one another, and promote discussion of common interests and collaboration.

iASeq
type: Resource
type: NamedIndividual
has db xref: OMICS_05505
synonym: iASeq: integrating multiple sequencing datasets for detecting allele-specific events
IAO_0000115: Software that uses a Bayesian hierarchical mixture model to learn correlation patterns of allele-specificity among multiple proteins.

Penn Hippocampus Atlas
type: Resource
type: NamedIndividual
has db xref: nlx_155920
IAO_0000115: Atlas of segmented and normalized high-resolution postmortem MRI of the human hippocampus. Additional data (raw images) is available through the SCM link. It requires knowing how to use CVS.

RapidArt
type: Resource
type: NamedIndividual
has db xref: nlx_155941
IAO_0000115: Software for detecting artifacts and performing individual region-of-interest based statistical analysis of fMRI data and enables users of fMRI technology to produce more detailed, consistent and reliable results.

Scribe
type: Resource
type: NamedIndividual
has db xref: nlx_155958
IAO_0000115: Scribe encodes papers to populate the BrainMap Database

ShapeWorks
type: Resource
type: NamedIndividual
has db xref: nlx_155961
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 2, 2022. Software that is an open-source distribution of a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wide range of shape analysis problems, including nonmanifold surfaces and objects of arbitrary topology. The proposed correspondence point optimization uses an entropy-based minimization that balances the simplicity of the model (compactness) with the accuracy of the surface representations. The ShapeWorks software includes tools for preprocessing data, computing point-based shape models, and visualizing the results.

d2-tools
type: Resource
type: NamedIndividual
has db xref: OMICS_02621
IAO_0000115: Software toolbox for counting the frequency of K-tuple from sequencing datasets and calculate the dissimilarity.

Vervet Probabilistic Atlas
type: Resource
type: NamedIndividual
has db xref: nlx_156015
IAO_0000115: Vervet (Chlorocebus aethiops sabaeus) probabilistic atlas that defines an anatomical space (template) with associated tissue and regional prior probability maps. The atlas was produced from whole head MRI of 10 normal adult animal subjects. The package consists of two atlases. The Biased directory contains the average template and probabilistic atlases for selected tissue classes constructed by registering the training population to one subject. The Unbiased directory contains the atlas constructed using unbiased estimation. The atlas is suitable for use in any segmentation tool using a probabilistic atlas, for example those in Slicer.

Altmetric Bookmarklet
type: Resource
type: NamedIndividual
has db xref: nlx_156030
synonym: The Altmetric Bookmarklet
IAO_0000115: Free bookmarklet for Chrome, Firefox and Safari that allows you to instantly get article level metrics for any recent paper. Simply drag the button below to your bookmarks bar, navigate to a journal article page, and hit Altmetric it!

Altmetric Explorer
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_156031
synonym: The Altmetric Explorer
IAO_0000115: Service to monitor, search and measure conversations about your publications and those of your competitors captured by Altmetric including tweets, blog posts, news stories and other content that mention scholarly articles. Use the Explorer to deliver insights, track mentions and measure levels of attention over time.

Epistemio
type: Resource
type: NamedIndividual
has db xref: nlx_156040
IAO_0000115: Database platform that aggregates post-publication peer reviews and ratings. It also includes a large-scale bibliographic database and features free reference management tools.

Hypothes.is
type: Resource
type: NamedIndividual
has db xref: nlx_156054
IAO_0000115: Non-profit organization working towards developing an open platform for the collaborative evaluation of knowledge. It will combine sentence-level critique with community peer-review to provide commentary, references, and insight on top of news, blogs, scientific articles, books, terms of service, ballot initiatives, legislation and regulations, software code and more.

PEPPER
type: Resource
type: NamedIndividual
has db xref: biotools:pepper
has db xref: OMICS_05485
synonym: Protein complex Expansion using Protein-Protein intERaction networks
synonym: Protein complex Expansion using Protein-Protein intERactions
IAO_0000115: A Cytoscape app designed to identify protein pathways / complexes as densely connected subnetworks from seed lists of proteins derived from pull-down assays (i.e AP-MS...).

RStudio
type: Resource
type: NamedIndividual
has db xref: SciRes_000113
IAO_0000115: Open source and enterprise ready professional software for R statistical computing environment. Integrated development environment for R. Includes console, syntax highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. Available in open source and commercial editions and runs on desktop Windows, Mac, and Linux or in browser connected to RStudio Server or RStudio Server Pro (Debian/Ubuntu, RedHat/CentOS, and SUSE Linux).

NINDS Disorder Index
type: Resource
type: NamedIndividual
has db xref: nif-0000-23200
synonym: Disorder Index: National Institute of Neurological Disorders and Stroke (NINDS)
synonym: Disorders index from the National Institute of Neurological Disorders and Stroke (NINDS)
synonym: National Institute of Neurological Disorders and Stroke Disorder Index
synonym: NINDS Disease List
synonym: NINDS Disorders A - Z
abbrev: NINDS Disorder List
IAO_0000115: Reference disease data set of neurological diseases along with their definitions, etiology, treatment, prognosis, ongoing research, clinical trials information and publications. The Disorder Index includes synonyms and research topics. Navigation is by letter of the alphabet., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

MNI brain and the Talairach atlas
type: Resource
type: NamedIndividual
has db xref: SciRes_000110
abbrev: mni2tal
IAO_0000115: Resource that discusses MNI brain, and the difference between the MNI brain and the brain in the Talairach atlas. Approaches to converting MNI coordinates to Talairach coordinates and a few other methods for locating your activation are also presented.Matlab function that transforms MNI coordinates to Talaraich coordinates. The inverse function, tal2mni is also available.

OLINgui
type: Resource
type: NamedIndividual
has db xref: BioTools:olingui
has db xref: OMICS_02030
synonym: OLINgui - Graphical user interface for OLIN
IAO_0000115: Software package providing a graphical user interface for the OLIN package.

OpenMM
type: Resource
type: NamedIndividual
has db xref: nif-0000-23334
synonym: OpenMM 4
synonym: OpenMM 7
synonym: OpenMM 8
IAO_0000115: Software toolkit to run modern molecular simulations. It can be used either as a standalone application for running simulations, or as a library that enables accelerated calculations for molecular dynamics on high-performance computer architectures.

NeuroJobs
type: Resource
type: NamedIndividual
has db xref: nif-0000-23424
IAO_0000115: A job search resource for careers in neuroscience. The website connects members with employment opportunities, professional development resources and educational materials about career paths.

Molecular Imaging Probes
type: Resource
type: NamedIndividual
has db xref: nif-0000-23695
abbrev: MIP
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2, 2022. A database of molecular imaging probes for various diseases, such as Parkinson's disease, dopamine disorder and prion disorders.

PsychoGenics Inc
type: Organization
type: NamedIndividual
has db xref: nif-0000-24069
synonym: PGI
IAO_0000115: PsychoGenics, a leader in preclinical neurobiology and in the provision of CNS drug discovery solutions, works with pharmaceutical companies and not-for-profit organizations to validate targets and select compounds to advance into clinical trials. PsychoGenics transforms drug discovery by combining expertise in behavioral neurobiology with the power of bioinformatics in conjunction with proprietary, high-throughput behavioral testing platforms that rapidly screen compound libraries for CNS activity.

TNO-DECO
type: Resource
type: NamedIndividual
has db xref: OMICS_02660
IAO_0000115: Matlab code for preprocessing gas chromatography mass spectrometry data.

EthoVision XT
type: Resource
type: NamedIndividual
has db xref: rid_000100
IAO_0000115: Video tracking software that tracks and analyzes the behavior, movement, and activity of any animal.

ALS Association
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100000971
has db xref: grid.430438.8
has db xref: ISNI: 0000 0004 0590 7963
has db xref: nif-0000-00449
has db xref: Wikidata: Q4652439
synonym: ALS Association - Fighting Lou Gehrig's Disease
synonym: Amyotrophic Lateral Sclerosis Association
IAO_0000115: Established in 1985, The ALS Association is the only national non-profit organization fighting Lou Gehrig's Disease on every front. By leading the way in global research, providing assistance for people with ALS through a nationwide network of chapters, coordinating multidisciplinary care through certified clinical care centers, and fostering government partnerships, The Association builds hope and enhances quality of life while aggressively searching for new treatments and a cure. As the preeminent ALS organization, The Association leads the way in research, care services, public education, and public policy giving help and hope to those facing the disease. The Association's nationwide network of chapters provides comprehensive patient services and support to the ALS community. The mission of The ALS Association is to lead the fight to treat and cure ALS through global research and nationwide advocacy, while also empowering people with Lou Gehrig's Disease and their families to live fuller lives by providing them with compassionate care and support. The ALS Association has committed more than $58 million to find effective treatments and a cure for Lou Gehrig's Disease. Our global research effort has helped increase the number of scientists working on ALS, advanced new discoveries and treatments, and has shed light on the complex genetic and environmental factors involved in ALS. Diversity exemplifies The ALS Association's research philosophy. The Association spearheads investigator-initiated projects that originate from the minds of scientists. It also has ALS Association-initiated projects in which research ideas come from a small, blue ribbon committee of scientists who reach out with specific projects for designated scientists in the field. The ALS Association offers multi-year grants to established investigators, as well as one-year starter research awards. The Association is proud to administer The Milton Safenowitz Post-Doctoral Fellowship for ALS Research, w…

OntoMorph Tab
type: Resource
type: NamedIndividual
has db xref: nif-0000-24916
synonym: OntoMorph
IAO_0000115: OntoMorph is a tab plugin for Protege-OWL 3 that allows a user to mark-up portions of a Neurolucida neuron morphology with OWL instances. A user loads a Neurolucida morphology file, either from their hard drive or from an arbitrary URL, into an interface that allows them to zoom, rotate, and translate the morphology. The interface allows them to select points on the morphology to indicate points, segments, or subtrees of the morphology they wish to assign to an OWL instance. After this selection has been made, OntoMorph saves the selection to the currently active OWL instance in the ontology that is currently loaded into Protege. No modifications are made to the Neurolucida file itself. As a result, an association is created between that portion of the morphology and the OWL instance, such that selecting the OWL instance allows retrieval of the portion. Upon retrieval, the morphology portion can be highlighted, so the user can keep track of what pieces each instance refer to.

SigFuge
type: Resource
type: NamedIndividual
has db xref: OMICS_05201
IAO_0000115: Algorithm for testing significance of clustering in RNA-seq data.

International Consortium for Brain Mapping
type: Resource
type: NamedIndividual
has db xref: nif-0000-00041
has db xref: nif-0000-00103
has db xref: SCR_001948
synonym: ICBM - International Consortium for Brain Mapping
synonym: ICBM Atlas
synonym: ICBM Subject Database
synonym: International Consortium for Brain Mapping (ICBM)
abbrev: ICBM
IAO_0000115: Probabilistic reference system for human brain, including tools to establish this reference system for structural and functional anatomy on both macroscopic (in vivo) and microscopic (post mortem) levels. Project has expanded neuroinformatics tools for data sharing and created Conforming Site System that allows laboratories worldwide to contribute data to evolving atlas. Through implementation of ICBM data sharing policy space, they are fostering data exchange while still providing for scientific credit assignment and subject confidentiality.ICBM atlas collection consists of ICBM Template, tool developed to provide reference that includes both set of coordinates and associated anatomical labels; the ICBM 452 T1 atlas, average of T1-weighted MRIs of normal young adult brains, ICBM probabilistic atlases, and Cytoarchitectonic Atlas. ICBM Subject Database is web-based database infrastructure that simplifies image dataset collection, organization and dissemination. Authorized users may view representations of data and form collections of datasets that can be downloaded or fed directly into Pipeline environment for distributed processing and analysis.

National Research Council
type: Resource
type: NamedIndividual
has db xref: nif-0000-00486
synonym: NRC
IAO_0000115: Private, non-profit institution dedicated to utilizing knowledge in science, engineering, technology and health to improve government decision making and public policy as well as increase public education and understanding. The council collects, analyzes and shares information and knowledge through activities such as consensus studies, meetings and workshops, and program and research management.

National Spasmodic Dysphonia Association
type: Resource
type: NamedIndividual
has db xref: nif-0000-00490
synonym: NSDA
IAO_0000115: The mission of the National Spasmodic Dysphonia Association is to advance medical research into the causes of and treatments for spasmodic dysphonia, promote physician and public awareness of the disorder, and provide support to those affected by spasmodic dysphonia.

Talairach Daemon
type: Resource
type: NamedIndividual
has db xref: nif-0000-00042
synonym: Talairach Software
abbrev: talairach.org
IAO_0000115: Software automated coordinate based system to retrieve brain labels from the 1988 Talairach Atlas. Talairach Daemon database contains anatomical names for brain areas using x-y-z coordinates defined by the 1988 Talairach Atlas.

stsPlots
type: Resource
type: NamedIndividual
has db xref: OMICS_05141
IAO_0000115: Software to plot primary analysis quality control metrics to assess potential SMRTcell loading problems.

Bio-Formats
type: Resource
type: NamedIndividual
has db xref: nif-0000-30175
synonym: Bio-Formats Library
synonym: BioFormats
synonym: The Bio-Formats Library
IAO_0000115: Standalone software Java library for reading microscopy image data files in any format and writing image data using standardized, open formats. It currently reads and converts more than 120 file formats to the OME-TIFF data standard.

CAGE Basic Viewer for Mus musculus
type: Resource
type: NamedIndividual
has db xref: nif-0000-30231
abbrev: CAGE Basic Viewer
IAO_0000115: A web system, which could search and display to current CAGE library information in CAGE Database.

Sulfinator
type: Resource
type: NamedIndividual
has db xref: OMICS_02436
synonym: The Sulfinator
IAO_0000115: Data analysis service that predicts tyrosine sulfation sites in protein sequences.

Rdisop
type: Resource
type: NamedIndividual
has db xref: biotools:rdisop
has db xref: OMICS_02416
synonym: Decomposition of Isotopic Patterns
synonym: Rdisop - Decomposition of Isotopic Patterns
synonym: Rdisop: Decomposition of Isotopic Patterns
IAO_0000115: Software for identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists.

pbcore
type: Resource
type: NamedIndividual
has db xref: OMICS_05135
IAO_0000115: Software Python library for reading and writing PacBio data files.

GeneExpressionSignature
type: Resource
type: NamedIndividual
has db xref: OMICS_04919
synonym: GeneExpressionSignature - Gene Expression Signature based Similarity Metric
IAO_0000115: An R package developed for the large-scale analysis of gene expression signatures. It gives the implementations of the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. And its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest.

RegenBase
type: Resource
type: NamedIndividual
has db xref: nlx_156707
synonym: Regen Base
synonym: RegenBase - repairing the injured nervous system
synonym: RegenBase KnowledgeBase
IAO_0000115: Information framework and knowledge base to facilitate research about nervous system regeneration. It includes minimal information standards, an ontology that is linked to other ontologies, and a knowledge base built with a triple store and a relational database.

sybil - Efficient Constrained Based Modelling in R
type: Resource
type: NamedIndividual
has db xref: OMICS_06008
synonym: sybil: sybil - Efficient Constrained Based Modelling in R
abbrev: sybil
IAO_0000115: A Systems Biology Library for R, implementing algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis). This is an implementation of COBRA toolbox in R language.

msbwt
type: Resource
type: NamedIndividual
has db xref: OMICS_05976
synonym: multi-string BWT
IAO_0000115: A software package for creating, merging, and querying multi-string BWTs.

MAXCHELATOR
type: Resource
type: NamedIndividual
has db xref: nlx_156862
abbrev: MAXC
IAO_0000115: A series of programs for determining the free metal concentration in the presence of chelators or total metal given a desired free concentration.

Sea Urchin Embryology
type: Resource
type: NamedIndividual
has db xref: nlx_156868
IAO_0000115: Laboratory modules designed for high school students covering sea urchin embryology including fertilization and development.

MetaDrug
type: Organization
type: NamedIndividual
has db xref: OMICS_01584
IAO_0000115: A leading systems pharmacology solution that incorporates extensive manually curated information on biological effects of small molecule compounds. Predictive and analytical algorithms look at chemical compounds from different angles in one integrated workflow are available for: * Individual previously described compounds to look up their known information and predict currently unknown properties * Individual newly synthesized or isolated compounds to predict their properties from its structures * Compound libraries to extract known and predict new properties of individual compounds and perform their comparison and prioritization

Genome BioInformatics Research Lab - gff2ps
type: Resource
type: NamedIndividual
has db xref: biotools:gff2ps
has db xref: nif-0000-30611
has db xref: OMICS_17140
synonym: gff2ps
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for visualizing annotations of genomic sequences. The program has features such as the ability to create comprehensive plots, customizable parameters, and flexibility in file format.

Reprever
type: Resource
type: NamedIndividual
has db xref: OMICS_01561
synonym: Reprever: resolving low-copy duplicated sequences using template drive
IAO_0000115: Software that identifies (a) the insertion breakpoints where the extra duplicons inserted into the donor genome and (b) the actual sequence of the duplicon for any genomic regions that are increased in copy number.

POPBAM
type: Resource
type: NamedIndividual
has db xref: biotools:popbam
has db xref: OMICS_01559
IAO_0000115: A tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome.

iSpyBio.com
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_156870
has db xref: nlx_157275
has db xref: SCR_010229
abbrev: iSpyBio
IAO_0000115: Search engine for Life scientists that ranks reagents by the amount of data available, such as publications, reviews, characterization images and tested applications. It displays reagents such as antibodies, proteins, ELISA kits and biomolecules. Its proprietary search algorithm is unique and rapidly analyzes the end-user's search query against its large database, while powerful filters allow the user to enhance search results. As iSpyBio syncs with supplier and other public databases, it is always up-to-date - allowing iSpyBio to exclude out of stock items, whilst also showing the most recent testing results and peer-reviewed publications.

Health Level Seven International
type: Organization
type: NamedIndividual
has db xref: grid.434932.b
has db xref: nlx_157307
has db xref: Wikidata: Q17054989
abbrev: HL7
IAO_0000115: ANSI-accredited standards developing organization providing a comprehensive framework and related standards for the exchange, integration, sharing, and retrieval of electronic health information that supports clinical practice and the management, delivery and evaluation of health services. HL7's 2,300+ members include approximately 500 corporate members who represent more than 90% of the information systems vendors serving healthcare. HL7 provides standards for interoperability that improve care delivery, optimize workflow, reduce ambiguity and enhance knowledge transfer among all of their stakeholders, including healthcare providers, government agencies, the vendor community, fellow SDOs and patients.

nmrML
type: Resource
type: NamedIndividual
has db xref: biotools:nmrml_converter
has db xref: nlx_157309
IAO_0000115: An open mark-up language for NMR data.

SAMBLASTER
type: Resource
type: NamedIndividual
has db xref: biotools:samblaster
has db xref: OMICS_04682
IAO_0000115: Software tool to mark duplicates and extract discordant and split reads from SAM files. This fast and flexible program for marking duplicates in read-id grouped paired-end SAM files can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.

SpeedSeq
type: Resource
type: NamedIndividual
has db xref: OMICS_04673
IAO_0000115: Software for a lightweight, flexible, and open source pipeline that identifies genomic variation (single nucleotide variants (SNVs), indels, and structural variants (SVs)).

Non-Human Genome Segmental Duplication Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-03194
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. It contains information about segmental duplications in the genomes of chimpanzee, mouse, and rat. The criteria used to identify regions of segmental duplication are: * Sequence identity of at least 90% * Sequence length of at least 5 kb * Not be entirely composed of repetitive elements. BACKGROUND: The high quality of the mouse genome draft sequence and its associated annotations are an invaluable biological resource. Identifying recent duplications in the mouse genome, especially in regions containing genes, may highlight important events in recent murine evolution. In addition, detecting recent sequence duplications can reveal potentially problematic regions of the genome assembly. We use BLAST-based computational heuristics to identify large (>/= 5 kb) and recent (>/= 90% sequence identity) segmental duplications in the mouse genome sequence. Here we present a database of recently duplicated regions of the mouse genome found in the mouse genome sequencing consortium (MGSC) February 2002 and February 2003 assemblies. RESULTS: We determined that 33.6 Mb of 2,695 Mb (1.2%) of sequence from the February 2003 mouse genome sequence assembly is involved in recent segmental duplications, which is less than that observed in the human genome (around 3.5-5%). From this dataset, 8.9 Mb (26%) of the duplication content consisted of "unmapped" chromosome sequence. Moreover, we suspect that an additional 18.5 Mb of sequence is involved in duplication artifacts arising from sequence misassignment errors in this genome assembly. By searching for genes that are located within these regions, we identified 675 genes that mapped to duplicated regions of the mouse genome. Sixteen of these genes appear to have been duplicated independently in the human genome. From our dataset we further characterized a 42 kb recent segmental duplication of Mater, a maternal-effect gene essential for embryogenesis in mice. CONCLUSION:…

pyQPCR
type: Resource
type: NamedIndividual
has db xref: OMICS_02326
IAO_0000115: A GUI application written in python that deals with quantitative PCR (QPCR) raw data. Using quantification cycle values extracted from QPCR instruments, it uses a proven and universally applicable model to give finalized quantification resu

RefFinder
type: Resource
type: NamedIndividual
has db xref: OMICS_02321
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Web-based tool for evaluating and screening reference genes from extensive experimental datasets. It integrates major computational programs (geNorm, Normfinder, BestKeeper, and the comparative delta-Ct method) to compare and rank the tested candidate reference genes. Based on the rankings from each program, it assigns an appropriate weight to an individual gene and calculated the geometric mean of their weights for the overall final ranking., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Gazetteer
type: Resource
type: NamedIndividual
has db xref: nlx_157412
abbrev: GAZ
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Description not available.

Denver University Department of Psychology
type: Organization
type: NamedIndividual
has db xref: nif-0000-01928
synonym: DU Dept. of Psychology
synonym: University of Denver Department of Psychology
IAO_0000115: The department of psychology at Denver University that offers degrees at the undergraduate, graduate and doctoral level. The doctoral programs have specializations such as Affect/Social, Child Clinical, Cognitive, and Developmental.

PGS
type: Resource
type: NamedIndividual
has db xref: biotools:pgs
has db xref: OMICS_04651
synonym: Penalized GEE with Grid Search
synonym: PGS: Penalized GEE with Grid Search
IAO_0000115: Software tool for association study of high-dimensional microRNA expression data with repeated measures. The penalized regression model incorporates a grid search method for analyzing associations of high-dimensional microRNA expression data with repeated measures.

Human Disease Ontology
type: Resource
type: NamedIndividual
has db xref: biotools:disease_ontology
has db xref: nif-0000-35926
has db xref: nlx_157432
has db xref: SCR_003491
synonym: Disease Ontology
synonym: Human Disease Ontology Knowledgebase
abbrev: DO
IAO_0000115: Comprehensive hierarchical controlled vocabulary for human disease representation.Open source ontology for integration of biomedical data associated with human disease. Disease Ontology database represents comprehensive knowledge base of inherited, developmental and acquired human diseases.

Information Artifact Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157441
abbrev: IAO
IAO_0000115: An ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch. Please note: The ontology metrics displayed by BioPortal do not distinguish IAO-developed terms from terms imported from other ontologies.

Neurosciences on the Internet
type: Resource
type: NamedIndividual
has db xref: nif-0000-00024
synonym: Neurosciences on the Internet http://www.neuroguide.com/
synonym: Neurosciences on the Internet Neuroguide.com
abbrev: Neuroguide.com
IAO_0000115: A searchable and browsable index of neuroscience resources available on the internet including neurobiology, neurology, neurosurgery, psychiatry, psychology, cognitive science sites and information on human neurological diseases. Two categories exist: Best Bets and Cutaneous Fields of Peripheral Nerves.

NCBITaxon
type: Resource
type: NamedIndividual
has db xref: nlx_157490
synonym: National Center for Biotechnology Information (NCBI) Organismal Classification
synonym: National Center for Biotechnology Information Organismal Classification
synonym: NCBI Organismal Classification
abbrev: NCBITAXON
IAO_0000115: Ontology that is an automatic translation of the NCBI taxonomy (a taxonomic classification of living organisms and associated artifacts) database into obo/owl.

miRprimer
type: Resource
type: NamedIndividual
has db xref: OMICS_02311
synonym: miRprimer - Automatic design of primers for miR-specific RT-qPCR
IAO_0000115: Software tool for automatic design of primers for PCR amplification of microRNAs using the method miR-specific RT-qPCR (Balcells, I., Cirera, S., and Busk, P.K. (2011). Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers. BMC Biotechnol. 11, 70).

iBMQ
type: Resource
type: NamedIndividual
has db xref: OMICS_04601
synonym: iBMQ - integrated Bayesian Modeling of eQTL data
IAO_0000115: Software for integrated Bayesian Modeling of eQTL data. It implements a joint hierarchical Bayesian model where all genes and SNPs are modeled concurrently.

NIMBL
type: Resource
type: NamedIndividual
has db xref: OMICS_02305
synonym: NIMBL: Numerical Identification of Methylation Biomarker Lists
synonym: Numerical Identification of Methylation Biomarker Lists
IAO_0000115: MATLAB code to quality control and prioritize differentially methylated markers from illumina infinium arrays.

Gene Bridges
type: Organization
type: NamedIndividual
has db xref: nlx_158134
synonym: Gene Bridges - The Recombineering Company
synonym: Gene Bridges GmbH
IAO_0000115: A biotech company that commercializes its patented Red/ET recombination worldwide as licenses and supplies several products for the pharmaceutical and biotech industry as well as academia. It operates from the Technologie Park in Heidelberg and provides customized in-house DNA modification of any kind. Recombineering with Red/ET allows cloning, subcloning and modification of DNA at any chosen position. It permits precise engineering of DNA molecules of any size, including very large ones such as BACs or the E.coli chromosome.

BrainNet Europe Sampling Protocols
type: Resource
type: NamedIndividual
has db xref: nlx_158157
abbrev: BNE Sampling protocols
IAO_0000115: Sampling protocols produced by the BrainNet Europe Consortium generally with five types of dissection and brain processing procedures defined in all disease related protocols. * Fresh brain dissection * Fresh brain processing * Dissection of formalin-fixed brain * Histology and immunohistochemistry * Processing fresh brain

Alzheimer Society of Canada
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100000143
has db xref: grid.453286.e
has db xref: ISNI: 0000 0001 0702 2390
has db xref: nlx_158162
has db xref: Wikidata: Q4738828
IAO_0000115: A nonprofit health organization that works to improve the quality of life of Canadians affected by Alzheimer's disease and other dementias. This organization also supports research on the cause and potential cures for the disease through education and funding.

Simulx
type: Resource
type: NamedIndividual
has db xref: nlx_158166
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 8, 2025. R function for computing predictions and simulating data from both Mlxtran and PharmML models that is based on MlxCompute, the model simulation engine developed by Lixoft. MlxCompute combines the Mlxtran language interpreter with the equation solvers to compute efficiently complex systems of ordinary differential equations (ODEs) and delayed differential equations (DDEs). Simulx takes advantage of the modularity of hierarchical models for simulating different components of a model: models for population parameters, individual covariates, individual parameters and longitudinal data, including continuous, count, categorical, and time-to-event data. It is also extremely flexible for defining complex dose regimens. Simulx will be the core of the next version of the DDMoRe Clinical Trial Simulator.

PharmML
type: Resource
type: NamedIndividual
has db xref: nlx_158169
synonym: Pharmacometrics Markup Language
abbrev: pharmML
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Standard for encoding of models, associated tasks and their annotation as used in pharmacometrics.

sigma-tau
type: Organization
type: NamedIndividual
has db xref: nlx_158258
synonym: Leadiant Biosciences
synonym: sigma-tau s.p.a.
IAO_0000115: Italian pharmaceutical company involved in research, manufacture and marketing of drugs. sigma-tau is present today in the most advanced research sectors, maintaining constant relations with scientific institutions with a world-wide reputation in the development of joint projects and in the implementation of original and innovative research programs.

Oncotest
type: Organization
type: NamedIndividual
has db xref: nlx_158264
synonym: Oncotest GmbH
IAO_0000115: A contract research organization (CRO) specializing in preclinical oncology services. As a pioneer in the field of patient derived tumor xenografts (PDX), they provide tailored solutions to the problems faced by preclinical oncology researchers. They assist with the identification of the best drug candidates and the validation of their targets and deliver in-depth bioinformatics analyses, laying the groundwork for the successful planning of clinical trials. Their diverse tumor model collection enables them to recommend the right assays and models to answer their customers' questions. Their AAALAC accredited facilities with IVC system, separate model development unit, large cage capacity of over 14,500 mice and proprietary electronic measurement system with an integrated database and by continuously maintaining important PDX models in mice, they are able to provide the highest standard of testing within a reasonable timeframe.

Bio-derived Feedstocks for Sustainable UK-Based Manufacture of Chemicals and Pharmaceutical Intermediates
type: NamedIndividual
has db xref: nlx_158450
abbrev: BFSUKMCPI
IAO_0000115: Project aiming to establish a range of new technologies to enable the synthesis of a range of chemicals from sugar beet pulp (SBP) in a cost-effective and sustainable manner. The chemical and pharmaceutical industries are currently reliant on petrochemical derived intermediates for the synthesis of a wide range of valuable products. Decreasing petrochemical reserves and concerns over costs and greenhouse gas emissions are driving the search for renewable sources of organic synthons. The UK is self-sufficient in the production of SBP which is a by-product of sugar beet production (8 million tonnes grown per year) and processing. The ability to convert SBP into chemicals and pharmaceutical intermediates will therefore have significant economic and environmental benefits. SBP is rich in carbohydrate (nearly 80% by weight) which is made up of roughly equal proportions of 2 biological polymers; cellulose and pectin. To be cost-effective it will be necessary to find uses for each of these substances. The consortium will develop a biorefinery approach for the selective breakdown of both polymers, purification of the breakdown compounds and their use to synthesize a range of added value products such as speciality chemicals, pharmaceuticals and biodegradable polymers. It is already known that cellulose can be broken down into hexose sugars and fermented to ethanol for use in biofuels. The focus is on the release of galacturonic acid and arabinose (from pectin) and their conversion, by chemical or enzymatic means, into added value products. Synthetic Biology methods will also be explored to test the feasibility of metabolically engineering microbial cells to simultaneously breakdown the polymeric feed material and synthesize a desired product, such as aromatic compounds, in a single integrated process. In conducting this research the consortium will adopt a holistic, systems-led, approach to biorefinery design and operation. Computer-based modelling tools will be used to ass…

Digital Asset Management System
type: Resource
type: NamedIndividual
has db xref: nlx_158282
synonym: UC San Diego Library DAMS repository
synonym: UC San Diego Library Digital Asset Management System
abbrev: DAMS
IAO_0000115: A digital repository designed to store and manage digital assets of UC San Diego. The flexible architecture can accept a variety of data formats, schemas and web services when ingesting digital assets. It stores digital content files and allows for the creation, indexing and searching of associated metadata to locate and retrieve the content files. Content can be composed of files in any format, including text, sound, video, and images. The DAMS is also designed to facilitate the transfer and submission of the Library's digital assets to Chronopolis and the California Digital Library's Merritt, and can easily be extended to serve other purposes. Additionally, the DAMS is able to export data in many formats, including METS, HTML, OAI, RSS, CSV. Future plans include linking data sets with other universities and organizations. For more information about the DAMS, including the data model and technical diagram, see Github, https://github.com/ucsdlib: * DAMS Manual, https://github.com/ucsdlib/dams/wiki/DAMS-Manual * DAMS Hydra Head, https://github.com/ucsdlib/damspas * DAMS REST API, https://github.com/ucsdlib/dams/wiki/REST-API * DAMS Ontology, https://github.com/ucsdlib/dams/tree/master/ontology Additional information on Hydra is available at Project Hydra and Duraspace.

AlzProtect
type: Organization
type: NamedIndividual
has db xref: nlx_158327
synonym: Alz Protect
synonym: AlzProtect - Therapeutic Solutions for Neurodegeneration
synonym: Alzprotect SAS
synonym: SAS AlzProtect
IAO_0000115: Commercial organization that develops drug candidates in the field of neurodegenerative diseases and particularly Alzheimer's. Their main objective is the development of a drug against Alzheimer's disease from molecules patented by Inserm and the University of Lille II.

Exonhit Therapeutics
type: Organization
type: NamedIndividual
has db xref: nlx_158329
synonym: Diaxonhit
synonym: ExonHit Therapeutics S.A.
synonym: Exonhit Therapeutics SA
IAO_0000115: A drug and diagnostic discovery company.

Royal Society of Chemistry
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100000704
has db xref: grid.431456.1
has db xref: ISNI: 0000 0001 0668 7091
has db xref: nlx_158344
has db xref: Wikidata: Q905549
abbrev: RSC
IAO_0000115: The UK's professional body for chemical scientists, supporting and representing members and bringing together chemical scientists from all over the world. This not-for-profit organisation has an international publishing business and their activities span education, conferences, science policy and the promotion of chemistry to the public. They have offices in Europe, Asia, North America and South America.

Open PHACTS Foundation
type: Resource
type: NamedIndividual
has db xref: nlx_158351
synonym: The Open PHACTS Foundation
abbrev: OPF
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 5,2025. A not-for-profit membership organization, supporting the Open PHACTS Discovery Platform: A sustainable, open, and interoperable information infrastructure for applied life science research and development. The foundation is the successor organization of the Open PHACTS project, and aims to ensure the sustainability of the Open PHACTS Discovery Platform infrastructure. OPF also acts as a hub for scientific research and development relevant to the life sciences, and serves as a forum for the scientific community, allowing idea exchange between the pharmaceutical industry, academia and SMEs. OPF is a UK-based not-for-profit membership organization, but operates in an international commercial environment.

Aging Portal
type: Resource
type: NamedIndividual
has db xref: nlx_158366
abbrev: Aging
IAO_0000115: Portal devoted to aging relevant scientific data and resources.

Drug Design Data Resource
type: Resource
type: NamedIndividual
has db xref: nlx_158375
synonym: Drug Design Data (D3R) Resource
abbrev: D3R
IAO_0000115: Project portal's database of protein-ligand data sets provided by pharmaceutical partners that provide atomic details of drug mechanisms that will be used to improve computer-aided drug-design methods and thus accelerate drug discovery. The project aims to help companies release the high-quality data they have generated, which has incredible value to researchers working to improve methods of computer-aided drug discovery. Everyone stands to benefit from the ability to develop new medications more quickly and inexpensively. What computational chemists globally are trying to do is to make faster, more accurate, more predictive programs to speed up the process. Part of their mission is to engage the community in these challenges to test newly developed predictive algorithms.

TDARACNE
type: Resource
type: NamedIndividual
has db xref: OMICS_02013
synonym: TDARACNE - Network reverse engineering from time course data
IAO_0000115: Software package to infer gene regulatory networks from time-series measurements. The algorithm is expected to be useful in reconstruction of small biological directed networks from time course data.

Heptares Therapeutics
type: Organization
type: NamedIndividual
has db xref: grid.450873.d
has db xref: ISNI: 0000 0004 0456 4700
has db xref: nlx_158498
synonym: Heptares
synonym: Heptares Therapeutics Limited
synonym: Heptares Therapeutics Ltd
IAO_0000115: A drug discovery company focused on small-molecule drugs targeting G-protein-coupled receptors (GPCRs), the largest family of druggable targets. Heptares creates new medicines targeting previously undruggable or challenging GPCRs, a superfamily of receptors linked to many diseases. They are pioneering a structure-based drug design approach to GPCRs, leveraging proprietary technologies for protein stabilization, structure determination, and fragment-based discovery. Their partners include Cubist, MorphoSys, AstraZeneca, MedImmune and Takeda. Their objective is to build a broad pipeline of novel medicines to transform the treatment of serious diseases, including Alzheimer's disease, schizophrenia, diabetes, ADHD and chronic migraine.

brainSCANr
type: Resource
type: NamedIndividual
has db xref: nlx_143546
synonym: Brain Systems Connections Associations and Network Relationships
IAO_0000115: A database of neuroscience-related concepts that utilizes visualization tools for the purpose of research, education and knowledge discovery. The data comes from PubMed abstracts and an algorithm that assumes related terms will appear together. The topics can include computational modeling, behavioral functions and neurological degeneration.

ECNP
type: Resource
type: NamedIndividual
has db xref: nlx_158605
synonym: ECNP - neuroscience applied
synonym: European College of Neuropsychopharmacology
IAO_0000115: A pan-European scientific association to encourage research across the neurosciences and to translate new knowledge on fundamental disease mechanisms into new medicines and clinical applications. As an interdisciplinary forum for the science and treatment of disorders of the brain, they promote the communication and cross- fertilization of high-quality experimental and clinical research across the field of neuroscience. ECNP is a non-profit member-based association, independently governed and self-funded. ECNP is a public-interest-serving entity.

Bitbucket
type: Resource
type: NamedIndividual
has db xref: nlx_158615
synonym: Atlassian Bitbucket
IAO_0000115: A hosting site for the distributed version control systems (DVCS) Git and Mercurial. The service offering includes an issue tracker and wiki, as well as integration with a number of popular services such as Basecamp, Flowdock, and Twitter.

Wordpress for Scientists
type: Resource
type: NamedIndividual
has db xref: nlx_18849
IAO_0000115: A list of Wordpress plugins that are useful for authoring scientific papers. Listed plugins include BibTeX Importer, Link to Link, Broken Link Checker, and Contact Info Options, among many others.

Brain Mysteries
type: Resource
type: NamedIndividual
has db xref: nlx_19443
IAO_0000115: A blog featuring articles on the brain, consciousness, cognitive science, psychology and neurology. This resource is in Russian.

IFTI-Mirage
type: Resource
type: NamedIndividual
has db xref: nlx_19877
synonym: Institute for Transcriptional Informatics-Molecular Informatics Resource for the Analysis of Gene Expression
synonym: MIRAGE
IAO_0000115: A resource for information pertaining to methodologies, tools and technologies of gene expression. The website offers resources for sequence analysis, database services, and other technologies of gene expression and regulation.

FluWikie.com
type: Resource
type: NamedIndividual
has db xref: nlx_22823
synonym: Flu Wikie
synonym: FluWikie
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. Flu Wikie is a topical portal on the flu. Major categories include health, Flu Symptoms, Avian Influenza, Swine Flu, Cold, Vaccination, Pandemic, Vitamin D, and Immune System. Many articles on topic are included.

BioEden Tooth Cell Bank
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_25195
abbrev: BioEDEN
IAO_0000115: International private stem cell storage bank to collect, assess and cryogenically store living tooth cells from deciduous baby teeth. Tooth cell banking is a safe, natural and completely noninvasive method of collecting and preserving valuable stem cells which could hold the key to your child's health. Simply enroll, send us your child's tooth when it falls out, and they'll do the rest. Stem cell treatment to repair or replace damaged tissues or organs is the cornerstone of future medical science. Children's milk teeth, (baby teeth) have been identified as a rich source of these stem cells and have the potential to treat some of the worst illnesses and diseases facing people today. Stem cells from teeth (mesenchymal stem cells) are different from those found in cord blood (hematopoietic stem cells). Cord blood cells can be used to treat blood disorders such as leukemia, but stem cells from teeth are different. Stem cells from teeth can be used to grow a range of tissues including bone, nerve, fat, muscle and cartilage and may one day be used to grow entire organs. It is widely believed that stem cells will be used to treat a wide variety of diseases and injuries within the next decade. Their UK facility is regulated by the Human Tissue Authority (HTA), and they hold a full license. They are also registered with the Food and Drug Administration (FDA) in the US. BioEDEN, Ltd is ISO 9001:2008 accredited by the British Assessment Bureau. When you enroll for the BioEDEN service, you will be offered the opportunity to consent to donate any excess cells. BioEDEN will provide these cells to leading academic and clinical research centers to help further the progression of this technology to useful clinical applications. BioEDEN will only provide cells to researchers that have full ethical approval for their research and will be guided by our Advisory team as to the most appropriate research to support. The cells will be donated in accordance with strict regulatory guidelines…

Karmanos Cancer Institute
type: Resource
type: NamedIndividual
has db xref: nlx_143656
synonym: Barbara Ann Karmanos Cancer Center
synonym: Barbara Ann Karmanos Cancer Institute
synonym: Karmanos Cancer Center
abbrev: Karmanos
IAO_0000115: Center for patient care, education and research on cancer. The institute focuses its research on prevention methods, early detection, treatment and finding cures.

Windber Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_29009
synonym: Windber Research Institute Tissue Bank
synonym: Windber Research Institute Tissue Banking
synonym: Windber Tissue Banking
synonym: WRI Tissue Banking
abbrev: WRI Tissue Bank
IAO_0000115: Under the direction of Stella Somiari, Ph.D., the tissue bank at Windber Research Institute acquires and banks large numbers of high quality and well annotated normal and diseased tissue specimens. These specimens are obtained from fully informed and consented donors using Institutional Review Board (IRB) approved protocols and are accompanied by detailed clinical, family history and demographic information. The tissue bank has established Standard Operating Procedures (SOPs) for tissue acquisition, handling, processing, packaging and shipping. All collaborators at participating clinics/medical centers utilize these procedures to ensure that the integrity of the specimen is maintained. Tissue types in our collection include plasma, serum, tissue embedded in optimum cutting temperature (OCT), formalin fixed paraffin embedded, and flash frozen. We also isolate and bank tissue derived products such as DNA, RNA and protein for research. Very stringent SOPs are in place for the process of extraction of these tissue-derived products and for quality control/quality assurance (QA/QC). The WRI tissue bank currently has 5 isothermal freezers each with the capacity to store 36,000 specimens. For all specimens obtained from surgical procedures, routine histology is performed to obtain representative Hematoxylin and Eosin (H & E) stained sections for imaging/archiving. All H & E sections are imaged on the Trestle SL-50 imaging system and these images are available online to designated collaborative sites. A certified pathologist verifies all tissue specimens and WRI has telepathology capabilities, which can also be utilized for pathology verification when a second pathologist opinion is required to confirm specimen diagnosis. Other uses of the telepathology capabilities include the verification of Laser Capture Microdissection (LCM) sections (by pathologist) to ensure the correct areas are captured for research. The telepathology system at WRI is the Trestle Corporation's Medmic…

bamova
type: Resource
type: NamedIndividual
has db xref: OMICS_01532
IAO_0000115: Software that implements a Bayesian Analysis of Molecular Variance and different likelihood models for three different types of molecular data (including two models for high throughput sequence data).

BAIT
type: Resource
type: NamedIndividual
has db xref: biotools:bait
has db xref: OMICS_01531
synonym: BAIT - Software to help analyse Strand-Seq data
IAO_0000115: Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data.

PubMed Health
type: Resource
type: NamedIndividual
has db xref: nlx_32805
synonym: Pub Med Health
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 9, 2022. A consumer health database that provides up-to-date information on diseases, conditions, injuries, drugs, supplements, treatment options, and healthy living, with a special focus on comparative effectiveness research from institutions around the world. PubMed Health includes * consumer guides summarizing comparative effectiveness research * fact sheets on diseases and conditions * information on drugs and supplements * encyclopedic overviews of health topics * links to external Web sites PubMed Health has a special focus on comparative effectiveness research, in particular that research which evaluates the available evidence of the benefits and harms of different treatment options for different groups of people. In Comparative Effectiveness Research, experts often synthesize the evidence from dozens, or even hundreds, of individual studies.

Boston University Alzheimer's Disease Center Neuropathology Core Facility
type: Resource
type: NamedIndividual
has db xref: nlx_33878
synonym: Boston University Alzheimer's Disease Center - Neuropathology
synonym: Boston University Alzheimer's Disease Center - Neuropathology Core
synonym: BU ADC Neuropathology
synonym: BU ADC Neuropathology Core
synonym: BU Alzheimer's Disease Center - Neuropathology
IAO_0000115: The Neuropathology Core leads neuropathological analyses of brains donated by research registry participants of the Boston University Alzheimer's Disease Center. The Core works with the Clinical Core to carry out the Brain Tissue Donation Program, which provides brain tissue for analyses that will help to understand the underlying pathology of AD. The Core also works closely with the Data Management and Statistics Core to maintain a comprehensive computerized database of information resulting from neuropathological analyses. The Boston University Brain Bank of the Neuropathology Core documents neuropathological findings of Center research registry participants, but also of brain donors from important related BUSM studies such as the Framingham Heart Study and the Centenarian Study.

ARNIE
type: Resource
type: NamedIndividual
has db xref: OMICS_01529
synonym: AVEXIS Receptor Network with Integrated Expression
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Database that integrates the extracellular protein interaction network generated in our lab using AVEXIS technology with spatiotemporal expression patterns for all genes in the network. The tool allows users to browse the network by clicking on individual proteins, or by specifying the spatiotemporal parameters. Clicking on connector lines will allow users to compare stage-matched expression patterns for genes encoding interacting proteins. Additionally, users can rapidly search for their genes in the network using the BLAST server provided.

ARB project
type: Resource
type: NamedIndividual
has db xref: OMICS_01515
synonym: The ARB project
abbrev: ARB
IAO_0000115: Software environment for maintaining databases of molecular sequences and additional information, and for analyzing the sequence data, with emphasis on phylogeny reconstruction. Programs have primarily been developed for ribosomal ribonucleic acid (rRNA) sequences and, therefore, contain special tools for alignment and analysis of these structures. However, other molecular sequence data can also be handled. Protein gene sequences and predicted protein primary structures as well as protein secondary structures can be stored in the same database. ARB package is designed for graphical user interface. Program control and data display are available in a hierarchical set of windows and subwindows. Majority of operations can be controlled using mouse for moving pointer and the left mouse button for initiating and performing operations.

fourSig
type: Resource
type: NamedIndividual
has db xref: OMICS_02628
IAO_0000115: A suite of software programs for analyzing and visualizing 4C-seq data.

UCL Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_36620
synonym: Biobanking at UCL
IAO_0000115: Two University College London (UCL) biobanks, one based at the Royal Free Hospital (RFH) Campus and the other based at Bloomsbury supporting Pathology and the Cancer Institute, will act as physical repositories for collections of biological samples and data from patients consented at UCLH, Partners Hospitals and external sources. This will incorporate collections of existing stored samples and new collections. UCL-RFH BioBank, the physical repository at the Royal Free, presents a unique opportunity to advance medical research through making access to research tissue easier, faster and much more efficient. The BioBank is both a physical repository, with capacity for up to 1 million cryogenically stored samples and a virtual repository for all tissue, cell, plasma, serum, DNA and RNA samples stored throughout UCLP. In particular, samples considered "relevant material", such as tissues and cells, that are licensed by the Human Tissue Authority, can be stored long term. Existing holdings of tissues and cells where appropriate can be transferred to the Physical BioBank at the Royal Free. UCL - Royal Free BioBank provides a flexible approach to banking, allowing the Depositor to pick and choose services that are tailored to fit their requirements. Collaborations arising from publicizing of the existence of the holdings are entirely at the discretion of the depositor, as the facility ensures that access to the deposits remains at the decision of the Depositor/User. UCL Biobank for studying Health and Disease (based at Pathology-Rockefeller building and the UCL-Cancer Institute will support projects principally involved in the study of human disease. The aim is to support primarily, research in the Pathology Department, UCLH and the UCL-Cancer Institute but it will also support other UCLH partners. The biobank will store normal and pathological specimens, surplus to diagnostic requirements, from relevant tissues and bodily fluids. Stored tissues will include; snap-frozen or…

LifeLegacy Foundation
type: Resource
type: NamedIndividual
has db xref: nlx_37185
synonym: LifeLegacy
IAO_0000115: A non-profit tissue bank that facilitates the distribution of non-transplantable tissue to the medical and research community. It provides snap frozen low post mortem interval (PMI) tissue, normal and diseased tissue, plastinated specimens, anatomical specimens, and specialty specimens. The foundation also works to increase public awareness of research tissue donation for medical research.

TFFACTOR
type: Resource
type: NamedIndividual
has db xref: nlx_39049
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 13, 2016. A dataset about transcriptional regulation in eukaryotic cells, including data such as transcription factors and their binding sites and profiles. Resource is in Chinese.

Quality of Medical Data
type: Resource
type: NamedIndividual
has db xref: nlx_39837
IAO_0000115: Portal serves as resource to understand the current state of medical data quality and the factors that affect it. The information is gathered from anecdotal and empirical examples from peer-reviewed journals, popular media and author contributions. Issues of importance include understanding and measuring medical data quality, contributing factors, best practices, and the effects of data quality on secondary uses of medical data.

WikiMD - The free Medical Encyclopedia
type: Resource
type: NamedIndividual
has db xref: nlx_40517
synonym: WikiMD
synonym: wikiMD.org
IAO_0000115: WikiMD is a free wiki based medical encyclopedia and medical wiki community that any registered user can edit. This medical encyclopedia with articles, links, images and information on everything related to medicine and health, has great potential to provide patients with reliable health information as wikiMD is edited by users with close supervision by medical professionals. WikiMD is a sister project of Residentscafe.com - a place for medical students, residency applicants, residents, fellows and attending physicians. Major categories of WikiMD: *Video of the day *Did you know? *Gray's Anatomy *USMLE (United States Medical Licensing Examination) Wiki *Disease Index *Medical Resources *Health Encyclopedia Use the info at your own risk!

Evidence-Based Medicine Librarian
type: Resource
type: NamedIndividual
has db xref: nlx_40990
synonym: EMB Librarian
IAO_0000115: A portal for developing a community of librarians that teach and support the practice of evidence-based medicine (EBM). The site offers a forum for sharing teaching materials, discussing issues and asking for advice from colleagues.

Mfuzz
type: Resource
type: NamedIndividual
has db xref: biotools:mfuzz
has db xref: OMICS_02012
synonym: Mfuzz - Soft clustering of time series gene expression data
IAO_0000115: Software package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

CCLG Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_51003
synonym: Children's Cancer and Leukaemia Group Tissue Bank
synonym: Children's Cancer and Leukemia Group Tissue Bank
IAO_0000115: Tissue bank that provides access to tissue samples and an anonymized version of the tissue bank database.Bank has large collection of tumour, DNA and other tissue samples from childhood cancer patients.

CARTA
type: Organization
type: NamedIndividual
has db xref: nlx_51231
synonym: Center for Academic Research & Training in Anthropogeny
synonym: Center for Academic Research and Training in Anthropogeny
IAO_0000115: A virtual organization that promotes transdisciplinary research into anthropogeny, or the study of human origins. The research interests are broad and include finding the structural and molecular differences between humans and apes, identifying and explaining external mechanisms, and defining the evolutionary origins of humans. The center hosts symposia as well as visiting professors for the anthropogeny graduate program.

NERC Environmental Bioinformatics Centre
type: Resource
type: NamedIndividual
has db xref: nlx_51307
synonym: NERC Environmental Bioinformatics Center
abbrev: NEBC
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Data sharing platform based on the ISA software suite - including an annotation tool and a database - that holds environmental omic data in standards-compliant format. It uses various approaches to provide new discovery, interoperability and integration opportunities for environmental scientists, including the development of tools, databases, standard and ontologies. The main tool for collecting environmental omics data from researchers is the EnvBase data catalogue. The NEBC Toolbox contains a range of tools developed by NEBC to support environmental researchers. The data include next generation sequencing, microarray and ABI sequencing technologies. ISAconfigurator and ISAcreator ensure that the extensive information relating to environmental sampling is consistently collected by the NERC experimentalists, according to the appropriate MIBBI checklist(s), and then reported centrally to NEBC. A local instance of the BII runs as an internal prototype database that will soon provide public and private access to NERC research projects outputs, as appropriate. In accordance with the NERC Data Policy, and when data sets are declared ready for public release, the NEBC team will use the ISAconverter to perform (combined) submissions to the appropriate public repositories (ENA, or SRA, ArrayExpress and PRIDE) to ensure long term stewardship.

ADA GENNID Study
type: Resource
type: NamedIndividual
has db xref: nlx_143803
synonym: ADA Genetics of non-insulin dependent diabetes mellitus Study
synonym: ADA Repository
synonym: ADA The GENNID Study: Genetics of Non-Insulin Dependent Diabetes
synonym: American Diabetes Association GENNID Study
synonym: Genetics of NIDDM Study
abbrev: GENNID Study
IAO_0000115: The purpose of the American Diabetes Association (ADA), GENNID Study (Genetics of non-insulin dependent diabetes mellitus, NIDDM) is to establish a national database and cell repository consisting of information and genetic material from families with well-documented NIDDM. The GENNID Study will provide investigators with the information and samples necessary to conduct genetic linkage studies and locate the genes for NIDDM. Non-Hispanic white, Hispanic, African-American, and Japanese-American multiplex NIDDM families, with a minimum of one affected sib-pair, are being collected by the eight Harold Rifkin Family Acquisition Centers. Detailed family and medical histories are obtained from all participants. Family members with diabetes have fasting blood samples drawn, while nondiabetic family members have an oral glucose tolerance test and, when possible, insulin sensitivity and insulin secretion measurements by frequently sampled intravenous glucose tolerance testing or euglycemic insulin clamp. Lymphoblastoid cell lines are established for all participants. DNA samples and extensive phenotypic data are available from the American Diabetes Association's GENNID study (Genetics of NIDDM). GENNID has collected detailed family histories and a broad array of data on 170 large pedigrees, all of which contain at least one affected sib pair, with a total of 650 affected individuals and approximately 1,200 total subjects. Included are approximately 65 Caucasian, 60 Hispanic, 25 African American, and 20 Japanese American pedigrees. In addition, GENNID also contains DNA and data on 1,000 additional affected sib pairs in each of three groups, African American, Caucasian, and Hispanic. DNA and phenotypic data, including race, gender and age, are available for all members of the pedigrees. The data set includes multiple metabolic factors, including carbohydrate metabolism, lipid metabolism, and body size measures, as well as lifestyle variables obtained by questionnaire (e.g., em…

MaryGold
type: Resource
type: NamedIndividual
has db xref: OMICS_01495
synonym: MaryGold - Variation analysis of metagenomic samples
IAO_0000115: Software package that enables detection of sequence variation between metagenomic samples.

Ohio State Leukemia Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_55663
synonym: OSU Comprehensive Cancer Center Leukemia Tissue Bank Shared Resource
synonym: OSUCCC Leukemia Tissue Bank Shared Resource
synonym: OSUCCC LTBSR
abbrev: LTBSR
IAO_0000115: The OSU Comprehensive Cancer Center Leukemia Tissue Bank Shared Resource (LTBSR) facilitates the successful translation of basic leukemia research to the clinical setting via an extensive repository of tissue samples and accompanying pathologic, cytogenetic and clinical data for ready correlation of clinical and biological results. The LTBSR, which is an NCI-sponsored biorepository, has more than 40,000 vials of cryopreserved viable cells and 13,000 vials of matched frozen plasma and/or serum samples from more than 4,000 patients treated for leukemia and other malignancies. Committed to furthering translational research efforts for OSUCCC - James members and the cancer research community, the LTBSR provides investigators with training and technical support as well as procurement, processing, storage, retrieval and distribution of clinical research materials. In many cases, the LTBSR serves as the central processing lab for multi-site trials in which the principal investigator is an OSUCCC - James member. The LTBSR's goals are to: * Provide a central collection, processing and a state-of-the-art repository for samples collected from leukemia patients treated on OSUCCC - James protocols, and * Provide materials to investigators involved in collaborative studies with OSU, who examine relevant cellular and molecular properties of leukemia and correlate these properties with clinical or population-based outcomes.

Neuroscience News: Neuroscience Videos
type: Resource
type: NamedIndividual
has db xref: nlx_143831
synonym: "Neuroscience Videos" Neuroscience Articles
abbrev: Neuroscience Videos
IAO_0000115: Neuroscience News provides "Neuroscience Videos" and corresponding articles.

Donate Life America
type: Resource
type: NamedIndividual
has db xref: nlx_63855
synonym: Donate Life
synonym: Donate Life Network
synonym: Donate Life Organization
IAO_0000115: Nonprofit alliance of national organizations and state teams dedicated to increasing organ, eye and tissue donation. Donate Life America manages and promotes the national brand for donation, Donate Life, and assists Donate Life State Teams and national partners in facilitating high-performing donor registries; developing and executing effective multi-media donor education programs; and motivating the American public to registeras organ, eye and tissue donors.

Trait Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_65829
synonym: Gramene Plant Trait Ontology
synonym: Gramene Trait Ontology
abbrev: TO
IAO_0000115: Database of controlled vocabulary to describe each trait as a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant (or individual). Some examples include: plant height, disease resistance, and photosensitivity.

TOPPAS
type: Resource
type: NamedIndividual
has db xref: OMICS_02640
synonym: The OpenMS Proteomics Pipeline Assistant
synonym: TOPP Pipeline Assistant
IAO_0000115: A graphical user interface (GUI) for rapid composition of HPLC-MS analysis workflows. Workflow construction is reduced to drag-and-drop of analysis tools and adding connections in between.

SPHINX
type: Resource
type: NamedIndividual
has db xref: OMICS_01466
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Hybrid binning tool that achieves high binning efficiency by utilizing both "compositional" and "similarity" features of the query sequence during the binning process. SPHINX can analyze sequences in metagenomic data sets as rapidly as composition based approaches, but nevertheless has the accuracy and specificity of similarity based algorithms., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Feinstein Biorepository
type: Resource
type: NamedIndividual
has db xref: nlx_67278
synonym: Feinstein Institute for Medical Research Biorepository
synonym: North Shore-LIJ Biorepository
IAO_0000115: The Biorepository was designed to collect, process, and distribute large numbers of high quality research specimens quickly and efficiently. The data that is collected is primarily human DNA from whole blood along with other human specimen types. The data are collected, processed, stored and later distributed to support a large number of research studies. Biobanking of other specimen types include cells, RNA, serum, plasma and tissue. The Biorepository serves as a storage facility for tracking specimen inventory using bar code technologies. The Biorepository also conducts most operations using modern laboratory automation and robotics, an efficient way to avoid processing errors inherent in the handling of larger numbers of specimens.

Neurology and Neurosurgery
type: Resource
type: NamedIndividual
has db xref: nlx_68689
synonym: Neurology and Neurosurgery (Wikibook)
IAO_0000115: A resource and online book on neurology and neurosurgery. The book covers topics such as neurological symptoms, consciousness and unconsciousness, trauma, seizure disorders and dementia.

This Week In Science
type: Resource
type: NamedIndividual
has db xref: nlx_70738
synonym: TWIS - This Week in Science
abbrev: TWIS
IAO_0000115: A podcast hosted by Kristin Sanford and Justin Jackson to explain recent scientific research and developments in a wide range of scientific phenomenon.

Ishtar
type: Resource
type: NamedIndividual
has db xref: nlx_71525
IAO_0000115: A program for designing primer pairs that amplify multiple target sequences using DNA thermodynamics and one class support vector machines. Written in Python.

IMPACT: International Mission for Prognosis and Analysis of Clinical Trials in TBI
type: Resource
type: NamedIndividual
has db xref: nlx_143883
synonym: International Mission for Prognosis and Analysis of Clinical Trials in TBI
synonym: TBI-IMPACT
abbrev: IMPACT
IAO_0000115: Project focused on advancing knowledge of prognosis, trial design and treatment in Traumatic Brain Injury. IMPACT has developed and validated prognostic models for classification and characterization of TBI series, and participated in development of standardization of data collection in TBI studies.

PhyloPythia
type: Resource
type: NamedIndividual
has db xref: OMICS_01459
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Data analysis service for accurate phylogenetic classification of variable-length DNA fragments.

MATCHCLIP
type: Resource
type: NamedIndividual
has db xref: OMICS_02289
synonym: MATCHCLIPS
synonym: matchclips2
IAO_0000115: Software program that detects the precise break points of Copy number variations (CNVs) through a fuzzy string matching algorithm using both CIGAR and POS information. In case the two break points of a CNV are in repeated regions and the break points are not unique, it reports the range where the break points can slide.

University of Michigan Human Breast Cancer Cell Lines
type: Resource
type: NamedIndividual
has db xref: nlx_84393
synonym: University of Michigan Human Breast Cancer Cell Lines (SUM-LINES)
synonym: University of Michigan SUM-LINES
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1, 2023. Asterand, Inc., the Detroit-based supplier of human tissue products and services, announces the distribution of eleven breast cancer cell lines, derived at the University of Michigan. The University has agreed to license the marketing of the breast cancer cell lines, known as the SUM lines, through Asterand in an effort to provide an exceptional tool to a broad base of researchers studying the disease. There are an estimated 1.2 million new diagnoses worldwide of breast cancer each year. The cell lines can be used to study all aspects of breast cancer biology, from new drug target identification to cell signaling to effects of novel drugs on cellular proliferation.

mzMatch
type: Resource
type: NamedIndividual
has db xref: biotools:mzmatch
has db xref: OMICS_02642
IAO_0000115: A software to provide small tools for common processing tasks for LC/MS data. It is an extension to the metabolomics analysis pipeline mzMatch.R. The software is modular, open source, platform independent and written in Java.

Sequence Search and Alignment by Hashing Algorithm
type: Resource
type: NamedIndividual
has db xref: biotools:ssaha2
has db xref: nlx_93831
has db xref: OMICS_00690
synonym: ssaha
synonym: ssaha2
abbrev: SSAHA2
IAO_0000115: A program designed for the efficient mapping of sequence reads onto genomic references. The software is capable of reading most sequencing platforms and giving a range of outputs are supported.

Science Talk
type: Resource
type: NamedIndividual
has db xref: nlx_94534
IAO_0000115: A weekly podcast hosted by Steve Mirsky on topics relating to developments in science and technology through interviews with leading scientists and journalists. This podcast is affiliated with Scientific American.

NEI Clinical Studies
type: Resource
type: NamedIndividual
has db xref: nif-0000-00237
synonym: National Eye Institute Clinical Studies
IAO_0000115: An archived portal of clinical studies, both ongoing and completed, that have been conducted and supported by the National Eye Institute (NEI) since 1970. The portal covers corneal diseases, glaucoma, epidemiology, lens and cataract, retinal diseases, strabismus, amblyopia and visual processing.

Indiana University-Bloomington Neuroscience Program
type: Resource
type: NamedIndividual
has db xref: nlx_95679
synonym: Indiana U Bloomington Neuroscience
synonym: Indiana University Bloomington Neuroscience
synonym: Indiana University Bloomington Neuroscience Program
synonym: IU Bloomington Neuroscience Program
IAO_0000115: A neuroscience PhD program based at Indiana University that focuses on technical skills and the conceptual framework needed to puruse a career of research and/or teaching in neuroscience. Faculty of the neuroscience department fall into one of four areas of research: Molecular and Cellular Neuroscience, Behavioral Neuroscience, Cognitive and Computational Neuroscience and Clinical and Translational Neuroscience.

Iowa Donor Network
type: Organization
type: NamedIndividual
has db xref: nlx_96684
abbrev: IDN
IAO_0000115: A nonprofit organ procurement agency based in Iowa. The organization facilitates both organ and tissue recovery in cooperation with local hospitals. The network also works to support public education, hospital development and family support services.

American Tissue Services Foundation - ATSF
type: Organization
type: NamedIndividual
has db xref: nlx_97074
synonym: American Tissue Services Foundation
abbrev: ATSF
IAO_0000115: A non-profit organization that facilitates the donation of tissues. It supports healthcare agencies, coroners, medical examiners and funeral professionals through donations and training, as well as partnering with organizations that utilize tissue in medical care and research.

National Disease Research Interchange
type: Resource
type: NamedIndividual
has db xref: nlx_99804
abbrev: NDRI
IAO_0000115: NDRI is a Not-For-Profit (501c3) Corporation dedicated to providing the highest quality human biomaterials for research. NDRI makes it easy for researchers to get the human tissues and organs they need, prepared, preserved and shipped precisely according to their specific scientific protocols, as quickly as possible, and in the largest available quantities. NDRI provides researchers with protocol specific human neurological tissues such as brain stem, spinal cord, and basal ganglia, among others. In addition to control specimens, NDRI recovers tissues from donors with a variety of diseases, including Down syndrome, Parkinsons disease, Alzheimers disease, schizophrenia, and dementia. Through the NDRI 24/7 referral and procurement system, research consented biospecimens can be provided from low post mortem interval donors preserved at 4ºC, frozen or snap frozen, fixed, paraffin embedded, or as unstained slides.

Emory ADRC Tissue and Biospecimen Banking Facility
type: Resource
type: NamedIndividual
has db xref: nlx_144036
synonym: Emory ADRC Tissue & Biospecimen Banking Facility
synonym: Emory Tissue & Biospecimen Banking Facility
synonym: Emory Tissue and Biospecimen Banking Facilities
IAO_0000115: The Alzheimer's Disease Research Center at Emery University maintains an active brain bank to facilitate the acquisition, storage, handling and distribution of well-characterized autopsy brain tissue and other materials to investigators. It contains frozen tissue and brain specimens, formalin fixed tissue, paraformaldehyde fixed tissue, and cryopreserved tissue. The ADRC also has access to tissues and samples related to other neurodegenerative diseases. It contains plasma samples, serum samples, lymphoblast cell lines, and cerebrospinal fluid.

ESPRIT
type: Resource
type: NamedIndividual
has db xref: OMICS_01444
synonym: Estimating Species Richness Using 16S rRNA Pyrosequences
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9, 2022. Software tool for estimating Species Richness Using 16S rRNA Pyrosequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

DySC
type: Resource
type: NamedIndividual
has db xref: OMICS_01443
synonym: DySC: Software for Greedy Clustering of 16S rRNA Reads
IAO_0000115: Software for Greedy Clustering of 16S rRNA Reads which uses a dynamic seeding strategy.

Purves Lab See For Yourself
type: Resource
type: NamedIndividual
has db xref: nlx_144063
synonym: purves-lab See For Yourself
abbrev: Purves-lab: See for Yourself
IAO_0000115: Interactive demonstrations of sensory perception phenomena from Dale Purves' website. You may read the empirical explanations and download high resolution images.

FPSAC
type: Resource
type: NamedIndividual
has db xref: biotools:fpsac
has db xref: OMICS_00041
synonym: Fast Phylogenetic Scaffolding of Ancient Contigs
synonym: Fast Phylogenetic Scaffolding of Ancient Contigs (FPSAC) and application to the medieval Black Death agent
synonym: FPSAC: fast phylogenetic scaffolding of ancient contigs
IAO_0000115: Sogftware for fast Phylogenetic Scaffolding of Ancient Contigs.

Scaffold builder
type: Resource
type: NamedIndividual
has db xref: OMICS_00046
abbrev: scaffold_builder
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Tool designed to generate scaffolds (super contigs of sequences joined by N-bases) using the homology provided by a closely related reference sequence. Scaffold_builder is an advanced wrapper for Nucmer, written in Python that resolves several situations that may arise when mapping contigs to the reference genome.

SNPiR
type: Resource
type: NamedIndividual
has db xref: OMICS_01362
synonym: SNPiR: Reliable Identification of Genomic Variants Using RNA-seq Data
IAO_0000115: Software for reliable Identification of Genomic Variants Using RNA-seq Data.

ACCUSA2
type: Resource
type: NamedIndividual
has db xref: OMICS_01360
IAO_0000115: Multi-purpose SNV calling software enhanced by probabilistic integration of quality scores.

MuTect
type: Resource
type: NamedIndividual
has db xref: biotools:mutect
has db xref: OMICS_00087
synonym: Mutect
IAO_0000115: Software for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.

Pindel
type: Resource
type: NamedIndividual
has db xref: biotools:pindel
has db xref: OMICS_00321
IAO_0000115: Software to detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

BAMS Connectivity
type: Resource
type: NamedIndividual
has db xref: nlx_144138
synonym: Brain Architecture Management System Connectivity Data
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9,2022. Database of information about brain region circuitry, it collates data from the literature on tract tracing studies and provides tools for analysis and visualization of connectivity between brain regions., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

rSeq
type: Resource
type: NamedIndividual
has db xref: biotools:rseq
has db xref: OMICS_01288
synonym: RNA-Seq Analyzer
synonym: rSeq: RNA-Seq Analyzer
IAO_0000115: A software toolkit for RNA sequence data analysis. It contains programs that cover several aspects of RNA-Seq data analysis such as read quality assessment, reference sequence generation, sequence mapping, and gene and isoform expressions estimations.

GERP
type: Resource
type: NamedIndividual
has db xref: OMICS_00174
synonym: Genomic Evolutionary Rate Profiling
synonym: Genomic Evolutionary Rate Profiling: GERP
synonym: GERP2
synonym: GERP++
IAO_0000115: Software that identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint. We refer to these deficits as Rejected Substitutions. Rejected substitutions are a natural measure of constraint that reflects the strength of past purifying selection on the element. GERP estimates constraint for each alignment column; elements are identified as excess aggregations of constrained columns. A false-positive rate (which is user-settable) is calculated using "shuffled" alignments in which the order of columns is randomized., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

SiPhy
type: Resource
type: NamedIndividual
has db xref: OMICS_00183
IAO_0000115: Software that implements rigorous statistical tests to detect bases under selection from a multiple alignment data. It takes full advantage of deeply sequenced phylogenies to estimate both unlikely substitution patterns as well as slowdowns or accelerations in mutation rates. It can be applied as an Hidden Markov Model (HMM), in sliding windows, or to specific regions.

wANNOVAR
type: Resource
type: NamedIndividual
has db xref: OMICS_00194
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web interface to the ANNOVAR software, a tool to annotate functional consequences of genetic variation from high-throughput sequencing data, to help biologists without bioinformatics skills to easily submit a list of mutations (even whole-genome variants calls) to the web server, select the desired annotation categories, and receive functional annotation back by emails. Given a list of single nucleotide variants (SNVs) and insertions / deletions in VCF or ANNOVAR input format, wANNOVAR annotates their functional effects on genes (such as amino acid changes for non-synonymous SNPs), calculate their predicted functional importance scores (such as SIFT and PolyPhen scores), retrieve allele frequencies in public databases (such as the 1000 Genomes Project and NHLBI-ESP 6500 exomes), and implement a variants reduction protocol to identify a subset of potentially deleterious variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

ViReMa
type: Resource
type: NamedIndividual
has db xref: OMICS_00225
synonym: Viral Recombination Mapper
IAO_0000115: Software Python package for detection, alignment and reporting of recombination events in Next-Generation Sequencing data. Detects and reports recombination or fusion events in virus genomes using deep sequencing datasets.

Lady Scientist
type: Resource
type: NamedIndividual
has db xref: nlx_144218
IAO_0000115: Lady Scientist chronicles the author's journey through grad school and navigating the so-called Two Body Problem. The author, Amanda (at) Lady Scientist, is a recent Ph.D. graduate in biochemistry and molecular biology.

Smart Dictionary Lookup
type: Resource
type: NamedIndividual
has db xref: OMICS_01198
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9, 2022. System that retrieves relevant UniProt IDs from BioThesaurus entries using a soft string matching algorithm.

VariantMaster
type: Resource
type: NamedIndividual
has db xref: OMICS_02261
synonym: VariantMaster - Extract causative variants for monogenic and sporadic genetic diseases
IAO_0000115: Software program that extracts causative variants in familial and sporadic genetic diseases. The algorithm takes into account predicted variants (SNPs and indels) in affected individuals or tumor samples and utilizes the row (BAM) data to robustly estimate the conditional probability of segregation in a family, as well as the probability of it being de novo or somatic. In familial cases, various modes of inheritance are considered: X-linked, autosomal dominant, and recessive (homozygosity or compound heterozygosity). Moreover, it integrates phenotypes and genotypes, and employs Annovar to produce additional information as allelic frequencies in general population and damaging scores.

Microbial Genetics Resource at JGI
type: Resource
type: NamedIndividual
has db xref: nlx_144369
synonym: Microbial Genetics Program - Exploration of Microbial Diversity
synonym: Microbial Genetics Program at JGI
abbrev: JGI Microbial Genetics Program
IAO_0000115: Mission: Dynamically evolve sequencing, finishing, annotation and analysis processes, exploit new technologies, and develop expertise to deliver high quality and high throughput sequence-based microbial science by listening to and responding to DOE Users and scientific community needs. GOALS 1. Expand product catalog and increase sample throughput while maintaining highest quality The MGP has been expanding its product catalog beyond a finished microbial genome and has projected to significantly up ramp throughput for the majority of its current products namely Draft Genomes, Single Cell Genomes, Quick Draft Genomes, Resequencing projects and RNAseq Project. This projected increase in microbial genomes is going hand-in-hand with and has been stimulated by new high throughput technologies and capabilities (de novo microbial Illumina assemblies, single cell genomics, Genologic sample tracking). The increased throughput will support the user community as well as JGI scientists by enabling DOE-relevant science at a grander scale. As the Program aims to generate hundreds of microbial genomes per year, our goal is to scale our production efficiency and maintain our trademark quality to best support our science mission. 2. Expand sequence space One of the ongoing missions of the MGP is to expand the coverage of the phylogenomic sequence space by generating reference genome datasets from highly diverse braches in bacterial and archaeal tree of life. The value of such effort includes the generation of phylogenetic anchors for metagenomic datasets, the improvement of annotation, an increased insight into phylogenetic distribution of functions, the discovery of novel genes, protein families, pathways and a better understanding on evolutionary diversication. 3. Make Single Cell Genomes a robust User product As the vast majority of microbes are uncultured to date, single cell genomics will be a crucial component of the MGP over the next several years to drive not only JGI scienc…

UCSCin
type: Resource
type: NamedIndividual
has db xref: nlx_144379
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Beta software used to align and browse a genome.

GeneWays
type: Resource
type: NamedIndividual
has db xref: nif-0000-30019
has db xref: OMICS_01182
synonym: GeneWays: A System for Extracting Analyzing Visualizing and Integrating Molecular Pathway Data
synonym: GeneWays: A System for Extracting Analyzing Visualizing Integrating Molecular Pathway Data
abbrev: Geneways
IAO_0000115: System for automatically extracting, analzying, visualizing and integrating molecular pathway data from the research literature. System focuses on interactions between molecular substances and actions, providing a graphical consensus view on the collected information. GeneWays is designed as open platform, allowing researchers to query, review and critique integrated information.

AdaptiveCrawler
type: Resource
type: NamedIndividual
has db xref: OMICS_01170
synonym: Adaptive Crawler
synonym: Smart Web Crawler
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9,2022. A web crawler that can intelligently acquire social media content on the Internet to meet the specific online data source acquisition needs of cancer researchers.

NGS-Cleaner
type: Resource
type: NamedIndividual
has db xref: OMICS_01166
IAO_0000115: Software application that provides cleaning of FASTQ/A formatted large DNA sequence files containing multiple short-reads sequences provided by Next Generation Sequencing platforms.

flowQ
type: Resource
type: NamedIndividual
has db xref: OMICS_05805
synonym: flowQ: Quality control for flow cytometry
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. Software that provides quality control and quality assessment tools for flow cytometry data.

ADHD-200 Preprocessed Data
type: Resource
type: NamedIndividual
has db xref: nlx_144425
IAO_0000115: Preprocessed versions of the ADHD-200 Global Competition data including both preprocessed versions of structural and functional datasets previously made available by the ADHD-200 consortium, as well as initial standard subject-level analyses. The ADHD-200 Sample is pleased to announce the unrestricted public release of 776 resting-state fMRI and anatomical datasets aggregated across 8 independent imaging sites, 491 of which were obtained from typically developing individuals and 285 in children and adolescents with ADHD (ages: 7-21 years old). Accompanying phenotypic information includes: diagnostic status, dimensional ADHD symptom measures, age, sex, intelligence quotient (IQ) and lifetime medication status. Preliminary quality control assessments (usable vs. questionable) based upon visual timeseries inspection are included for all resting state fMRI scans. In accordance with HIPAA guidelines and 1000 Functional Connectomes Project protocols, all datasets are anonymous, with no protected health information included. They hope this release will open collaborative possibilities and contributions from researchers not traditionally addressing brain data so for those whose specialties lay outside of MRI and fMRI data processing, the competition is now one step easier to join. The preprocessed data is being made freely available through efforts of The Neuro Bureau as well as the ADHD-200 consortium. They ask that you acknowledge both of these organizations in any publications (conference, journal, etc.) that make use of this data. None of the preprocessing would be possible without the freely available imaging analysis packages, so please also acknowledge the relevant packages and resources as well as any other specific release related acknowledgements. You must be logged into NITRC to download the ADHD-200 datasets, http://www.nitrc.org/projects/neurobureau

TarBase
type: Resource
type: NamedIndividual
has db xref: nif-0000-03534
synonym: DIANA-TarBase
synonym: TarBase v7.0
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 3,2023. Collection of miRNA target interactions. Manually curated collection of experimentally supported microRNA targets in several animal species of central scientific interest, plants and viruses. Database is functionally linked to several other relevant and useful databases such as Ensembl, Hugo, UCSC and SwissProt., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Inner Ear Proteins in Health and Disease
type: Resource
type: NamedIndividual
has db xref: nif-0000-00078
synonym: Inner Ear Protein Database
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 06, 2013. The fully federated database provides information on proteins identified in inner ear structures and fluids in health and disease. in addition, protein maps derived from 2d electrophoresis/mass spectrometry are displayed.

Jefferson Hospital for Neuroscience Alzheimers Disease and Dementia Center
type: Resource
type: NamedIndividual
has db xref: nlx_144497
synonym: Jefferson Hospital for Neuroscience Alzheimer's Disease and Dementia Center
synonym: Jefferson Hospital for Neuroscience Alzheimer's Disease Dementia Center
synonym: Jefferson Hospital for Neuroscience Alzheimers Disease Dementia Center
abbrev: Jefferson Alzheimer's Disease and Dementia Center
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. If you or someone you love has been diagnosed with dementia caused by Alzheimer's disease, you'll be in good hands at Jefferson. Our neurologists and psychiatrists are dedicated to: Compassionate care for individuals with Alzheimer's disease; Supporting families; Advancing care through research into the epidemiology and treatment of neurodegenerative diseases. We interact with patients very early in the disease progression, when impairment is typically mild; deliver state-of-the-art care; provide information; build care-giving skills; and help caregivers connect with community support and plan for the future.

MUSC Health News
type: Resource
type: NamedIndividual
has db xref: nlx_144508
synonym: Medical University of South Carolina Health News
synonym: MUSC Health News RSS Feeds
IAO_0000115: MUSC's Health News RSS Feeds includes topic of a interest you can subscribe to by copying the corresponding URL into your preferred RSS software. You will automatically receive this feed each time it's published. Topics include: Brain Waves, Diabetes Health, Kids Health, Heart Care, Men's Health, Women's Health, and Community Blog.

Database Enabled Code for Ideal Probe Hybridization Employing R
type: Resource
type: NamedIndividual
has db xref: OMICS_01114
abbrev: DECIPHER
IAO_0000115: A software toolset that can be used for deciphering and managing DNA sequences efficiently using the R statistical programming language., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Whole Brain Catalog Blog
type: Resource
type: NamedIndividual
has db xref: nlx_144534
abbrev: WBC Blog
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. The blog of the Whole Brain Catalog.

NGSmethPipe
type: Resource
type: NamedIndividual
has db xref: OMICS_00611
synonym: NGSmethPipe - A tool to generate high-quality methylation maps
IAO_0000115: A software tool which generates high-quality methylation maps.

Pyrocleaner
type: Resource
type: NamedIndividual
has db xref: OMICS_01069
IAO_0000115: A software module for cleaning 454 pyrosequencing reads using filters such as read duplication, length, complexity, base-pair quality and number of undetermined bases. The software also uses flowgram files of paired-end sequences to validate paired-ends files of another file.

DecGPU
type: Resource
type: NamedIndividual
has db xref: biotools:decgpu
has db xref: OMICS_01060
has db xref: OMICS_01101
has db xref: SCR_011850
synonym: Distributed short read Error Correction on GPUs
IAO_0000115: Software tool as parallel and distributed error correction algorithm for high-throughput short reads using CUDA and MPI parallel programming models.

drFAST
type: Resource
type: NamedIndividual
has db xref: biotools:drfast
has db xref: OMICS_00661
synonym: di-base read Fast Alignment Search Tool
synonym: drFAST: di-base read Fast Alignment Search Tool
IAO_0000115: A software which maps di-base reads (SOLiD color space reads) to reference genome assemblies in a fast and memory-efficient manner.

MPscan
type: Resource
type: NamedIndividual
has db xref: biotools:mpscan
has db xref: OMICS_00670
synonym: MPscan: index free mapping of multiple short reads on a genome
IAO_0000115: Web tool for index free mapping of multiple short reads on a genome.

TAPyR
type: Resource
type: NamedIndividual
has db xref: biotools:tapyr
has db xref: OMICS_00693
synonym: Tool for Alignment of Pyrosequencing Reads
IAO_0000115: An efficient software tool for the local alignment of pyrosequencing reads produced by the GS FLX (454) Genome Analyzer technology against a reference genome sequence. The approach explores the characteristics of the data in re-sequencing applications and uses state of the art BWT-based indexing techniques combined with a flexible seed-based approach, leading to a fast and accurate algorithm which needs very little user parameterization. Although initially developed having this specific technology in mind, this software performs equally well on any other platform that can return its sequencing reads in the FASTA, FASTQ or SFF formats, including Illumina, Ion Torrent and Pacific Biosciences technologies.

BioLexicon
type: Resource
type: NamedIndividual
has db xref: nlx_54008
synonym: BOOTStrep Bio-Lexicon
IAO_0000115: A large-scale English terminological database that contains over 2.2.M lexical entries (3.3M semantic relations), terminological variants and rich linguistic information (subcategorization frames) which supports text mining systems. It is primarily intended to support text mining and information retrieval in the biomedical domain. The BioLexicon provides specific information to help determine the relevant facts to be extracted. BioLexicon is available in a relational database format (MySQL dump format) and it adheres to the EAGLES/ISO standards for lexical resources.

LORIS - Longitudinal Online Research and Imaging System
type: Resource
type: NamedIndividual
has db xref: nlx_144608
synonym: Longitudinal Online Research and Imaging System
synonym: Longitudinal Online Research Imaging System
abbrev: LORIS
IAO_0000115: A modular and extensible web-based data management system that integrates all aspects of a multi-center study, from heterogeneous data acquisition to storage, processing and ultimately dissemination, within a streamlined platform. Through a standard web browser, users are able to perform a wide variety of tasks, such as data entry, 3D image visualization and data querying. LORIS also stores data independently from any image processing pipeline, such that data can be processed by external image analysis software tools. LORIS provides a secure web-based and database-driven infrastructure to automate the flow of clinical data for complex multi-site neuroimaging trials and studies providing researchers with the ability to easily store, link, and access significant quantities of both scalar (clinical, psychological, genomic) and multi-dimensional (imaging) data. LORIS can collect behavioral, neurological, and imaging data, including anatomical and functional 3D/4D MRI models, atlases and maps. LORIS also functions as a project monitoring and auditing platform to oversee data acquisition across multiple study sites. Confidentiality during multi-site data sharing is provided by the Subject Profile Management System, which can perform automatic removal of confidential personal information and multiple real-time quality control checks. Additionally, web interactions with the LORIS portal take place over an encrypted channel via SSL, ensuring data security. Additional features such as Double Data Entry and Statistics and Data Query GUI are included.

neurodudes
type: Resource
type: NamedIndividual
has db xref: nlx_144623
synonym: neurodudes - at the intersection of neuroscience and AI
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Neurodudes is intended to be an open forum at the intersection of neuroscience and ai. regular readers are encouraged to post appropriate material. make sure to put your name somewhere in the post. The ultimate neurodudes RSS feed combines neuro/ai/cogsci-related RSS feeds from many sources, sometimes filtering along the way so as to minimize offtopic posts.

Brain Evolution in the News
type: Resource
type: NamedIndividual
has db xref: nlx_144625
IAO_0000115: Brain Evolution in the News pulls in blogs from a variety of resources on topic.

SWORD
type: Resource
type: NamedIndividual
has db xref: nlx_144633
synonym: Simple Web-service Offering Repository Deposit
IAO_0000115: A software that is used for the management of data and to deposit content between different locations. A request from an authenticated user is sent to implement for the "service document", which returns details of the collection that user is allowed to deposit within the repository. At this point, the user can deposit their file into a collection, which can then be accessed at a different location.

MutPred Splice
type: Resource
type: NamedIndividual
has db xref: OMICS_02257
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Tool for identifying coding region variants which disrupt pre-mRNA splicing and the underlying mechanism.

ContEst
type: Resource
type: NamedIndividual
has db xref: biotools:contest
has db xref: OMICS_01038
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 8,2025. A software tool (and method) for estimating the amount of cross-sample contamination in next generation sequencing data.

Mini Analysis Guide for Microarrays
type: Resource
type: NamedIndividual
has db xref: OMICS_00772
abbrev: MAGMA
IAO_0000115: A collection of cook-book like manuals for various microarray designs. MAGMA is a collaboration between the Norwegian Microarray Consortium NMC and MolMine AS

DDBJ Omics Archive
type: Resource
type: NamedIndividual
has db xref: OMICS_01026
synonym: Ddbj Omics aRchive
abbrev: DOR
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between ArrayExpress at EBI and DOR in common MAGE-TAB format. Supports MIAME and MINSEQE-compliant data submissions. DOR issues accession numbers, E-DORD-n to experiment and A-DORD-n to array design. DOR exchanges public data with the EBI ArrayExpress in common MAGE-TAB format. Note: At present, DOR does not accept submissions. DDBJ will announce launch of DOR when it is ready. (2013/01/31) The data can be kept private until your paper is published. You can set the hold date for a maximum of 1 year and can change it. Registered records are released according to the Data Release Policy.

Chromas
type: Commercial Organization
type: NamedIndividual
has db xref: biotools:chromas
has db xref: OMICS_01016
IAO_0000115: Software ideal for the most basic of sequencing projects, where assembly of multiple sequences is not required., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Yeast Transfactome Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-03577
synonym: TransfactomeDB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A repository of sequence specificity models and condition-specific regulatory activities for a large number of DNA- and RNA-binding proteins in Saccharomyces cerevisiae. Accurate and comprehensive information about the nucleotide sequence specificity of trans-acting factors (TFs) is essential for computational and experimental analyses of gene regulatory networks. The sequence specificities in TransfactomeDB, represented as position-specific affinity matrices (PSAMs), are directly estimated from genomewide measurements of TF-binding using our previously published MatrixREDUCE algorithm, which is based on a biophysical model. For each mRNA expression profile in the NCBI Gene Expression Omnibus, we used sequence-based regression analysis to estimate the post-translational regulatory activity of each TF for which a PSAM is available. The trans-factor activity profiles across multiple experiments available in TransfactomeDB allow the user to explore potential regulatory roles of hundreds of TFs in any of thousands of microarray experiments.

NVM
type: Resource
type: NamedIndividual
has db xref: nlx_149080
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Software tool for quantitative neuroanatomical measurements in volumetric image data. Used to draw regions of interest for subsequent fMRI analysis.

Onto-Design
type: Resource
type: NamedIndividual
has db xref: nlx_149109
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Many Laboratories chose to design and print their own microarrays. At present, the choice of the genes to include on a certain microarray is a very laborious process requiring a high level of expertise. Onto-Design database is able to assist the designers of custom microarrays by providing the means to select genes based on their experiment. Design custom microarrays based on GO terms of interest. User account required. Platform: Online tool

OnEx - Ontology Evolution Explorer
type: Resource
type: NamedIndividual
has db xref: nlx_149129
has db xref: OMICS_02273
synonym: Ontology Evolution Explorer
synonym: Ontology Evolution Explorer (OnEx)
abbrev: OnEx
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Web-based application that integrates versions of 16 life science ontologies including the Gene Ontology, NCI Thesaurus and selected OBO ontologies with data leading back to 2002 in a common repository to explore ontology changes. It allows to study and apply the evolution of these integrated ontologies on three different levels. It provides global ontology evolution statistics and ontology-specific evolution trends for concepts and relationships and it allows the migration of annotations in case a new ontology version was released

Cardiovascular Proteomics Center
type: Resource
type: NamedIndividual
has db xref: nlx_149148
synonym: Boston University School of Medicine Cardiovascular Proteomics Center
synonym: BU Cardiovascular Proteomics Center
synonym: BUSM Cardiovascular Proteomics Center
abbrev: BUSM CPC
abbrev: CPC
IAO_0000115: The Cardiovascular Proteomics Center is a research center funded by the NIH/NHLBI to analyze and identify proteins that may be modified or created by oxidative stress. The CPC is developing and applying new proteomics methodology and instrumentation to the analysis of known proteins and those yet to be discovered.

Baylor College of Medicine - Shaw Laboratory
type: Resource
type: NamedIndividual
has db xref: nlx_149156
abbrev: BCM - Shaw Laboratory
abbrev: BCM Shaw Lab
abbrev: BCM Shaw Laboratory
IAO_0000115: The mission of the Baylor College of Medicine - Shaw Laboratory is to apply methods of statistics and bioinformatics to the analysis of large scale genomic data. Our vision is data integration to reveal the underlying connections between genes and processes in order to cure disease and improve healthcare.

USP Molecular Genetics and Bioinformatics Laboratory
type: Resource
type: NamedIndividual
has db xref: nlx_149158
synonym: University of Sao Paulo Molecular Genetics and Bioinformatic Laboratory
synonym: University of Sao Paulo Molecular Genetics and Bioinformatics Laboratory
synonym: USP Laboratorio de Genetica Molecular e Bioinformatica
synonym: USP Molecular Genetics and Bioinformatic Laboratory
synonym: USP Molecular Genetics Bioinformatics Laboratory
IAO_0000115: Laboratory portal of the University of Sao Paulo Molecular Genetics and Bioinformatic Laboratory.

Zebrafish Brain Atlas
type: Resource
type: NamedIndividual
has db xref: nlx_149455
synonym: zebrafishbrain.org
IAO_0000115: Collates and curates neuroanatomical data and information generated both in-house and by community to communicate current state of knowledge about neuroanatomical structures in developing zebrafish. Most of data come from high resolution confocal imaging of intact brains in which neuroanatomical structures are labelled by combinations of transgenes and antibodies. Community repository for image based data related to neuroanatomy of zebrafish.

KI Biobank - Amphetamine dependence
type: Resource
type: NamedIndividual
has db xref: nlx_149466
synonym: Amphetamine dependence study
synonym: KI Amphetamine dependence
IAO_0000115: The primary objective of this study is to establish a biobank of blood samples from amphetamine dependent patients in order to study genetic risk factors for this disease. This may ultimately shed new light on the pathophysiology of substance dependence and its relation to other psychiatric disorders, and suggest new approaches to prevention and treatment. Types of samples * EDTA whole blood * DNA Number of sample donors: 104 (June 2010)

Model: Hebbian Mirror Neuron System (H-MNS) (Keysers - Perrett)
type: Resource
type: NamedIndividual
has db xref: nlx_149493
synonym: Hebbian Mirror Neuron System
synonym: Model: Hebbian Mirror Neuron System
abbrev: H-MNS
abbrev: Model: H-MNS
IAO_0000115: A conceptual model of how Hebbian learning between the areas STS, PF, F5 allows recognition of the actions of others by associating them with self-produced actions.

Craig Mod
type: Resource
type: NamedIndividual
has db xref: nlx_149495
synonym: at craigmod
synonym: craigmod.com
abbrev: @craigmod
IAO_0000115: Blog by Craig Mod: Thinking about the future of books and publishing and story telling.

KI Biobank - PAIN
type: Resource
type: NamedIndividual
has db xref: nlx_149607
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Aims to investigate the relation between specific genetic variations, personality factors and pain experience in healthy subjects.

Annotator
type: Resource
type: NamedIndividual
has db xref: nlx_149635
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Annotator is an open-source JavaScript library and tool that can be added to any webpage to make it annotatable. Annotations can have comments, tags, users and more. Moreover, the Annotator is designed for easy extensibility so its a cinch to add a new feature or behavior. Adding annotation to your webpage using the Annotator is easy. Full instructions are in the Getting Started section of the docs, but it is just two short steps. First, you need to download the Annotator library (or link to the hosted version), include it on your page along with jQuery. Then add the following line to initialize the annotator. $("#content").annotator(); Plug-ins can be included for adding functionality such as user accounts, tags, filtering and formatting. You'll need to store your data somewhere, luckily we've made this very simple to do using AnnotateIt, a hosted web service for storing annotations. Alternatively if you'd like to integrate the annotator with your own storage system check out the Docs for more information on the annotation format and store plugin. The bookmarklet is a simple tool that allows you to add the annotator to any webpage and save your annotations to AnnotateIt. Check it out at http://annotateit.org/.

MacArthur Foundation
type: Resource
type: NamedIndividual
has db xref: nlx_151326
synonym: John D. and Catherine T. MacArthur Foundation
IAO_0000115: The John D. and Catherine T. MacArthur Foundation supports creative people and effective institutions committed to building a more just, verdant, and peaceful world. In addition to selecting the MacArthur Fellows, the Foundation works to defend human rights, advance global conservation and security, make cities better places, and understand how technology is affecting children and society. MacArthur is one of the nation's largest independent foundations. Through the support it provides, the Foundation fosters the development of knowledge, nurtures individual creativity, strengthens institutions, helps improve public policy, and provides information to the public, primarily through support for public interest media. The Foundation makes grants and loans through four programs. * International Programs focus on international issues, including human rights and international justice, peace and security, conservation and sustainable development, higher education in Nigeria and Russia, migration, and population and reproductive health. MacArthur grantees work in about 60 countries; the Foundation has offices in India, Mexico, Nigeria, and Russia. * U.S. Programs address issues in the United States, including community and economic development; housing, with a focus on the preservation of affordable rental housing; juvenile justice reform; education, with an emerging interest in digital media and learning; and policy research and analysis. * Media, Culture, and Special Initiatives support public interest media, including public radio, documentary programming, and work to explore the use of digital technologies to reach and engage the public. Grants are also made to arts and cultural institutions in the Chicago area and for special initiatives. * The MacArthur Fellows Program awards five-year, unrestricted fellowships to individuals across all ages and fields who show exceptional merit and promise of continued creative work. It is limited to U.S. citizens and residents. John…

Maps4Mipav (Exploratory JIST)
type: Resource
type: NamedIndividual
has db xref: nlx_151345
synonym: MedIC Automated Pipeline Scheduler Medical Image Processing Analysis and Visualization
abbrev: Maps4Mipav
IAO_0000115: The exploratory development tree of Java Image Science Toolkit (JIST), an extension to the MIPAV (Medical Image Processing, Analysis, and Visualization) plug-in framework that allows the user to design and execute pipelines, which are multi-stage processing tasks.. New features and designs are tested here before general release into the JIST project. JIST was formerly known as the MedIC Automated Pipeline Scheduler (MAPS).

HIV Databases
type: Resource
type: NamedIndividual
has db xref: nlx_151409
has db xref: SCR_014940
IAO_0000115: Contains comprehensive data on HIV genetic sequences and immunological epitopes. This collection of databases contains tools to visualize and analyze HIV-related data.

PRACSIS - Prognosis and Risk in Acute Coronary Syndromes In Sweden
type: Resource
type: NamedIndividual
has db xref: nlx_151442
synonym: KI Biobank - PRACSIS
synonym: PRACSIS - Prognosis Risk in Acute Coronary Syndromes In Sweden
synonym: Prognosis and Risk in Acute Coronary Syndromes In Sweden
abbrev: PRACSIS
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. PRACSIS (Prognosis and Risk in Acute Coronary Syndromes In Sweden) aims to study prognosis and its predictors in a consecutive series of patients with acute coronary syndrome (ACS). The study is comprised of patients between 18 and 80 years diagnosed at the coronary care unit at the Sahlgrenska University Hospital with unstable angina, non-ST-elevation MI or ST-elevation MI. Extensive information on medical history and blood samples for analyses of biochemical markers and genetic factors have been collected.

CEA; Gif sur Yvette; France
type: Resource
type: NamedIndividual
has db xref: nlx_151454
synonym: Commissariat a l''Energie Atomique
synonym: Commissariat a l''Energie Atomique et aux Energies Alternatives
synonym: Commissariat �� l''��nergie Atomique
synonym: Commissariat �� l''��nergie atomique et aux ��nergies alternatives
synonym: French Alternative Energies and Atomic Energy Commission
abbrev: CEA
IAO_0000115: A French government-funded technological research organization and ensures that the nuclear deterrent remains effective in the future. A prominent player in the European Research Area, it is involved in setting up collaborative projects with many partners around the world. The CEA is active in four main areas: low-carbon energies, defense and security, information technologies and health technologies. In each of these fields, the CEA maintains a cross-disciplinary culture of engineers and researchers, building on the synergies between fundamental and technological research.

Neurocarta
type: Resource
type: NamedIndividual
has db xref: nlx_151502
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Neurocarta is a knowledgebase that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of the associations. The system enables automatic and manual curation of evidence supporting each association, as well as user-enabled entry of their own annotations. Phenotypes are recorded using controlled vocabularies such as the Disease Ontology to facilitate computational inference and linking to external data sources. The gene-to-phenotype associations are filtered by stringent criteria to focus on the annotations most likely to be relevant. Neurocarta is constantly growing and currently holds more than 30,000 lines of evidence linking over 6,800 genes to 1,800 different phenotypes. Neurocarta is a one-stop shop for researchers looking for candidate genes for any disorder of interest. In Neurocarta, they can review the evidence linking genes to phenotypes and filter out the evidence they're not interested in. In addition, researchers can enter their own annotations from their experiments and analyze them in the context of existing public annotations. Neurocarta's in-depth annotation of neurodevelopmental disorders makes it a unique resource for neuroscientists working on brain development.

Gatsby Charitable Foundation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100000324
has db xref: grid.453189.2
has db xref: ISNI: 0000 0001 0199 6389
has db xref: nlx_151556
synonym: Gatsby
IAO_0000115: Gatsby is a Foundation set up by David Sainsbury to realize his charitable objectives. Gatsby works in areas that David Sainsbury and the Trustees are particularly passionate about and where they believe charitable funding can make a real difference. Gatsby is currently active in six tightly-focused areas: * Plant science research * Neuroscience research * Science and engineering education * Economic development in Africa * Public policy research and advice * The Arts We have also supported significant programs in mental health - in particular through the founding of the Centre for Mental Health - although we are no longer focusing on this area. Across all areas, we aim to be more than a funder. We act as an enabler for projects, designing, developing, overseeing and, in some cases, delivering activities. We are proactive in putting together projects to achieve our aims. Rather than wait for third-party proposals, we identify areas of need, commission research and design interventions in partnership with sector and industry experts. We take a long-term view as we do not think much can be achieved by short, one-off projects. We build long relationships with the organizations we support, allowing both them and us to learn from successes and failures and to develop sustainable change. We are particularly enthusiastic about supporting innovation. David Sainsbury has long believed that private foundations have an important role to play in testing imaginative models and new ideas that governments may see as too risky for public funding, even when they have significant potential to benefit the public if they succeed. Gatsby can incubate such models, giving them the support they need to prove themselves and build the track-records that will encourage others to scale them up. We will continue to support and undertake both large- and small-scale work, employing different methods and models depending on the different challenges, but always ultimately looking to deliver long-te…

ProQuest Dissertations and Theses Global
type: Resource
type: NamedIndividual
has db xref: nlx_151559
synonym: ProQuest Dissertations & Theses Database
synonym: ProQuest Dissertations Theses Database
abbrev: PQDT
IAO_0000115: ProQuest Dissertations and Theses Full text is a comprehensive collection of dissertations and theses, as well as the official digital dissertations archive for the Library of Congress and the database of record for graduate research. PQDT Full Text includes nearly 3 million searchable citations to dissertations and theses available for download in PDF format. The database offers full text for most of the dissertations added since 1997 and strong retrospective full-text coverage for older graduate works. Full-text dissertations are archived as submitted by the degree-granting institution. Each dissertation published since July 1980 includes a 350-word abstract written by the author. Masters theses published since 1988 include 150-word abstracts. Simple bibliographic citations are available for dissertations dating from 1637. ProQuest Dissertations and Theses Full Text also offers researchers unlimited access to digital copies from their own institutions as well as affordable copies from others.

Sarah Jane Brain Project
type: Resource
type: NamedIndividual
has db xref: nlx_151578
synonym: Sarah Jane Brain Foundation
abbrev: SJBF
IAO_0000115: The Mission of the Sarah Jane Brain Project is to create a model system of care for children and young adults suffering from all Pediatric Acquired Brain Injuries in order to advance our knowledge of the brain fifty years over the next five years! As a father of a child suffering from a Pediatric Acquired Brain Injury (PABI), I have spent countless hours searching the internet and speaking with Sarah Jane's development team (doctors, therapists and other professionals) trying to improve the development of my daughter. What I found was that while there are a countless number of wonderful and informative prevention sites for Shaken Baby Syndrome and advocacy sites for brain injuries, there is no one centralized resource for research and rehabilitation for PABI. Furthermore, many of the issues families and children face are the same whether the brain injury was caused by a car crash, a sports-related concussion, an assault or by a tumor. No one person or organization has all the answers to the questions that parents of children suffering from PABI face. Yet through my own experience, I learned that the coordination and dissemination of Sarah Jane's medical and therapy records and data in an orderly manner greatly helps her development team better help her. These wonderful individuals are constantly looking for additional ways to improve Sarah Jane's progress by speaking with their colleagues, reading literature on brain injury, and collaborating with other parents. But they all admit there is a considerable amount that still needs to be learned about the human brain, particularly the developing brain. The field of neuroscience today is similar to the computer science field of the 1950s and 1960s: you have a diverse group of very smart people working independently of one another throughout the United States and the world, yet few know what the others are doing behind closed doors. Fast- forward 50 years and many of the breakthroughs in the computer industry have been ma…

BEBaC
type: Resource
type: NamedIndividual
has db xref: OMICS_01440
synonym: Bayesian estimation of bacterial communities
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for Bayesian estimation of bacterial communities.

ProGlycProt
type: Resource
type: NamedIndividual
has db xref: biotools:proglycprot
has db xref: nlx_151583
synonym: ProGlycProt - A Repository of Experimentally Characterized GlycoProteins of Prokaryotes
synonym: Prokaryotic Glycoproteins
IAO_0000115: Manually curated, comprehensive repository of experimentally characterized bacterial glycoproteins and archaeal glycoproteins, generated from an exhaustive literature search. This is the focused effort to provide concise relevant information derived from rapidly expanding literature on prokaryotic glycoproteins, their glycosylating enzyme(s), glycosylation linked genes, and genomic context thereof, in a cross-referenced manner. The database is arranged into two sections namely, ProCGP and ProUGP. ProCGP is the main section containing characterized prokaryotic glycoproteins, defined as entries with at least one experimentally known glycosylated residue (glycosite). Whereas, ProUGP is the supplementary section, presenting uncharacterized prokaryotic glycoproteins, defined as entries with experimentally identified glycosylation but unidentified glycosites. The ProGlycProt has been developed with to aid and advance the emerging scientific interests in understanding the mechanisms, implications, and novelties of protein glycosylation in prokaryotes that include many pathogenic as well as economically important bacterial species. The website supports a dedicated structure gallery of homology models and crystal structures of characterized glycoproteins in addition to two new tools developed in view of emerging information about prokaryotic sequons (conserved sequences of amino acids around glycosites) that are never or rarely seen in eukaryotic glycoproteins. ProGlycProt provides an extensive compilation of experimentally identified glycosites (334) and glycoproteins (340) of prokaryotes that could serve as an information resource for research and technology applications in glycobiology. A general data update policy is once in three months. Existing entries are updated in real-time.

e-mouse.org
type: Resource
type: NamedIndividual
has db xref: nlx_151621
abbrev: e mouse
abbrev: e-mouse
IAO_0000115: The e-mouse.org is an online resource that aims to bring together and provide users with all information related to the laboratory mouse and its use as a model organism. Users can find direct links to MRB, a resource management project that provides a dynamic and interactive view of most world wide available mouse resources, as well as the CreZOO, MMdb and Fleming Databases, three more specialized mouse repositories, all developed and hosted at the B.S.R.C. Alexander Fleming Institute. Additionally e-mouse.org provides links to major European and international mouse resources like the Mouse Genome Informatics (MGI), European Mouse Mutant Archive (EMMA), International Mouse Strain Resource (IMSR) and Ensembl. Users interested in retrieving information regarding the use of mouse models are encouraged to visit MRB which provides an index of publicly available mouse resources intended for both bench scientists and bioinformaticians. * Mouse Resource Browser (MRB) is a resource management project that provides a dynamic and interactive view of most world wide available mouse resources, classified in 22 categories. * CreZOO is the European virtual repository of Cre and other targeted conditional driver strains. Its aim is to capture and disseminate extant and new information on all Cre driver strains. * MUGEN Mouse Database (MMdb) is a virtual and fully searchable repository of murine models of immune processes and immunological diseases. * Fleming Database is a fully searchable resource developed to host all mouse strains developed and/or housed in BSRC Al. Fleming's animal house. * MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. * EMMA is a non-profit repository for the collection, archiving (via cryopreservation) and distribution of relevant mutant strains essential for basic biomedical research. * IMSR is a searchable online database of …

Neuroamer
type: Resource
type: NamedIndividual
has db xref: nlx_151649
IAO_0000115: Neuroamer is a researcher-oriented blog about neuroscience, psychiatry, and psychology. It is an attempt to fill the space between journal articles and pop science journalism.

FlipFlop
type: Resource
type: NamedIndividual
has db xref: biotools:flipflop
has db xref: OMICS_04028
synonym: flipflop - Fast lasso-based isoform prediction as a flow problem
IAO_0000115: Software that discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data.

PredSL
type: Resource
type: NamedIndividual
has db xref: nlx_151739
synonym: PREDiction of Subcellular Location from the N-terminal Sequence
IAO_0000115: Web tool using an algorithm that exploits neural networks, Markov Chains, and HMMs for the prediction of the subcellular localization of proteins in eukaryotic cells from the N-terminal amino acid sequence and aims to classify proteins into five groups: Chloroplast, Thylakoid, Mitochondrion, Secreted proteins, and Other. As input PredSL requires the protein's sequence in fasta format.

IRIS DMC Web Services
type: Resource
type: NamedIndividual
has db xref: SciRes_000178
synonym: Incorporated Research Institutions for Seismology Data Management Center Web Services
synonym: Incorporated Research Institutions for Seismology DMC Web Services
synonym: IRIS Data Management Center Web Services
IAO_0000115: Web services provided by the Incorporated Research Institutions for Seismology (IRIS) Data Management Center (DMC) to acquire data and metadata.

CAST
type: Resource
type: NamedIndividual
has db xref: nlx_151779
synonym: CAST - Compositional Bias Detection Algorithm
IAO_0000115: A novel algorithm for low-complexity region detection and selective masking. The algorithm is based on multiple-pass Smith-Waterman comparison of the query sequence against twenty homopolymers with infinite gap penalties. The output of the algorithm is both the masked query sequence for further analysis, e.g. database searches, as well as the regions of low complexity.

BioWiki
type: Resource
type: NamedIndividual
has db xref: nif-0000-06715
IAO_0000115: A meta-list that is a compilation of other biology related wikipedia pages. These listings include the wiki name, description, year of inception, pages, new pages, users, active users, new edits, and wiki logo. The table can also be downloaded in a csv formatted table.

Psychology Corner
type: Resource
type: NamedIndividual
has db xref: nlx_151806
IAO_0000115: A blog by a Romanian clinical psychologist and psychotherapist Lucia Grosaru. Major categories include: General, lifestyle, news, pensees, psychologists, psychotherapy, self-help and video. Lucia Grosaru is the President and a Founding Member of the Romanian Institute Sic Cogito, Founding Member for The Romanian Center of Psychology and a Founding Editor of The Romanian Journal of Psychology, Psychotherapy and Neuroscience. Lucia is an integrative psychotherapist, clinical psychologist and a Certified Rorschach Inkblot Test Specialist (Method: Scuola Romana Rorschach, Italy). She has graduated the Psychology and Educational Science Faculty at the University of Bucharest in 2008 and the Cognitive Psychodiagnosis and Counseling Master's Programme in 2010.

Quantum Lobe Chronicles
type: Resource
type: NamedIndividual
has db xref: nlx_151810
synonym: The Quantum Lobe Chronicles
IAO_0000115: A blog covering psychology, neuroscience, philosophy, quantum physics, and anything else worth writing about, by William Lu. William Lu is currently a postdoctoral fellow specializing in neuropsychology and rehabilitation psychology

Albinism database
type: Resource
type: NamedIndividual
has db xref: nif-0000-06691
abbrev: Albinism Database
IAO_0000115: Database of mutations associated with all major known forms of oculocutaneous and ocular albinism. The Albinism Database is part of the Locus Specific Mutation Databases of the Human Genome Variation Society and accepts the submission of new mutations. A link is provided for submission of new mutations. Columns in the database include: type of albinism, human locus, omim link, link to table of mutations and polymorphisms, and map of mutation locations.

Phosphor Antibody Array Data Analysis
type: Resource
type: NamedIndividual
has db xref: OMICS_04025
synonym: PANDA: Phosphor Antibody Array Data Analysis
abbrev: PANDA
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6, 2023. Web-based software program for analyzing phosphorylation antibody arrays. It identifies phosphorylated antibodies in the microarray and statistically quantifies the extent of phosphorylation for these antibodies.

Neo
type: Resource
type: NamedIndividual
has db xref: nlx_151874
abbrev: neo
IAO_0000115: A Python package for representing electrophysiology data, together with support for reading a wide range of neurophysiology file formats, including Spike2, NeuroExplorer, AlphaOmega, Axon, Blackrock, Plexon, Tdt, and support for writing to a subset of these formats plus non-proprietary formats including HDF5. The goal of Neo is to improve interoperability between Python tools for analyzing, visualizing and generating electrophysiology data (such as OpenElectrophy, NeuroTools, G-node, Helmholtz, PyNN) by providing a common, shared object model. In order to be as lightweight a dependency as possible, Neo is deliberately limited to represention of data, with no functions for data analysis or visualization. Neo implements a hierarchical data model well adapted to intracellular and extracellular electrophysiology and EEG data with support for multi-electrodes (for example tetrodes). Neo's data objects build on the quantities package, which in turn builds on NumPy by adding support for physical dimensions. Thus Neo objects behave just like normal NumPy arrays, but with additional metadata, checks for dimensional consistency and automatic unit conversion.

Pathline
type: Resource
type: NamedIndividual
has db xref: nlx_151898
synonym: Pathline: A Tool For Comparative Genomics
IAO_0000115: Software visualization tool for comparative functional genomics that supports analysis of three types of biological data at once: functional data such as gene activity measurements; pathway data that presents a series of reactions within a cellular process; and phylogenetic data describing ancestral relationships between species. The design of Pathline includes two new visual encoding techniques. The first is an encoding of a linearized metabolic pathway representation that provides appropriate topological information and supports the comparison of quantitative data along the pathway. The second is a curvemap, a matrix layout of temporal expression data for enhanced perception of trends in gene and cell activity levels across multiple species.

National Addiction and HIV Data Archive Program (NAHDAP)
type: Resource
type: NamedIndividual
has db xref: DOI:10.3886
has db xref: nif-0000-06713
has db xref: r3d100010261
synonym: ICPSR/NAHDP
synonym: NAHDAP
synonym: National Addiction & HIV DATA Archive Program
synonym: National Addiction & HIV DATA Archive Program (NAHDAP)
synonym: National Addiction and HIV DATA Archive Program
synonym: National Addiction and HIV DATA Archive Program (NAHDAP)
synonym: National Addiction HIV Data Archive Program
IAO_0000115: Archive that acquires, preserves and disseminates data relevant to drug addiction and HIV research. Collection of data on drug addiction and HIV infection in United States. Most of datasets are raw data from surveys, interviews, and administrative records. They were originally gathered in research projects and for administrative purposes. Some datasets have been used in published studies. Bibliographies of these studies are available . Provides access to research data and technical assistance for data depositors. Provides e-workshops on data preparation and data systems.

FEED
type: Resource
type: NamedIndividual
has db xref: nlx_151995
synonym: FEED: Feeding Experiments End-User Database
synonym: Feeding Experiments End-User Database
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of physiologic data and associated metadata related to feeding behavior for a number of mammalian species, including human. The data contain information on muscle activity, bone and muscle strain, jaw and oropharyngeal apparatus motion, and intra-oral pressure and were generated using several techniques (e.g., electromyography, cineradiography, sonomicrometry). The data are searchable and can be downloaded into csv format.

Africa Centre Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_152011
synonym: Africa Center Biobank
synonym: Africa Centre for Health and Population Studies Biobank
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented November 30, 2015. Extensive collection of biological specimens of various kinds that are mostly collected from the population around the Africa Centre in northern KwaZulu-Natal, but there are also specimens collected from populations in and around Durban and elsewhere in KwaZulu-Natal. The results of tests carried out on these specimens are generally stored in the main databases of the various studies involved, and are linkable back to the demographic and other data collected from the individuals concerned. The Biobank is curated by staff of the Africa Centre's Virology Laboratory in Durban, where all the specimens are currently stored, mostly in -80C freezers. A particular strength of its holdings are the dried blood spot (DBS), specimens five drops of blood on a filter-paper card, obtained via a finger-prick - of which there are now nearly 115,000. The following is a list of its holdings (May 2011): * 67,700 DBS specimens collected since late 2002 primarily for HIV prevalence estimation of the population covered by the Africa Centre Demographic Surveillance population. All have at least been tested for HIV, and just over 21% give a Positive result. Specimens are collected annually, so for some individuals we might have a sequence of 8-10 specimens covering 2002-2011. * 36,601 DBS specimens collected by the Vertical Transmission Study (VTS) between Sep 2001 and Dec 2006. This study focussed on mother-child pairs and investigated the vertical transmission of HIV from mother to child. DBS specimens were collected from both the mothers (at initial screening, and then from their children at Birth, 6, 10, 14, 18, 22 weeks, and 7, 8, 9, 12, 15, 18, 21 and 24 months. * 6,585 DBS specimens collected as part of the KZN IMPACT study of PMTCT effectiveness in six districts of kwaZulu-Natal. The specimens were collected during 2004-2006 from infants aged 4-8 weeks when mothers brought them to clinics for immunisation. These DB…

University of Neurosurgery Webinar Series
type: Resource
type: NamedIndividual
has db xref: nif-0000-06723
synonym: CNS Webinar Series
synonym: Congress of Neurological Surgeons Webinar Series
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. A series of of webinars offered directly to users' computers. The webinars are offered in a variety of subjects, including neurotrauma, spine, tumor and vascular. Each webinars costs $35 US and offers CME credit.

PhenoFam
type: Resource
type: NamedIndividual
has db xref: biotools:phenofam
has db xref: OMICS_02230
IAO_0000115: A web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms.

UC3 Merritt
type: Resource
type: NamedIndividual
has db xref: nlx_152126
has db xref: r3d100010747
synonym: University of California Curation Center Merritt
abbrev: Merritt
IAO_0000115: Data repository service from the University of California Curation Center (UC3) that lets the UC community manage, archive, and share its valuable digital content. Merritt provides long-term preservation of digital assets, allows researchers to share data with others, or meet the data sharing and preservation requirements of a grant-funded project.

forqs
type: Resource
type: NamedIndividual
has db xref: OMICS_02196
synonym: and Selection
synonym: Forward-in-time simulation of Recombination
synonym: Quantitative traits
IAO_0000115: Software for forward-in-time population genetics simulation that tracks individual haplotype chunks as they recombine each generation. It also also models quantitative traits and selection on those traits.

Avadis
type: Resource
type: NamedIndividual
has db xref: nlx_149208
has db xref: OMICS_01120
synonym: Access Visualize Analyze Discover
synonym: Avadis NGS
IAO_0000115: Software integrated platform that provides analysis, management and visualization tools for next-generation sequencing data. It supports workflows for RNA-Seq, DNA-Seq, ChIP-Seq and small RNA-Seq experiments. Avadis has a built-in Gene Ontology browser to view ontology hierarchies. There are common ontology paths for multiple genes. Platform has collection of data / text mining algorithms, data visualization libraries, workflow/application automation layers, and enterprise data organization functions. These functions are available as libraries that allow developers to rapidly build software prototypes, applications and off-the-shelf products. The collection of algorithms and visualizations in AVADIS grows as new applications using the platform are developed. Currently, the algorithms that AVADIS platform contains range from general purpose statistical mining and modelling algorithms, to text mining algorithms, to very application-specific algorithms for microarray / NGS data analysis, QSAR modelling and biological networks analysis. AVADIS has a collection of powerful mining algorithms like PCA, ANOVA, T-test, clustering, classification and regression methods. The range of visualizations includes most statistical and data modelling related graphing views, and very application-specific visualizations. Some of the statistical views include 2D/3D scatter plots, profile plots, heat maps, histograms and matrix plot; data modelling relevant views include dendrograms, cluster profiles, similarity images and SOM U-matrices. Application-specific views in AVADIS include pathway network views, genome browsers, chemical structure views and pipe-line views. Platform: Windows compatible, Mac OS X compatible, Linux compatible,

Wake Forest Primate Center
type: Resource
type: NamedIndividual
has db xref: nif-0000-24363
synonym: Wake Forest University Primate Center
abbrev: WFPC
abbrev: WFUPC
IAO_0000115: A research center whose primary functions are research, training, and outreach using nonhuman primates to study six of the ten major causes of death in the United States. Educational training includes programs designed to teach both pre- and postdoctoral veterinarians how to conduct biomedical research. Scientific outreach extends to investigators at Wake Forest School of Medicine and across the nation who require expertise, infrastructure, and monkeys to be used in studies that advance human health and well-being.

GMcloser
type: Resource
type: NamedIndividual
has db xref: biotools:gmcloser
has db xref: OMICS_00042
synonym: Gmcloser - Closing the gaps in scaffolds with preassembled contigs
IAO_0000115: Software that fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads. Unlike other gap-closing tools that use only NGS reads, GMcloser uses preassembled contig sets or long read sets as the sequences to close gaps and uses paired-end (PE) reads and a likelihood-based algorithm to improve the accuracy and efficiency of gap closure. The efficiency of gap closure can be increased by successive treatments with different contig sets.

UCSF Brain Tumor Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_143683
synonym: UCSF Brain Tumor Research Center Tissue Bank
synonym: UCSF Brain Tumor Research Center Tissue Core
synonym: UCSF BTRC Tissue Core
synonym: UCSF Neurological Surgery Tissue Bank
synonym: UCSF Neurosurgery Tissue Bank
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Brain Tumor Research Center Tissue Bank began collecting tissue in 1978 and has established an organized repository of characterized tissues--frozen, paraffin-embedded, blood and cultures--that are maintained in a manner useful for a wide range of studies. Samples are collected only from patients who have agreed to have their tissues banked and used for future research. Consent documents are maintained in a secure area and associated clinical data are held in a double-password protected computer database. Each sample received into the Tissue Bank is non-identifying number. No protected health information (PHI) is released. To obtain samples, investigators submit a request form to the Manager. The request form requires an explanation of the tissue requested (type, number of samples, justification), description of the study, CHR approval (see new policy regarding human vs. non-human research) and Project Leader authorization. The Manager reviews each request for feasibility before presentation to the Scientific Core Committee. The UCSF Neurosurgery Tissue Bank makes its inventory of stock cell lines available to all investigators. Requested cells are grown in T-25 flasks and shipped FedEx Priority Overnight at the receipient's expense. However, if you prefer, we can ship the frozen cells, packed in dry ice. (Note: some countries restrict dry ice shipments.)

F1000 Reports
type: Resource
type: NamedIndividual
has db xref: nlx_36964
synonym: Faculty of 1000 Reports
IAO_0000115: The open access F1000 Reports journals add an extra dimension to F1000, providing unique, peer-reviewed reports on emerging themes in biology and medicine. F1000 Section Heads ensure coverage of the latest advances by selecting topics and nominating experts to provide context for the evaluated literature. These open access journals are freely available to all users without barriers or the need for a subscription, and are currently indexed and/or abstracted by PubMed, PubMed Central, Scopus, Embase, Global Health and CAB Abstracts.

Wired Science
type: Resource
type: NamedIndividual
has db xref: nlx_144196
synonym: Wired Science - News for Your Neurons
IAO_0000115: Wired Science covers what's new on the front lines of science, from deep space to DNA sequencing.

GenomeWeb
type: Resource
type: NamedIndividual
has db xref: nif-0000-10238
has db xref: OMICS_01731
synonym: GenomeWeb LLC
IAO_0000115: An independent, privately-held online and print publisher based in New York that serves the global community of scientists, technology professionals, and executives who use and develop the latest advanced tools in molecular biology research and molecular diagnostics. GenomeWeb's editorial mission is to serve readers with exclusive, in-depth coverage of the technology, institutions, and scientists that make up the worldwide research enterprise of molecular biology. We operate the largest online news organization focused on advanced research tools in genomics, proteomics, and bioinformatics. Our expert editors report and write with precision and clarity. GenomeWeb users can be found in major scientific organizations around the world, including biopharmaceutical companies, important research universities, biomedical institutes, and government laboratories. Our advertisers include leading suppliers of research tools, analytical instruments, and information technology. Getting started is easy - just register, and use your workplace e-mail address to maximize your access to content. Once you're logged in, you'll have complete free access to GenomeWeb Daily News, The Daily Scan, all of Genome Technology magazine, every GenomeWeb blog, and much more. GenomeWeb Free Content * GenomeWeb Daily News offers breaking news as well as feature articles on genomics, proteomics, bioinformatics, and more. Daily News covers not only the science and business news, but also regulatory and policy updates. Published online and twice daily by e-mail bulletin. * The Daily Scan is a roundup of the most interesting mainstream media articles, blog posts, and peer-reviewed literature relevant to genomic and proteomic scientists. Published daily online and by e-mail bulletin. * Genome Technology: GenomeWeb's magazine covers news, trends, people, and technologies in the systems biology field. It also includes Tech Guides, which feature expert troubleshooting advice on specific lab challenges, and R…

Autism Tissue Program
type: Resource
type: NamedIndividual
has db xref: nif-0000-10160
abbrev: ATP
IAO_0000115: Autism research program that makes available post-mortem brain tissue to qualified scientists all over the world. Working directly with tissue banks, organ procurement agencies, medical examiners and the general public, this is the largest program dedicated to increasing and enhancing the availability of post-mortem brain tissue for basic research in autism. To date, the ATP has collected and stored more than 170 brains in their repositories at Harvard (US) and Oxford (UK). These brains are processed by formalin fixation and/or snap frozen to properly provide high quality tissue of all brain regions, in support of biological research in autism. The ATP is unique in that they diligently pursue all available clinical data (pre and post mortem) on tissue donors in order to create the most biologically relevant brain repository for autism research. These data, together with tissue resources from both banks and associated repositories, are presented to all interested researchers through their extensive web-based data portal (login required). The ATP is not a brain bank, but works directly with the Harvard Brain Tissue Resource Center in Boston (HBTRC), Massachusetts to serve as its tissue repository. This program augments brain bank functions by: * Creating the most biologically relevant brain tissue repository possible * Fully covering all costs associated with brain extraction and transfer to the repositories at Harvard (US and Canada) and Oxford (UK). * Providing scientific oversight of tissue distributions * Overseeing and managing all tissue grants * Clinically phenotyping and acquiring extensive medical data on all of their donors * Providing continuing family support and communication to all of their donors * Directly supporting researchers to facilitate autism research * Maintaining a robust web based data management and secure on-line global interface system * Developing and supporting ATP established scientific initiatives * Actively providing public outreach a…

CENtral Science
type: Resource
type: NamedIndividual
has db xref: nlx_144206
IAO_0000115: Blogs for all things chemistry, hosted by Chemical & Engineering News (C&EN) magazine, where you will find blogs written by both C&EN staff and non-staff contributors on topics ranging from jobs to natural products chemistry to safety to the businesses of chemistry. CENtral Science currently includes the following blogs: * Artful Science: C&EN science writer Sarah Everts peers in to the laboratories that help museums and galleries authenticate, conserve, and restore art and artifacts. * Cleantech Chemistry: C&EN business writer Melody Voith looks at the business and technology strategies of companies that hope to serve the world's need for renewable energy, sustainable agriculture, clean water, and non-polluting manufacturing and transportation, among other cleantech sectors. * IYC 2011: CENtral Science's home for all things IYC 2011. * Just Another Electron Pusher: Contributors Christine Herman and Glenn Ernst profile people who've pursued professions away from the bench. They also write about their own personal quests for satisfying jobs that use their degrees but may not involve running any %$@& columns. * Newscripts: The companion blog to the like-named weekly C&EN column. Written primarily by C&EN science writers Lauren Wolf and Beth Halford, with contributions from the C&EN staff. * Terra Sigillata: Molecular cancer pharmacologist David Kroll writes about natural products, focusing on chemistry and pharmaceutical issues. * The Chemical Notebook: C&EN business writer Alex Tullo shares interesting tidbits from his reporter's notebook. * The Editor's Blog: The companion blog to the weekly print column by editor-in-chief Rudy Baum and deputy editor-in-chief Maureen Rouhi. * The Haystack: C&EN business writer Lisa Jarvis and science writer Carmen Drahl weed through pharma's molecular mountain to pluck out the drug developments worth noting. Also features frequent contributions from SeeArrOh, a Ph.D chemist working in industry. * The Safety Zone: C&EN science writer…

GONUTS
type: Resource
type: NamedIndividual
has db xref: nlx_30164
has db xref: OMICS_02268
synonym: Gene Ontology Normal Usage Tracking System
synonym: GONUTS wiki
IAO_0000115: A wiki where users of the Gene Ontology can contribute and view notes about how specific GO terms are used. GONUTS can also be used as a GO term browser, or to search for GO annotations of specific genes from included organisms. The rationale for this wiki is based on helping new users of the gene ontology understand and use it. The GONUTS wiki is not an official product of the the Gene Ontology consortium. The GO consortium has a public wiki at their website, http://wiki.geneontology.org/. Maintaining the ontology involves many decisions to carefully choose terms and relationships. These decisions are currently made at GO meetings and via online discussion using the GO mailing lists and the Sourceforge curator request tracker. However, it is difficult for someone starting to use GO to understand these decisions. Some insight can be obtained by mining the tracker, the listservs and the minutes of GO meetings, but this is difficult, as these discussions are often dispersed and sometimes don't contain the GO accessions in the relevant messages. Wikis provide a way to create collaboratively written documentation for each GO term to explain how it should be used, how to satisfy the true path requirement, and whether an annotation should be placed at a different level. In addition, the wiki pages provide a discussion space, where users can post questions and discuss possible changes to the ontology. GONUTS is currently set up so anyone can view or search, but only registered users can edit or add pages. Currently registered users can create new users, and we are working to add at least one registered user for each participating database (So far we have registered users at EcoliHub, EcoCyc, GOA, BeeBase, SGD, dictyBase, FlyBase, WormBase, TAIR, Rat Genome Database, ZFIN, MGI, UCL and AgBase...

RetractionWatch.com
type: Resource
type: NamedIndividual
has db xref: nif-0000-06675
synonym: Retraction Watch
synonym: retractionwatch
IAO_0000115: Retraction Watch is a blog of retractions in the scientific literature. It is maintained by Adam Marcus and Ivan Oransky and has been operating since August 2010.

UNSW Embryology
type: Resource
type: NamedIndividual
has db xref: nlx_151968
synonym: University of New South Wales Embryology
IAO_0000115: A wiki / educational resource for learning concepts in embryological development with sections including medicine, science, movies - audio, human embryo, systems, abnormal and animals. Pages on developmental topics can be added by experts in that specific research area and the content subject to easy review and update. Students can also contribute and several undergraduate courses use content on this site. Editing of pages will be restricted to registered users and all changes are logged.

Drugs.com
type: Resource
type: NamedIndividual
has db xref: nif-0000-21133
IAO_0000115: The Drugs.com mission is to be the Internets most trusted resource for drug and related health information. We will achieve this aim by presenting independent, objective, comprehensive and up-to-date information in a clear and concise format for both consumers and healthcare professionals. Their goal is to provide clear information about drugs sold in the USA, at a level everyone can comprehend. For consumers, we provide product information in non-technical language. Health professionals will find what they need in the FDA Product Label Professional Information database. The Care Guide provides information about the treatment of common illnesses and injuries. The Drug Interactions checker details drug-drug interaction mechanisms, severity and management, and also outlines drug-food interactions. Drugs.com is NOT an online pharmacy and does not condone the sale of prescription medicines over the Internet without a prescription. Drugs.com simply provides a free drug-information service to help you better understand how medicines work: their uses, side effects and potential to interact with other medicines. For information on purchasing prescription medicines online please visit the FDAs Buying Prescription Medicine Online: A Consumer Safety Guide. Drugs.com medical dictionary is powered by Stedmans. Since 1911, Stedmans Medical Dictionary has been the medical professions most trusted source for medical definitions. A complete medical terms dictionary, Steadmans Electronic Medical Dictionary contains over 107,000 medical terms taken directly from Stedmans Medical Dictionary, 28th Edition. Most search engines cover the entire Internet, and searches on these engines may produce many results that are not specific to your drug question. On Drugs.com, you can search by medical condition or by drug, and get the answer you need right away. Searches by drug can be made using the brand name or the generic name of the drug. Searches by medical condition will return a list of med…

Lab Times
type: Resource
type: NamedIndividual
has db xref: nlx_153833
synonym: Lab Times Online
IAO_0000115: News magazine for the European life sciences. The mixture of content, spirit and language works to make both Lab Times and www.labtimes.eu a good read as demonstrated by steadily rising reader counts and click rates, and the positive researcher feedback we've received, including an email from Tim Hunt, winner of the 2001 Nobel Prize in Physiology or Medicine, in which he stated, I like your magazine, and I wanted to let you know how much I enjoy reading it.

Pediatric Brain Tumor Consortium
type: Resource
type: NamedIndividual
has db xref: grid.477819.4
has db xref: nlx_143885
abbrev: PBTC
IAO_0000115: The PEDIATRIC BRAIN TUMOR CONSORTIUM (PBTC) is a multidisciplinary cooperative research organization devoted to the study of correlative tumor biology and new therapies for primary CNS tumors of childhood. PBTC's mission is to contribute rapidly and effectively to the understanding and cure of these tumors through the conduct of multi-center, multidisciplinary, innovative studies with designs and analyses based on uniformly high quality statistical science. While the primary mission of the PBTC is to identify through laboratory and clinical science superior treatment strategies for children with brain cancers, the PBTC investigators recognize their profound responsibility to meet the special needs of the children and families as they face this enormous challenge. Members are committed to working within their institutions and communities to improve support services and follow up care for these patients and their families. The PBTC's primary objective is to rapidly conduct novel phase I and II clinical evaluations of new therapeutic drugs, new biological therapies, treatment delivery technologies and radiation treatment strategies in children from infancy to 21 years of age with primary central nervous system (CNS) tumors. A second objective is to characterize reliable markers and predictors (direct or surrogate) of brain tumors' responses to new therapies. The Consortium conducts research on brain tumor specimens in the laboratory to further understand the biology of pediatric brain tumors. A third objective is to develop and coordinate innovative neuro-imaging techniques. Through the PBTC's Neuro-Imaging Center, formed in May 2000, research to evaluate new treatment response criteria and neuro-imaging methods to understand regional brain effects is in progress. These imaging techniques can also advance understanding of significant neuro-toxicity in a developing child's central nervous system. The Neuro-Imaging Center is supported in part by private sources - grants …

Bycom
type: Resource
type: NamedIndividual
has db xref: OMICS_00594
IAO_0000115: A software which can perform methylcytosine calling from BS-seq (WGBS and RRBS), and permits either unmapped reads (FASTQ) or mapped reads (SAM/BAM) to be used as the input data. Certain SNPs (C>A/G) can also be selected in the output.

CorQ
type: Resource
type: NamedIndividual
has db xref: OMICS_01039
IAO_0000115: A set of perl programs that correct errors in 454 pyrosequences by identifying and flagging poor quality insertions, deletions and substitutions within an alignment. The algorithm utilizes the inherent base quality in sequence-specific context to correct for homopolymer and non-homopolymer insertion and deletion errors. CorQ also takes uneven read mapping into account for correcting pyrosequencing miscall errors and it identifies and corrects carry forward errors.

MEG Tools
type: Resource
type: NamedIndividual
has db xref: nlx_155792
IAO_0000115: A software program for source imaging Magnetoencephalographic data. Now MEG tools has added Imaged Coherence mapping, Talairach and MNI coordinates, Grainger Causality. MEG Tools also includes MR-FOCUSS, ECD, Beamformers and many other useful MEG tools. This is a Matlab-based software module that is used to image MEG data onto a patient's MRI. This software imports all MEG manufacture's data (4D-Neuroimaging/BTi, CTF and Neuromag/Elekta).

Wnt homepage
type: Resource
type: NamedIndividual
has db xref: nlx_156863
synonym: the Wnt homepage
IAO_0000115: A resource for members of the Wnt community, providing information on progress in the field, maps on signaling pathways, and methods. The page on reagents lists many resources generously made available to and by the Wnt community. Wnt signaling is discussed in many reviews and in a recent book. There are usually several Wnt meetings per year.

Southern California Earthquake Data Center
type: Resource
type: NamedIndividual
has db xref: nlx_154718
has db xref: r3d100011575
abbrev: SCEDC
IAO_0000115: Archive of earthquake data for research in seismology and earthquake engineering in Southern California recorded or processed by the Southern California Seismic Network (SCSN). Users can access information on: * Recent earthquakes detected by the SCSN * Significant southern California earthquakes and faults * The southern California earthquake catalog, spanning from 1933 to present * Waveform and metadata files of SCSN seismic stations from 1977 to present * Data sets created by SCEC scientists to assist in ongoing and future research

NGS tools for the novice
type: Resource
type: NamedIndividual
has db xref: OMICS_01063
synonym: NGS tools for the novice - Handy tools for processing of next generation sequencing (NGS) data
IAO_0000115: A collection of simple Perl scripts adressed to scientists doing research that bases on high throughput genomic/transcriptomic data. It does not require any bioinformatic expertise. The scripts perform fundamental processing steps like sorting sequences by TAGs, FASTQ to FASTA conversion, filtering and counting of redundant sequences, individually adjustable FASTQ quality filtering or basic analyses like base count and analysis of sequence length distribution.

Opera
type: Resource
type: NamedIndividual
has db xref: biotools:opera
has db xref: OMICS_00045
synonym: OPERA-LG
synonym: Optimal Paired-End Read Assembler
IAO_0000115: A sequence assembly software program that uses information from paired-end reads to optimally order and orient contigs assembled from shotgun-sequencing reads.

Virginia Commonwealth University, Department of Pharmacology
type: Organization
type: NamedIndividual
has db xref: nif-0000-02004
synonym: VCU Department of Pharmacology and Toxicology
synonym: VCU Department of Pharmacology Toxicology
synonym: VCU Pharmacology and Toxicology
synonym: VCU School of Medicine; Department of Pharmacology and Toxicology
synonym: VCU SOM Pharmacology and Toxicology
IAO_0000115: A graduate program for pharmacology and toxicology that is a component of the Virginia Commonwealth University. This organization also performs studies on medical disorders, and new pharmacology agents and their effects on human health.

MEGA
type: Resource
type: NamedIndividual
has db xref: nlx_156838
has db xref: SCR_023017
synonym: MEGA11
synonym: Molecular Evolutionary Genetics Analysis
synonym: Molecular Evolutionary Genetics Analysis 4
synonym: Molecular Evolutionary Genetics Analysis 6
abbrev: MEGA4
abbrev: MEGA6
abbrev: MEGA 4
abbrev: MEGA 11
IAO_0000115: Software integrated tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web based databases, estimating rates of molecular evolution, and testing evolutionary hypotheses. Used for comparative analysis of DNA and protein sequences to infer molecular evolutionary patterns of genes, genomes, and species over time. MEGA version 4 expands on existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. MEGA version 6 enables inference of timetrees, as it implements RelTime method for estimating divergence times for all branching points in phylogeny.

Tennenbaum Center for the Biology of Creativity
type: Resource
type: NamedIndividual
has db xref: nif-0000-10497
synonym: UCLA CBC
IAO_0000115: The purpose of this center is to study the molecular, cellular, systems and cognitive mechanisms that result in cognitive enhancements and explain unusual levels of performance in gifted individuals, including extraordinary creativity. Additionally, by understating the mechanisms responsible for enhancements in performance we may be better suited to intervene and reverse disease states that result in cognitive deficits. One of the key topics addressed by the Center is the biological basis of cognitive enhancements, a topic that can be studied in human subjects and animal models. In the past much of the focus in the brain sciences has been on the study of brain mechanisms that degrade cognitive performance (for example, on mutations or other lesions that cause cognitive deficits). The Tennenbaum Center for the Biology of Creativity at UCLA enables an interdisciplinary team of leading scientists to advance knowledge about the biological bases of creativity. Starting with a pilot project program, a series of investigations was launched, spanning disciplines from basic molecular biology to cognitive neuroscience. Because the concept of creativity is multifaceted, initial efforts targeted refinement of the component processes necessary to generate novel, useful cognitive products. The identified core cognitive processes: 1.) Novelty Generation the ability to flexibly and adaptively generate products that are unique; 2.) Working Memory and Declarative Memory the ability to maintain, and then use relevant information to guide goal-directed performance, along with the capacity to store and retrieve this information; and 3.) Response Inhibition the ability to suppress habitual plans and substitute alternate actions in line with changing problem-solving demands. To study the basic mechanisms underlying these complex brain functions we use translational strategies. Starting from foundational studies in basic neuroscience, we forged an interdisciplinary strategy that permits th…

SRMA
type: Resource
type: NamedIndividual
has db xref: biotools:srma
has db xref: OMICS_01079
synonym: Short Read Micro re-Aligner
IAO_0000115: A post-alignment micro re-aligner for next-generation high throughput sequencing data.

DeNovoGear
type: Resource
type: NamedIndividual
has db xref: OMICS_00083
IAO_0000115: A software for detecting de novo mutations using sequencing data. It utilizes likelihood-based error modeling to reduce the false positive rate of mutative discovery in exome analysis. It also uses fragment information to identify the parental origin of germ-line mutations.

VarB
type: Resource
type: NamedIndividual
has db xref: OMICS_00898
IAO_0000115: A variation browsing and analysis tool for variants derived from next-generation sequencing data.

BAMseek
type: Resource
type: NamedIndividual
has db xref: OMICS_00877
synonym: bamseek - Browse large BAM and SAM alignment files.
IAO_0000115: A Large File Viewer for BAM and SAM alignment files.

Southampton Tumour Bank
type: Resource
type: NamedIndividual
has db xref: nlx_14010
synonym: Cancer Research UK Center Tumor Bank
synonym: Cancer Research UK Centre Tumour Bank
synonym: Southampton Tumor Bank
synonym: University of Southampton Cancer Research UK Centre Tumour Bank
synonym: University of Southampton Tumor Bank
synonym: University of Southampton Tumour Bank
IAO_0000115: Collects and distributes human tissue for ethically approved studies to aid the study of cancer biology and other associated research. All tissue is collected with patient consent and tissue is distributed only to ethically approved studies. The purpose of the Tissue Bank is to source, organize, collect, prepare, store and distribute a diverse collection of human tissues and biological products. This valuable core resource is available to all local academics and researchers. The on-site bank allows for rapid access to a plethora of biological materials supported by an informatics system of databases acting as an inventory management system. In addition, the Tissue Bank provides a licensed facility to store surplus tissue when studies close. Tissues currently available include normal and malignant snap frozen blocks, freshly prepared spleen and lymph nodes, fresh biopsy tissues, blood products and biological fluids. Collections can be organized by bank staff or ran in parallel with current research activities and include a wide variety of cancer classifications. We currently hold over 38,000 vials. Tissue Availability: Lymphoma - solid tissue and cells - 843; Breast - solid tissue and cells - 540; Colon - solid tissue and cells - 238; Lung - solid tissue and cells - 43; Upper Gi - BIOPSY tissue - 114; Pleural fluid and cells - 14

The Guardian: Science Weekly
type: Resource
type: NamedIndividual
has db xref: nlx_144241
synonym: Science Weekly with Alok Jha
synonym: The Guardian - Science Weekly
synonym: The Guardian: Science Weekly with Alok Jha
IAO_0000115: Alok Jha and the Guardian's science team bring you the best analysis and interviews from the worlds of science and technology.

TriageTools
type: Resource
type: NamedIndividual
has db xref: biotools:triagetools
has db xref: nlx_156740
IAO_0000115: A collection of tools for partitioning raw data (fastq reads) from high-throughput sequencing projects. The tools are designed for basic data management as well for prioritizing analysis of certain subsets.

EUCOMMTOOLS
type: Resource
type: NamedIndividual
has db xref: nlx_152804
synonym: EUCOMM - Tools for Functional Annotation of the Mouse Genome
synonym: EUCOMM: Tools for Functional Annotation of the Mouse Genome
IAO_0000115: Functional Annotation of the Mouse Genome, it will complete the International Knockout Mouse Consortium (IKMC) resource of mutations for all protein coding genes. Furthermore, it will maximize the utility of the conditional IKMC resource by generating up to 250 different, mostly inducible Cre driver mouse lines. In addition, EUCOMMTOOLS will develop novel tools to enhance the versatility of the IKMC resource. EUCOMMTOOLS vectors, mutant ES cells and mutant mice are distributed worldwide: EUCOMMTOOLS mutant ES cells and vectors can be obtained from the European Mouse Mutant Cell Repository (EuMMCR). EUCOMMTOOLS mutant mice are archived and distributed by the European Mouse Mutant Archive (EMMA). Knockout-first Mutant Alleles: EUCOMMTOOLS will create 3500 C57Bl/6 conditional mutant alleles for single-exon (or otherwise previously conditionally untargeted) protein-coding mouse genes. These alleles will be made predominantly by introducing an "artificial intron", containing a standard EUCOMM promoter-driven targeting cassette, into the coding sequence of the single-exon gene. Cre Resources: EUCOMMTOOLS will engineer 500 new Cre C57Bl/6 ES cell lines by Cre knock-ins into genes with useful expression patterns. The resource will be made with inducible forms of Cre recombinase such as CreERT2. Up to 250 lines of Cre driver mice on a pure C57Bl/6N background will be generated and the Cre expression patterns documented and annotated in day P14 and P56. These mice will form a matched Cre driver resource for C57Bl/6N mice produced from conditional IKMC resources. Research, Technology and Complementary Reagents: EUCOMMTOOLS will develop novel technologies to add value, depth and flexibility to existing IKMC ES cell and mouse resources. Key areas include: * Development of novel recombinase based regulatory switches * Exploration of zinc-finger nuclease stimulated homologous recombination strategies in fertilized oocytes * Development and validation of complementary modular vecto…

WHO Collaborating Centre for Drug Statistics Methodology
type: Resource
type: NamedIndividual
has db xref: nif-0000-10553
synonym: WHOCC
IAO_0000115: The official compendium for the Anatomical Therapeutic Chemical Classification System (ATC)-code descriptions. The Centre's main tasks are development and maintenance of the ATC/DDD system, including: * To classify drugs according to the ATC system. * Priority will be given to the classification of single substances, while combination products available internationally (i.e. important fixed combinations) will be dealt with as far as possible. * To establish DDDs for drugs which have been assigned an ATC code. * To review and revise as necessary the ATC classification system and DDDs. * To stimulate and influence the practical use of the ATC system by co-operating with researchers in the drug utilization field. Support: The WHO Collaborating Centre for Drug Statistics Methodology was established in 1982. The Centre is situated in Oslo at the Norwegian Institute of Public Health. The Centre is funded by the Norwegian government.

clipcrop
type: Resource
type: NamedIndividual
has db xref: biotools:clipcrop
has db xref: OMICS_00310
synonym: ClipCrop
IAO_0000115: Software tool for detecting structural variations with single-base resolution using soft-clipping information from SAM files.

Clinical Trials Registry - India
type: Resource
type: NamedIndividual
has db xref: nlx_151507
has db xref: r3d100010980
synonym: Clinical Trials Registry - India (CTRI)
synonym: Clinical Trials Registry-India
synonym: Clinical Trials Registry-India (CTRI)
abbrev: CTRI
IAO_0000115: Free, online public record system for registration of clinical trials being conducted in India. Initiated as a voluntary measure, trial registration in the CTRI has been made mandatory by the Drugs Controller General (India) (DCGI) (http://www.cdsco.nic.in/). Moreover, Editors of Biomedical Journals of 11 major journals of India declared that only registered trials would be considered for publication. Today, any researcher who plans to conduct a trial involving human participants, of any intervention such as drugs, surgical procedures, preventive measures, lifestyle modifications, devices, educational or behavioral treatment, rehabilitation strategies as well as trials being conducted in the purview of the Department of AYUSH (http://indianmedicine.nic.in/) is expected to register the trial in the CTRI before enrollment of the first participant. Trial registration involves public declaration and identification of trial investigators, sponsors, interventions, patient population etc before the enrollment of the first patient. Submission of Ethics approval and DCGI approval (if applicable) is essential for trial registration in the CTRI. Multi-country trials, where India is a participating country, which have been registered in an international registry, are also expected to be registered in the CTRI. In the CTRI, details of Indian investigators, trial sites, Indian target sample size and date of enrollment are captured. After a trial is registered, trialists are expected to regularly update the trial status or other aspects as the case may be. After a trial is registered, all updates and changes will be recorded and available for public display. The CTRI is working with the WHO ICTRP to ensure that results of all trials registered with the CTRI are adequately reported and publicly available.

Eide Neurolearning Blog
type: Resource
type: NamedIndividual
has db xref: nlx_144589
IAO_0000115: Weekly articles related to brain-based learning and learning styles, problem-solving and creativity, kids, families, and parenting, gifted and visual learners, dyslexia, attention deficit disorders, autism, and more.

detecttd
type: Resource
type: NamedIndividual
has db xref: OMICS_00315
synonym: detecttd - Tool to detect tandem duplications in NGS reads
IAO_0000115: Software tool to detect tandem duplications in sequencing reads. It is written in Python and requires NCBI Blast standalone.

FastUniq
type: Resource
type: NamedIndividual
has db xref: OMICS_01044
IAO_0000115: A software tool for removal of de novo duplicates in paired short DNA sequences.

Canadian Online CME Sites
type: Resource
type: NamedIndividual
has db xref: nif-0000-23612
abbrev: Canadian Online CME
IAO_0000115: Annotated list of online CME (continuing medical education) with links to, and descriptions of, Web Sites offering courses and CME credit specifically aimed at Canadian physicians. All Canadian Online CME offering MainPro-M1 credit includes an online group discussion format. You must participate in these discussions as well as go though the didactic material to earn credit.

GEUVADIS
type: Resource
type: NamedIndividual
has db xref: OMICS_01779
synonym: Genetic European Variation in Health and Disease
synonym: Genetic European Variation in Health and Disease - A European Medical Sequencing Consortium
synonym: GEUVADIS Consortium
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 6,2023. A European Medical Sequencing Consortium committed to gaining insights into the human genome and its role in health and medicine by sharing data, experience and expertise in high-throughput sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Cystic Fibrosis Mutation Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-21105
has db xref: r3d100012093
abbrev: CFMDB
abbrev: CFTR1
IAO_0000115: Collection of mutations in CFTR gene for international cystic fibrosis genetics research community. Provides up to date information about individual mutations in CFTR gene. All known CFTR mutations and sequence variants have been converted to standard nomenclature recommended by Human Genome Variation Society. On line process for submission of new mutations has been added.While they continue to ensure quality of data, they urge international community to give them feedback and suggestions. Clinical information in this database relates only to details of discovery of specific mutations. As part of 2010 upgrade, CFTR1 joined new project called CFTR2 - Clinical and Functional TRanslation of CFTR. Links to CFTR2 for many mutations in CFTR1 will provide up-to-date summaries of genotype-phenotype information from patient registries around the world.

H2SO4Hurts
type: Resource
type: NamedIndividual
has db xref: nlx_144220
synonym: H2SO4 Hurts - Brian Krueger PhD
synonym: H2SO4 Hurts: And Other Pearls of Science Wisdom
synonym: H2SO4Hurts - Brian Krueger PhD
IAO_0000115: Blog about technology, molecular biology, and editorial comments on the current state of science on the internet. Brian Krueger PhD, is the owner, creator and coder of LabSpaces by night and a Molecular biologist by day. His posts are presented as opinion and commentary and do not represent the views of LabSpaces Productions, LLC, his employer, or his educational institution.

TMAP
type: Resource
type: NamedIndividual
has db xref: OMICS_00694
synonym: TMAP - torrent mapping alignment program
synonym: Torrent Mapping Alignment Program
IAO_0000115: Alignment software for short and long nucleotide sequences produced by next-generation sequencing technologies.

BISMA
type: Resource
type: NamedIndividual
has db xref: OMICS_00592
synonym: BISMA: Analysis of primary bisulfite sequencing data manual
synonym: Bisulfite Sequencing DNA Methylation Analysis
IAO_0000115: An online tool for the analysis of bisulfite sequencing DNA methylation data. The software has specificity and quality control functions that allow the user to compile a set of sequences.

SOAP
type: Resource
type: NamedIndividual
has db xref: biotools:soap
has db xref: nlx_154652
synonym: Short Oligonucleotide Analysis Package
synonym: SOAP: short oligonucleotide alignment program
IAO_0000115: Software package that provides full solution to next generation sequencing data analysis consisting of an alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder ( SOAPindel ), a structural variation scanner ( SOAPsv ), a de novo short reads assembler ( SOAPdenovo ), and a GPU-accelerated alignment tool for aligning short reads with a reference sequence. (SOAP3/GPU)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Consortium for Radiologic Imaging Studies of Polycystic Kidney Disease
type: Resource
type: NamedIndividual
has db xref: nlx_152795
synonym: Consortium of Radiologic Imaging Study of PKD
abbrev: CRISP
IAO_0000115: A five-year prospective cohort study following 240 patients who have autosomal-dominant polycystic kidney disease (PKD) to determine whether changes in anatomic characteristics of their kidneys as measured by magnetic resonance imaging will be useful in providing surrogate measures for disease progression. CRISP's overall goal is to develop methods that would facilitate shortening the observation period necessary to determine efficacy of treatment interventions in PKD patients. Specific goals of this study are to: * Quantify cyst growth and ascertain severity of renal parenchymal involvement by sequential measurement of total kidney volume and the ratio of intact parenchyma to renal parenchyma occupied by cysts over time * Establish useful clinical correlations of imaging data with other markers of disease progression * Identify and test other potential markers or indices of disease progression, for example, assessment of loss of heterozygosity of renal cells shed in the urine, or other markers, in cohorts of patients with PKD * Gain information about the cost-effectiveness, patient acceptability, and advantages and disadvantages of different imaging techniques used serially in patients with PKD. Some experience has been gained in establishing that repeat imaging of the same PKD patient, using these techniques, yields reproducible estimates of kidney size and the proportion of renal parenchyma occupied by cysts. MRI may also have the advantage of permitting simultaneous estimation of GFR. Ultrasound has the advantage of being more cost-effective and perhaps more acceptable to patients for repetitive studies, but the measurements may be less accurate and reproducible. Nonetheless, there is very limited experience in applying these techniques to follow progression of the renal disease. Development of improved, reproducible imaging methods that assess cyst growth and provide markers of disease progression could markedly improve the feasibility of clinical trials. Parti…

FineSplice
type: Resource
type: NamedIndividual
has db xref: OMICS_03274
IAO_0000115: A software pipeline based on TopHat2 combined with a splice junction detection algorithm.

PiNGO
type: Resource
type: NamedIndividual
has db xref: nlx_149330
has db xref: OMICS_02281
IAO_0000115: A Java-based tool to easily find unknown genes in a network that are significantly associated with user-defined target Gene Ontology (GO) categories. PiNGO is implemented as a plugin for Cytoscape, a popular open source software platform for visualizing and integrating molecular interaction networks. PiNGO predicts the categorization of a gene based on the annotations of its neighbors, using the enrichment statistics of its sister tool BiNGO. Networks can either be selected from the Cytoscape interface or uploaded from file. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

PyNIfTI
type: Resource
type: NamedIndividual
has db xref: nlx_155929
synonym: PyNIfTI - Pythonic access to NIfTI and ANALYZE files
synonym: Pythonic access to NIfTI and ANALYZE files
IAO_0000115: PyNIfTI is no longer actively developed. At has been superseded by NiBabel -- a pure-Python package that provides everything that PyNIfTI could do, and a lot more. The PyNIfTI module is a Python interface to the NIfTI I/O libraries. Using PyNIfTI, one can easily read and write NIfTI and ANALYZE images from within Python. The NiftiImage class provides pythonic access to the full header information and for a maximum of interoperability the image data is made available via NumPy arrays.

California Academy of Sciences Blogs
type: Resource
type: NamedIndividual
has db xref: nlx_144243
abbrev: Academy Blogs
IAO_0000115: Academy scientists, journalists, adventurers and other staff members are blogging their stories and inviting questions and comments. Read current science news, hear from researchers in the field (Philippines, Sao Tome, Papua New Guinea), ask a question of an Academy naturalist, and much more.

RMAP
type: Resource
type: NamedIndividual
has db xref: OMICS_00681
IAO_0000115: Software for short-read mapping to accurately map reads from the next-generation sequencing technology. It can map reads with or without error probability information (quality scores) and supports paired-end reads or bisulfite-treated reads mapping. There is no limitaions on read widths or number of mismatches. RMAP can now map more than 8 million reads in an hour at full sensitivity to 2 mismatches.

California National Primate Research Center Analytical and Resource Core
type: Resource
type: NamedIndividual
has db xref: nlx_151305
synonym: California National Primate Research Center Analytical Resource Core
abbrev: CNPRC Analytical and Resource Core
IAO_0000115: The Analytical and Resource Core provides services and resources to the scientific research community in areas including hematology, clinical chemistry, genetics, immunology, endocrinology, flow cytometry, and pathogen detection. Available resources include biological specimens, viral stocks, DNA, and species-specific reagents. Scientists and staff associated with each of the seven Core Laboratories provide consultation in experimental design, sample collection, and data analysis, and offer assays that utilize species-specific reagents wherever possible. Core Laboratory scientists can also work with users to develop new assays to meet research needs. Training is available for all assays, and Core Laboratories equipment can be made available, typically on a recharge basis. Nonhuman primate resources developed at CNPRC are available to qualified individuals via the Resource Services component of the Core. * Clinical Laboratory * Endocrine Core Laboratory * Flow Cytometry Core Laboratory * Genetics Core Laboratory * Infectious Diseases Immunology Core Laboratory * Pathogen Detection Core Laboratory * Respiratory Disease Immunology Core Laboratory * Affiliated Laboratory: Clinical Proteomics Core Laboratory * Affiliated Laboratory: Microarray Core Facility * Resource Services: The following research resources of CNPRC are available to scientists on a recharge basis. ** Allergen: Characterized protein extracts of house dust mite (Dermatophagoides pteronyssinus and Dermatophagoides farinae) are available for allergen sensitization projects. ** Biological Specimens: Tissues collected at necropsy are available from rhesus monkeys (Macaca mulatta), cynomolgus monkeys (Macaca fascicularis), and titi monkeys (Callicebus cupreus). Contact: Biospecimens (at) primate.ucdavis.edu Blood samples are available through our blood donor program. ** Data: Data for colony animals are available from our computerized database. Data include birth records, weights, reproductive history, reloc…

Semantic Web Applications in Neuromedicine (SWAN) Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_149502
synonym: Semantic Web Applications in Neuromedicine Ontology
abbrev: SWAN Ontology
IAO_0000115: The SWAN (Semantic Web Applications in Neuromedicine) ontology is an ontology for modeling scientific discourse and has been developed in the context of building a series of applications for biomedical researchers, as well as extensive discussions and collaborations with the larger bio-ontologies community. Developing cures for highly complex diseases, such as neurodegenerative disorders, requires extensive interdisciplinary collaboration and exchange of biomedical information in context. Our ability to exchange such information across sub-specialties today is limited by the current scientific knowledge ecosystem's inability to properly contextualize and integrate data and discourse in machine-interpretable form. This inherently limits the productivity of research and the progress toward cures for devastating diseases such as Alzheimer's and Parkinson's. The SWAN ontology is organized in three types of modules: * basic: basic modules represent the ontology building blocks. They cover topics that are general enough to be included in every ontology distribution. The current basic modules are: ** collections ** provenance, authoring and versioning (PAV) ** discourse relationships ** FOAF (in OWL-DL) ** SKOS (in OWL-DL) ** qualifiers ** scientific discourse * extension: extensions modules are covering topics (a) that can be related only to some fields of science (b) for which there could be more than one implementation (c) for which a temporary solution has been provided and it is possible to forecast its substitution. The current extensions modules are: ** life science entities ** citations ** qualifiers extension modules * distribution: distributions are modules that are including all the basic modules and extensions necessary for serving a specific domain (i.e. the SWAN ontology for the Alzheimer knowledge base or the generic distribution that is not binded to any specific scientific domain). The current available distributions are: ** swan-scientific-discourse ** sw…

KLEIO
type: Resource
type: NamedIndividual
has db xref: nlx_44954
has db xref: OMICS_01186
IAO_0000115: An information retrieval system that provides knowledge enriched searching facilities across the ever growing MEDLINE collection, the world's most comprehensive source of life sciences and biomedical bibliographic information. The semantic faceted search, using named entity recognition, can be accessed from your browser. By combining a selection of software services they can provide enhanced results through a process that identifies key entities within the text, such as gene names or proteins, and improves the querying method with unique identifiers by automatically including synonyms, spelling variants and even disambiguating acronyms. This combines with the traditional features found in other interfaces to provide a much needed solution to the growing problem of finding valuable information within the ever increasing volume of modern publications. The current available categories: * PROTEIN, GENE, METABOLITE, DISEASE, SYMPTOM, ORGAN, * DIAG_PROC, THERAPEUTIC_PROC, (diagnostic/therapeutic procedure, e.g. MRI, cerebral blood flow) * GENERAL_PHENOM, HUMAN_PHENOM, NATURAL_PHENOM, (Medical phenomenon or process, e.g. UV radiation ) * INDICATOR (Reagent or diagnostic aid, e.g. hydrogen peroxide, sulfhydryl reagent) * ACRONYM, AUTHOR, PUBLICATIONTYPE (e.g. Journal Article, Technical Report) Reference: C. Nobata, P. Cotter, N. Okazaki, B. Rea, Y. Sasaki, Y. Tsuruoka, J. Tsujii and S. Ananiadou. Kleio: a knowledge-enriched information retrieval system for biology. In Proc. of the 31st Annual International ACM SIGIR Conference, pp. 787--788, 2008

De Humani Corporis Fabrica
type: Resource
type: NamedIndividual
has db xref: nlx_149200
synonym: Andreas Vesalius De Humani Corporis Fabrica
synonym: Andreas Vesalius' De Humani Corporis Fabrica
synonym: Fabric of the Human Body
synonym: On the Fabric of the Human Body
synonym: The Fabric of the Human Body
IAO_0000115: English translation of Andreas Vesalius' Renaissance anatomical atlas On the Fabric of the Human Body (1543, 1555) and an explanation of the work in progress at Northwestern University to translate and annotate this historic work (by Daniel Garrison and Malcolm Hast). This detailed account of human anatomy transformed its subject and forever changed medical education in the West. Its woodcut illustrations became the basis of medical art and illustrations for generations to come, and continue to influence the way we look at the human body. * Book One -- The things that sustain and support the entire body, and what braces and attaches them all. (the bones and the ligaments that interconnect them) * Book Two -- All the ligaments and muscles, instruments of voluntary and deliberate motion * Book Three -- The series of veins and arteries throughout the body * Book Four -- The nerves * Book Five -- The organs of nutrition and generation * Book Six -- The heart and organs serving the heart (Chiefly the heart and lungs) * Book Seven -- The brain and organs of sense Note: Only introduction, images, and essays appear to be available.

Asper Biotech
type: Resource
type: NamedIndividual
has db xref: nif-0000-30125
synonym: AsperBio
IAO_0000115: A genetic testing company for rare and complex disorders and syndromes. The company specializes in retinal disorders, reproductive medicine and oncology. They also offer custom genotyping services.

Spinal Research
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100000334
has db xref: grid.468536.a
has db xref: ISNI: 0000 0000 9820 9830
has db xref: nif-0000-00473
synonym: International Spinal Research Trust
abbrev: ISRT
IAO_0000115: Spinal Research committed to funding international research into cure for spinal cord paralysis. Charity that funds medical research for treating and curing spinal cord paralysis. Supports basic science, clinical research and funds PhD students. ISRT also hosts Annual Network Meetings.

Cross Validation
type: Resource
type: NamedIndividual
has db xref: nlx_19901
IAO_0000115: A model evaluation method for training someone to read data. There are three methods: the holdout method, K-fold cross validation, and leave-one-out cross validation.

Catalyst Framework
type: Resource
type: NamedIndividual
has db xref: nif-0000-30301
synonym: Catalyst
IAO_0000115: A web application framework that helps build applications or run protocols for the web. It allows the user to manage various tasks being run on the web both manually and through existing Perl modules.

Backyard Brains
type: Commercial
type: NamedIndividual
has db xref: nif-0000-01870
IAO_0000115: A commercial company that sells affordable brain recording kits geared for neuroscience education purposes. Their products are meant to mimic electroencephalograms, a tool that measures the electrical activity of neurons.

Using our Brains Tissue Donor Program
type: Organization
type: NamedIndividual
has db xref: nif-0000-30212
abbrev: UoB
IAO_0000115: An Australian brain bank which aims to collect, store, characterize and provide tissue to national and international researchers studying disorders of the brain such as alcohol-related brain damage and mental illness, like schizophrenia. The program encourages those who are medically healthy to donate.

FlyBrain
type: Resource
type: NamedIndividual
has db xref: nif-0000-00031
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Interactive database of Drosophila melanogaster nervous system. Used by drosophila neuroscience community and by other researchers studying arthropod brain structure.

Comprehensive Drug Self-administration and Discrimination Bibliographic Databases
type: Resource
type: NamedIndividual
has db xref: nif-0000-00090
synonym: Drug Self-administration and Discrimination Bibliographic Databases
IAO_0000115: Database of bibliographic details of over 9,000 references published between 1951 and the present day, and includes abstracts, journal articles, book chapters and books replacing the two former separate websites for Ian Stolerman's drug discrimination database and Dick Meisch's drug self-administration database. Lists of standardized keywords are used to index the citations. Most of the keywords are generic drug names but they also include methodological terms, species studied and drug classes. This index makes it possible to selectively retrieve references according to the drugs used as the training stimuli, drugs used as test stimuli, drugs used as pretreatments, species, etc. by entering your own terms or by using our comprehensive lists of search terms. Drug Discrimination Drug Discrimination is widely recognized as one of the major methods for studying the behavioral and neuropharmacological effects of drugs and plays an important role in drug discovery and investigations of drug abuse. In Drug Discrimination studies, effects of drugs serve as discriminative stimuli that indicate how reinforcers (e.g. food pellets) can be obtained. For example, animals can be trained to press one of two levers to obtain food after receiving injections of a drug, and to press the other lever to obtain food after injections of the vehicle. After the discrimination has been learned, the animal starts pressing the appropriate lever according to whether it has received the training drug or vehicle; accuracy is very good in most experiments (90 or more correct). Discriminative stimulus effects of drugs are readily distinguished from the effects of food alone by collecting data in brief test sessions where responses are not differentially reinforced. Thus, trained subjects can be used to determine whether test substances are identified as like or unlike the drug used for training. Drug Self-administration Drug Self-administration methodology is central to the experimental analysis of …

Mouse Models For Alzheimer's Disease Research
type: Resource
type: NamedIndividual
has db xref: nif-0000-00183
synonym: MMFADR
IAO_0000115: An information resource about several models for mice to develop Alzheimer's-related characteristics as they age.

DCSearch
type: Resource
type: NamedIndividual
has db xref: nif-0000-00284
has db xref: nif-0000-00285
synonym: DCViewer
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 09, 2013. A java tool to search published activation data. All data from papers submitted to the fMRI Data center are included, and may be referenced online or via flat file. Users may create their own data files, by saving subsets of original data or creating their own comma seperated value files (with simple formatting information included on the top row). Searches may be made based on coordinate space (MNI or T-space), anatomical area, author, and a number of other fields. Searched points may be displayed on a 3-d brain representation, as well.

MRI Watcher
type: Resource
type: NamedIndividual
has db xref: nif-0000-00332
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. A visualization tool for MRI images which handles several formats (.gipl,.mha,.hdr). It uses integrated coupled cursors to show the differences between images. It can load an overlay image and make screenshots.

Americans for Medical Progress
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100005411
has db xref: grid.468272.d
has db xref: ISNI: 0000 0004 4659 713X
has db xref: nif-0000-00456
has db xref: Wikidata: Q4745618
abbrev: AMP
IAO_0000115: A non-profit charity dedicated to providing education about animal research for the purpose of protecting medical and scientific progress. The organization seeks to provide accurate and incisive information to foster a balanced public debate on animal research issues. They work to do outreach by distributing timely and relevant news, information and analysis about animal rights extremism to the research community.

BRAINnet-Brain Research And Integrative Neuroscience Network
type: Resource
type: NamedIndividual
has db xref: nif-0000-00502
synonym: Brain Research And Integrative Neuroscience Network
abbrev: BRAINnet
IAO_0000115: A neuroscience network providing access to a database of brain, cognitive, genomic and clinical data for research and scientific publication. Data include genomic information, electrical measures of brain and body function, structural and functional MRI, and cognitive and medical history. All data are collected using a standardized assessment protocols. These data are from healthy people and those experiencing a range of brain-related illnesses.

NIH - Rapid Access to Interventional Development
type: Resource
type: NamedIndividual
has db xref: nif-0000-00543
synonym: NIH-RAID
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 14, 2025.NIH-RAID makes available at no cost to researchers and organizations certain critical resources needed for the development of new therapeutic agents. This program, part of the Translational Research component of Reengineering the Clinical Research Enterprise, uses resources of NCI's Developmental Therapeutics Program and the National Heart Lung and Blood Institutes (NHLBI) Gene Therapy Resource Program. The services provided will depend upon the stage of the project and the strength of the preliminary data. Services available include: production, bulk supply, GMP manufacturing, formulation, development of an assay suitable for pharmacokinetic testing, and animal toxicology. Assistance also will be provided in the regulatory process, through access to independent product development planning expertise. Proposals in support of animal efficacy studies or synthesis and formulation of recombinant proteins or monoclonal antibodies will not be accepted. NIH-RAID is not a grant program. Successful projects will gain access to the governments contract resources, as well as the assistance of the NIH in establishing and implementing a product development plan. Funds to support individual projects will come both from the Roadmap and from individual Institutes, with Institutes assuming the bulk of support in the specific disease areas germane to their mission. This co-sponsorship is critical because of the resource and expertise needs and because NIH-RAID cannot support the full developmental pipeline; an Institute partnership may therefore be important for subsequent translational efforts. To obtain access to NIH-RAID resources, applications must be submitted electronically through Grants.gov using SF424. Applications are initially screened to determine whether the resources requested are appropriate for this program. Then they are reviewed by the NIH Center for Scientific Research. The results of that evaluat…

Science Leaks
type: Resource
type: NamedIndividual
has db xref: nif-0000-01872
synonym: ScienceLeaks
IAO_0000115: A blog for peer-reviewed scientific papers taken from behind journal-subscription paywalls. It serves as a resource for those who cannot access these resources.

Oregon State University College of Pharmacy
type: Organization
type: NamedIndividual
has db xref: nif-0000-02038
synonym: Oregon State
IAO_0000115: The college of pharmacy at Oregon State University that offers professional education in pharmacy. The foundational goals are to provide professional education, foster research to contribute to public health initiatives and promote safe and affordable medication access.

Queens College, Neuroscience
type: Organization
type: NamedIndividual
has db xref: nif-0000-02047
synonym: CUNY
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 14,2025. A neuroscience program that provides research-based, rigorous training in neuroscience that prepares students for neuroscience-related graduate, masters or PhD programs. This program is competitive and only accepts a limited number of students each year.

Scripps Women's College, Neuroscience Department
type: Organization
type: NamedIndividual
has db xref: nif-0000-02059
synonym: Scripps College Neuroscience
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 14,2025. A neuroscience program that prepares the student for graduate work in biology, psychology, neuroscience, or preparation for medical school or a career in the health services.

Sequencing Analysis Software
type: Resource
type: NamedIndividual
has db xref: OMICS_01814
IAO_0000115: A software that gives the user the ability to basecall, trim, display, edit, and print data for the entire line of capillary DNA sequencing instruments for data analysis and quality control. This software benefits from being able to obtain longer read lengths, greater accuracy on the 5' end, and the ability to filter out low-quality sequence ends.

Stanford University Psychiatry and Behavioral Sciences
type: Organization
type: NamedIndividual
has db xref: nif-0000-02073
synonym: Stanford
IAO_0000115: A Stanford-affiliated organization which is primarily concerned with the study and treatment of sleep disorders, the treatment of psychological illnesses, and the training of medical students, residents and research fellows in psychiatry and sleep medicine.

Temple University School of Medicine, Department of Neuroscience
type: Organization
type: NamedIndividual
has db xref: nif-0000-02090
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 14,2025. A department within the Temple University School of Medicine, which focuses on the education and research. This organization also hosts seminar series in neuroscience, sponsors annual lectures in neuroscience, and organizes bi-annual one-day workshops. This department has collaborative projects with researchers from the microbiology, immunology, pharmacology, radiology and the center for substance abuse research departments.

University of Texas Medical Branch Neurobiology
type: Organization
type: NamedIndividual
has db xref: nif-0000-02110
synonym: The University of Texas Medical Branch Neuroscience and Cell Biology
abbrev: UTMB NCB
IAO_0000115: A department within the University of Texas which is concerned with researching basic and translational research in neuroscience and cell biology, as well as providing training in those disciplines for graduate, medical and post-doctoral students.

University of California, Irvine, Department of Anatomy and Neurobiology
type: Organization
type: NamedIndividual
has db xref: nif-0000-02137
synonym: UCI
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 14,2025. A department within UC Irvine which supports studies in anatomy and neurobiology, and provides education at the medical, graduate and postgraduate levels.

University of Miami, Department of Neuroscience
type: Organization
type: NamedIndividual
has db xref: nif-0000-02209
IAO_0000115: A department within the University of Miami which offers both undergraduate and postgraduate programs in neuroscience. The graduate program provides neuroscience research training in biological, behavioral, and physical sciences. This organization also conducts research through 55 active laboratories.

University of Vermont College of Medicine, Pharmacology
type: Organization
type: NamedIndividual
has db xref: nif-0000-02281
synonym: UVM
IAO_0000115: A department within the University of Vermont which offers a undergraduate minor, and a graduate program in pharmacology.

Biozon
type: Resource
type: NamedIndividual
has db xref: nif-0000-02613
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Biozon is a unified biological resource on DNA sequences, proteins, complexes and cellular pathways. It currently provides data on pairwise similarities between proteins, the domain structure of proteins, structural similarities, threading-based and profile-profile similarities between protein families. Additional information about 3D models, predicted protein-protein interactions, assignment of genes to pathways and expression data analysis, as well as local and global maps of the protein space will be gradually added to Biozon.

Perlegen/NIEHS National Toxicology: Mouse Genome Resequencing Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-21746
abbrev: Mouse Resequencing Project
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, Documented on August 12, 2014. Data, grouped by chromosome, available as flat files for download, of identified DNA polymorphisms (SNPs) in 15 commonly used strains of inbred laboratory mice. Perlegen's SNP, genotype (empirical and imputed), haplotype, trace, and PCR primer data has been compiled with NCBI Mouse Build information to produce data files for public use. Using high-density oligonuclueotide array technology, the study identified over 8 million SNPs and other genetic differences between these strains and the previously sequenced C57BL/6J reference strains (Phase 1). By leveraging data provided by Mark Daly's research team at the Broad Institute, genotypes were also predicted for 40 other common strains (Phase 2). Under an extension to the contract, Eleazar Eskin's group at UCLA has used this data to evaluate SNP associations with phenotypes from the Mouse Phenome Project (the Mouse Phenome Database), and to construct haplotype maps for a total of 94 inbred strains (the Mouse HapMap Project). SNP and genotype positions have been mapped from their original reference coordinates to NCBI Mouse Build 37 coordinates. Note that C57BL6/J strain was not selected for re-sequencing as this data would have been almost entirely redundant with the NCBI reference sequence. Since we did not actually determine genotypes for C57BL6/J, we did not submit genotypes for this strain to dbSNP. However, implicit genotypes for C57BL6/J can be obtained from the reference sequence at each SNP position (the reference allele is the first allele in the ALLELES column). The data is available for download in two different compressed file formats. The files are saved as both PC .zip files and Unix compressed .gz files. At this website, you can: * Learn more about the goals of the Perlegen mouse resequencing project. * Learn more about the array-based resequencing technology used in the project. * Download the SNPs, genotypes, and other data generated…

ButterflyBase
type: Resource
type: NamedIndividual
has db xref: nif-0000-02627
IAO_0000115: An open-access Genomic Database for Lepidoptera. It includes all the Lepidoptera cDNA sequences available in NCBI's dbEST. Support for genomic-DNA sequences such as BACs and the Bombyx mori genome is being generated. Tools available on this website include BLAST search, Annotation search, Primer design, and Microsatellite repeat finders. Users can also download all data and sequences. Within the site, the Expressed Sequence Tag sequences are made with Trace2dbest from raw sequence data if available or downloaded from NCBI. We cluster them using PartiGene into gene-objects to reduce redundancy. Subsequently, we perform hierarchical BLAST searches to provide accurate similarity annotation and a robust protein translation protocol using prot4EST. Putative proteins objects have been further annotated with the Gene Ontology biological vocabulary (GO terms) and InterPro (EBI) domains to facilitate gene-hunters. The repository is open for all Lepidopteran researchers.

Cancer GEnome Mine
type: Resource
type: NamedIndividual
has db xref: nif-0000-02636
has db xref: r3d100010559
synonym: CanGEM
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September23, 2022. Cancer GEnome Mine is a public database for storing clinical information about tumor samples and microarray data, with emphasis on array comparative genomic hybridization (aCGH) and data mining of gene copy number changes. Within the website, users can browse microarray data or perform searches by hospital/disease classification/pathology/clinical presentation and other methods.

Cre-X-Mice: A Database of Cre Transgenic Lines
type: Resource
type: NamedIndividual
has db xref: nif-0000-02696
synonym: Cre-X-Mice
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Cre-X-Mice is a database of Cre transgenic mouse lines and mice genes. Users can search the database by anatomical area, cell type, stage, promoter locus, transgene type, or other properties. Users can also view anatomical areas by stage, or submit transgenic mouse lines.

Catalogue for Transmission Genetics in Arabs
type: Resource
type: NamedIndividual
has db xref: nif-0000-02705
synonym: CTGA
IAO_0000115: The CTGA database is a database for genetic disorders in Arab populations. It hosts entries for Mendelian disorders and related genes, and currently contains nearly 1290 entries. Its goal is to facilitate further research on Arab genomic diseases.

Domain Interaction MAp
type: Resource
type: NamedIndividual
has db xref: nif-0000-02752
synonym: DIMA
IAO_0000115: DIMA, the Domain Interaction Map, aims at becoming a comprehensive resource for functional and physical interactions among conserved protein-domains. The scope of the resource comprises both experimental data and computational predictions. Several methods and datasets have been integrated, already and inclusion of others is under way.

EGO - Eukaryotic Gene Orthologs
type: Resource
type: NamedIndividual
has db xref: nif-0000-02790
synonym: EGO
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. EGO is a database of eukaryotic gene orthologs generated by pair-wise comparison between the Tentative Consensus (TC) sequences that comprise the Dana Farber Gene Indices from individual organisms.

Drosophila RNAi Screening Center
type: Resource
type: NamedIndividual
has db xref: nif-0000-02846
synonym: Development of Validated Drosophila in vivo RNAi Models of Human Diseases
abbrev: DRSC
IAO_0000115: Database that provides free online tools to users to allow the retrieval of information related to the Drosophila genome and allows access to genome-wide and related cell-based screening of Drosophila at Harvard Medical School (for a fee) . Tools available include SnapDragon, and RNAi designer, a heat map tool for viewing screen data, and gene and amplicon search and download tools. The DRSC mainly exists to provide Drosophila genome screening services, including help with assay development and optimization, data and image analysis, and planning of follow-up assays.

FUGOID: a Database for Functional Genomics of Organelle Introns
type: Resource
type: NamedIndividual
has db xref: nif-0000-02855
synonym: FUGOID
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. FUGOID is a database for functional genomics of organelle introns. The taxonomically broad organelle intron database contains comprehensive functional and structural information on organellar (mitochondria and chloroplast) introns. FUGOID collects and integrates various structural and functional data on organellar (mitochondrial and chloroplast) introns, particularly functional information about intron splicing and mobility. It is implemented in a relational database management system and can be searched either by intron information or by a major reference. Data entry and revision systems have also been developed.

Gene Aging Nexus
type: Resource
type: NamedIndividual
has db xref: nif-0000-02875
abbrev: GAN
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A data mining platform for the biogerontological-geriatric research community. It enables users to analyze, query, and visualize the aging-related genomic data. Our goal is to facilitate the digestion and usage of the public genomic data. A current focus is on integrative analysis of microarray gene expression data. We are establishing a central database for aging microarray data of six species: human (H. sapiens), rat (R. norvegicus), mouse (M. musculus), "fly" (D. melanogaster), "worm" (C. elegans), and yeast (S. cerevisiae). GAN is equipped with a set of bioinformatics tools for analysis of the microarray data sets, cross-platform and cross-species.

GOLD.db - Genomics Of Lipid-associated Disorders
type: Resource
type: NamedIndividual
has db xref: nif-0000-02919
synonym: Genomics Of Lipid-associated Disorders database
synonym: GOLD.db
synonym: GOLD.db Genomics Of Lipid-associated Disorders
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented July 22, 2016. A database that integrates information on the function and properties of genes and their protein products relevant to lipid-associated disorders. GOLD.db provides information such as the biology, diagnosis management, treatment and prevention of such disorders like non-insulin dependent diabetes, various hyperlipedemias, high blood pressure and atherosclerosis. Resources include the biological pathways, data sets, microarray protocols and other experimental standards, analytical tools, and reagents.

Infectious Disease Biomarker Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-03007
abbrev: IDBD
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented July 22, 2016. A database of biomarkers for diagnosis, detection, protection and characterization of infectious diseases. It provides information on pathogens and biomarkers, such as nucleic acids, proteins, carbohydrates, and immune epitopes. The site links to global news and life science journal search engines as well as provides links to tool functions for gene sequence and protein structure analyses.

MeGX
type: Resource
type: NamedIndividual
has db xref: nif-0000-03109
has db xref: nif-0000-21260
has db xref: r3d100011324
synonym: Marine Ecological GenomiX
synonym: Megx.net
synonym: megx: marine ecological genomics
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Set of databases and tools that handle genomic and metagenomic sequences in their environmental contexts.Includes geographic information system to systematically store and analyse marine genomic and metagenomic data in conjunction with contextual information; environmental genome browser with fast search functionalities; database with precomputed analyses for selected complete genomes; database and tool to classify metagenomic fragments based on oligonucleotide signatures.

MitoProteome
type: Resource
type: NamedIndividual
has db xref: nif-0000-03146
IAO_0000115: A database of object-relational mitochondrial protein sequences, which contains both mitochondrial and nuclear encoded entries. This database that was generated from experimental evidence and other public databases. Each protein is annotated with data from external databases, including: Locuslink, Ensembl, OMIM, MINT, DIP, PFAM, InterPro, PRINTS and NCBI NR.

PMAP
type: Resource
type: NamedIndividual
has db xref: nif-0000-03318
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. A database of proteolytic pathways. Its goal is to contribute to the scientific community and the understanding of proteolysis by providing better tools and data to researchers and medical researchers.

QTL Matchmaker
type: Resource
type: NamedIndividual
has db xref: nif-0000-03382
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A database used for high throughput mapping of genes to QTL and comparative genome analysis between different humans, mice, and rats. This database is designed for the analysis of larger sets of data using genome-scale experimental approaches, and to organize information from various websites and publications.

Retinoblastoma Genetics
type: Resource
type: NamedIndividual
has db xref: nif-0000-03389
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A website that provides access to a database, nomenclature, fac sheets, downloadable slides, and other information regarding RB1 gene mutations.

Rice Proteome Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-03409
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented July 22, 2016. A database on the proteome of rice that contains reference maps based on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) of proteins from rice tissues and subcellular compartments.

SNPlogic
type: Resource
type: NamedIndividual
has db xref: nif-0000-03481
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. It provides comprehensive interactive SNP annotation, as well as a selection and prioritization system for focused genotyping projects and/or analysis and interpretation of SNP data. The user can create one or more SNP lists and populate them by adding SNPs either directly or by picking genes, pathways, chromosomal locations or by uploading own SNP lists. Additionally, users can design one or more SNP scoring systems based on any available SNP annotations. After that, SNP scores can be computed for any user SNP list using any of the designed scoring systems. Those scores can be used to prioritize SNPs. Sorted/filtered SNP lists can be exported in tab-delimited text format. The SNP lists and scoring rules can be kept private or shared within the workgroup or made public.

VectorDB- Molecular Biology Vector Sequence Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-03625
synonym: vectorDB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. A database with information about a variety of vectors, including phage, plasmid, phagemid, phasmid, cosmid, virus and YAC vectors. It also contains information on drosophilia, C. elegans, yeast and drosophilia vectors, including vector functions, hosts and copy number.

NeuroImages YouTube Channel
type: Resource
type: NamedIndividual
has db xref: nif-0000-07647
synonym: NeuroImage's Channel
IAO_0000115: A platform for posting and viewing videos related to all areas of neuroimaging.

Genboree Discovery System
type: Resource
type: NamedIndividual
has db xref: nif-0000-08906
abbrev: Genboree
IAO_0000115: A software application and database viewing system for genomic research, more specifically formulti-genome comparison and pattern discovery via genome self-comparison. Data are available for a range of species including Human Chr3, Human Chr12, Sea Urchin, Tribolium, and cow. The Genboree Discovery System is the largest software system developed at the bioinformatics laboratory at Baylor in close collaboration with the Human Genome Sequencing Center. Genboree is a turnkey software system for genomic research. Genboree is hosted on the Internet and, as of early 2007, the number of registered users exceeds 600. While it can be configured to support almost any genome-centric discovery process, a number of configurations already exist for specific applications. Current focus is on enabling studies of genome variation, including array CGH studies, PCR-based resequencing, genome resequencing using comparative sequence assembly, genome remapping using paired-end tags and sequences, genome analysis and annotation, multi-genome comparison and pattern discovery via genome self-comparison. Genboree database and visualization settings, tools, and user roles are configurable to fit the needs of specific discovery processes. Private permanent project-specific databases can be accessed in a controlled way by collaborators via the Internet. Project-specific data is integrated with relevant data from public sources such as genome browsers and genomic databases. Data processing tools are integrated using a plug-in model. Genboree is extensible via flexible data-exchange formats to accommodate project specific tools and processing steps. Our Positional Hashing method, implemented in the Pash program, enables extremely fast and accurate sequence comparison and pattern discovery by employing low-level parallelism. Pash enables fast and sensitive detection of orthologous regions across mammalian genomes, and fast anchoring of hundreds of millions of short sequences produced by next-gener…

Bio Resource for Array Genes Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-10165
synonym: BioRag
IAO_0000115: Bio Resource for array genes is a free online resource for easy access to collective and integrated information from various public biological resources for human, mouse, rat, fly and c. elegans genes. The resource includes information about the genes that are represented in Unigene clusters. This resource provides interactive tools to selectively view, analyze and interpret gene expression patterns against the background of gene and protein functional information. Different query options are provided to mine the biological relationships represented in the underlying database. Search button will take you to the list of query tools available. This Bio resource is a platform designed as an online resource to assist researchers in analyzing results of microarray experiments and developing a biological interpretation of the results. This site is mainly to interpret the unique gene expression patterns found as biological changes that can lead to new diagnostic procedures and drug targets. This interactive site allows users to selectively view a variety of information about gene functions that is stored in an underlying database. Although there are other online resources that provide a comprehensive annotation and summary of genes, this resource differs from these by further enabling researchers to mine biological relationships amongst the genes captured in the database using new query tools. Thus providing a unique way of interpreting the microarray data results based on the knowledge provided for the cellular roles of genes and proteins. A total of six different query tools are provided and each offer different search features, analysis options and different forms of display and visualization of data. The data is collected in relational database from public resources: Unigene, Locus link, OMIM, NCBI dbEST, protein domains from NCBI CDD, Gene Ontology, Pathways (Kegg, Genmapp and Biocarta) and BIND (Protein interactions). Data is dynamically collected and compiled twice …

VISAGES Research
type: Resource
type: NamedIndividual
has db xref: nif-0000-10223
synonym: VISAGES
synonym: VisAGeS
synonym: Vision Action and information manaGEment System in health
IAO_0000115: Research team focused on research and development of new algorithms in medical imaging, information processing and computer assisted intervention in the context of the pathologies of the central nervous system. Research team jointly affiliated to INSERM (National Institute of Health and Scientific Research), Inria (National Institute of Research in Computer Sciences and Automation) and IRISA / UMR CNRS 6074, University of Rennes I. Multidisciplinary team merging researchers in image processing and medical doctors.

Interactome Wiki
type: Resource
type: NamedIndividual
has db xref: nif-0000-10260
synonym: Interactome
IAO_0000115: This Wiki page provides information about Interactome of various species. An interactome of a species provides an important clues on how to interpret metabolic pathways of constituent enzymes and global protein network, which facilitates in turn to understand the mechanism responsible for the cellular functions.

Royal Institute of Technology: Research Project Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-10409
synonym: KTH Research Database
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The KTH Research Project Database is intended to contain all the currently on-going projects at KTH. Sponsors: This resource is supported by the Royal Institute of Technology, Sweden,

Salk Institute for Biological Studies
type: Organization
type: NamedIndividual
has db xref: grid.250671.7
has db xref: ISNI: 0000 0001 0662 7144
has db xref: nif-0000-10414
has db xref: Wikidata: Q1351061
synonym: Salk Institute
IAO_0000115: The Salk Institute conducts research within three major areas of study: Molecular Biology and Genetics; Neurosciences; and Plant Biology. Six key areas represent strategic research priorities: Chemistry and Proteomics; Stem Cell Biology; Cell Biology; Regulatory Biology; Metabolic Research; and Computational and Theoretical Biology.

Sullivan Lab Evidence Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-10439
abbrev: SLEP
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of genetic and gene expression data from the published literature on psychiatric disorders. Users can search the accumulated data to find the evidence in support of the involvement of a particular genomic region with a set of important psychiatric disorders, ADHD, autism, bipolar disorder, eating disorder, major depressive disorder, schizophrenia, and smoking behavior. It contains findings from manual reviews of 144 papers in psychiatric genetics, 136 primary reports and 8 meta-analyses. Disorders covered include schizophrenia (44 papers), autism (24 papers), bipolar disorder (24 papers), smoking behavior (24 papers), major depressive disorder and neuroticism (14 papers), ADHD (8 papers), eating disorders (3 papers), and a combined schizophrenia-bipolar phenotype (3 papers). The unbiased searches integrated into SLEP include genomewide linkage (117 papers), genomewide association (15 papers), copy number variation (9 papers), and gene expression studies of post-mortem brain tissue (3 meta-analyses courtesy of the Stanley Foundation). In total, SLEP captures 3,741 findings from these 144 papers. SLEP also contains over 70,000 SignPosts. These annotations derive from many different sources and are designed to try to capture current state of knowledge about disease associations in the human genome. SignPosts can be searched simultaneously with the psychiatric genetics literature in order to integrate these two bodies of knowledge. The SignPosts include: accumulated GWAS findings from the human genetics literature, the OMIM database, candidate gene association study literature, CNV location and frequency data, SNPs that influence gene expression in brain, genes expressed in brain, genes with evidence of imprinting and random monoalleleic expression, genes mutated in breast or colorectal cancer, and pathway data from BioCyc.

DNA-Protein Interaction Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-20838
synonym: NPIDB
IAO_0000115: The database NPIDB (Nucleic acid Protein Interaction DataBase) contains information derived from structures of DNA-protein and RNA-protein complexes extracted from Protein Data Bank (PDB) (1932 complexes in the end of 2007). It is equipped with a web-interface and a set of tools for extracting biologically meaningful characteristics of complexes. They are committed to satisfy all potential database users in order to: 1. Provide an essential information on structural features of DNA-protein and RNA-protein interaction for the users who need to get acquainted with the problem. 2. Give an effective access to the reasonably structured information about all DNA-protein and RNA-protein complexes containing in PDB. 3. Allow all visitors a quick access to our own research.

Interolog/Regulog Database
type: Resource
type: NamedIndividual
has db xref: biotools:interolog
has db xref: nif-0000-20863
synonym: Interolog
IAO_0000115: Interolog/Regulog quantitatively assess the degree to which interologs can be reliably transferred between species as a function of the sequence similarity of the corresponding interacting proteins.

Abysis Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-20947
synonym: Abysis
IAO_0000115: A database of antibody structure containing sequences from Kabat, IMGT and the Protein Databank (PDB), as well as structure data from the PDB. It provides search of the sequence data on various criteria and display of results in different formats. For data from the PDB, sequence searches can be combined with structural constraints. For example, one can ask for all the antibodies with a 10-residue Kabat CDR-L1 with a serine at H23 and an arginine within 10A of H36. The site also has software for structure analysis and other information on antibody structure available.

Common naming project
type: Resource
type: NamedIndividual
has db xref: nif-0000-20972
synonym: Shared names
IAO_0000115: Science Commons, OBO Foundry, and several other groups working with biological information on the Semantic Web have initiated an effort to establish shared community-maintained URIs for important data integration points such as life sciences database records (example: the record in the Entrez Gene database that has GeneID 1003064). We are attempting to determine the right technical and organizational recipe that will lead to the uptake of these URIs by a as many RDF-using bioinformatics projects as possible. Were this to be a success, one would be able to mash up information from multiple sources in a wide variety of ways, using the shared URIs to forge links between pieces. Information could be extracted from one source for inclusion in another; information could be combined in SPARQL queries using multiple FROM clauses; extractions from several triple stores could be combined to create a new one. Without shared URIs, this kind of integration would still be possible, but it would be significantly more difficult as it would require some kind of plumbing or mapping to get the two result sets to link up. Requirements We are limiting our concern for now to URIs for records in databases mentioned in external links from the Gene Ontology (GO), such as those from Enzyme or Pfam, with possible extension to other databases such as those in the LSRN (Life Science Resource Name) registry. The URIs we propose are meant to serve the community of Semantic Web-enabled bioinformatics projects that need URIs that refer to or denote database records. We identify the following requirements for URIs to serve a community and to be shared among Semantic Web projects: 1. It must be clearly stated what the intended referent of each URI is supposed to be, i.e. that the URI denotes some particular record from some particular database. 2. Information about the URI and its referent, including such a statement, must be made available, and in order to leverage existing protocol stacks, it must …

AMPDB: Arabidopsis Mitochondrial Protein Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-21026
synonym: AMPDB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 23,2022. The Arabidopsis Mitochondrial Protein Database is an Internet-accessible relational database containing information on the predicted and experimentally confirmed protein complement of mitochondria from the model plant Arabidopsis thaliana. This database, and the proteomic data contained in it for Arabidopsis mitochondria, have been accepted for publication in The Plant Cell.

Collecting Duct Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-21078
abbrev: CDDB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. This database is intended to serve as a learning tool to obtain curated information for the design of microarray targets to scan collecting duct tissues (human, rat, mouse). The database focuses on regulatory and transporter proteins expressed in the collecting duct, but when collecting duct proteins are a member of a larger family of proteins, common additional members of the family are included even if they have not been demonstrated to be expressed in the collecting duct. An Internet-accessible database has been devised for major collecting duct proteins involved in transport and regulation of cellular processes. The individual proteins included in this database are those culled from literature searches and from previously published studies involving cDNA arrays and serial analysis of gene expression (SAGE). Design of microarray targets for the study of kidney collecting duct tissues is facilitated by the database, which includes links to curated base pair and amino acid sequence data, relevant literature, and related databases. Use of the database is illustrated by a search for water channel proteins, aquaporins, and by a subsequent search for vasopressin receptors. Links are shown to the literature and to sequence data for human, rat, and mouse, as well as to relevant web-based resources. Extension of the database is dynamic and is done through a maintenance interface. This permits creation of new categories, updating of existing entries, and addition of new ones. CDDB is a database that organizes lists of genes found in collecting duct tissues from three mammalian species: human, rat, and mouse. Proteins are divided into categories by family relationships and functional classification, and each category is assigned a section in the database. Each section includes links to the literature and to sequence information for genes, proteins, expressed sequence tags, and related information. The user …

Disease Genes Conserved Sequence Tags Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-21121
synonym: DG CST Database
IAO_0000115: A database of conserved sequence elements, identified by a systematic genomic sequence comparison between a set of human genes involved in the pathogenesis of genetic disorders and their murine counterparts. Human and mouse genomic sequences were compared by BLASTZ. Sequences longer than 100 and with identity better than 70 were selected as CSTs and imported into the database. CSTs are extensively annotated with respect to exon/intron structure and other biological parameters. CST counterparts in other species were identified by using BLAST to scan genomes from other species, and selecting on the basis of homology and co-linearity. The database can be accessed by gene, chromosomal location, graphic browser, DNA features, and coding regions.

HighWire Press
type: Resource
type: NamedIndividual
has db xref: nif-0000-21191
IAO_0000115: A division of the Stanford University Libraries, which produces the online versions of journals and other scholarly content.

Histology World: Nervous System Histology
type: Resource
type: NamedIndividual
has db xref: nif-0000-21193
synonym: Histology Photo Album
IAO_0000115: This website contains a lot of images and slides of the nervous system. Most images are of the central nervous system histology and peripheral nervous system histology. Computation Neuroscience

MAboya Gene Expression Patterns and Sequence Tags
type: Resource
type: NamedIndividual
has db xref: nif-0000-21247
synonym: MAboya Gene Expression Patterns and Sequence Tags (MAGEST)
abbrev: MAGEST
IAO_0000115: A database for maternal gene expression information for ascidia, colloquially known as sea squirts. Information available includes DNA sequences, expression patterns of ESTs, and cDNA data from uncleaved fertilized eggs. The goal is to utilize the database to understand molecular mechanisms of establishment of embryonic body plans of chordates and to understand evolution from invertebrates to vertebrates in the future.

BLASR
type: Resource
type: NamedIndividual
has db xref: biotools:blasr
has db xref: OMICS_05134
synonym: Basic Local Alignment with Successive Refinement
synonym: BLASR: The PacBio long read aligner
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. C++ long-read aligner for PacBio reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

LONI Visualization Tool
type: Resource
type: NamedIndividual
has db xref: nif-0000-23313
synonym: LONI Visualization Environment
synonym: LONI Viz environment
synonym: LOVE
abbrev: LONI Viz
abbrev: LONI_Viz
IAO_0000115: A versatile 1D, 2D and 3D data viewer geared for cross-platform visualization of stereotactic brain data. It is a 3-D viewer that allows volumetric data display and manipulation of axial, sagittal and coronal views. It reads Analyze, Raw-binary and NetCDF volumetric data, as well as, Multi-Contour Files (MCF), LWO/LWS surfaces, atlas hierarchical brain-region labelings ( Brain Trees). It is a portable Java-based software, which only requires a Java interpreter and a 64 MB of RAM memory to run on any computer architecture. LONI_Viz allows the user to interactively overlay and browse through several data volumes, zoom in and out in the axial, sagittal and coronal views, and reports the intensities and the stereo-tactic voxel and world coordinates of the data. Expert users can use LONI_Viz to delineate structures of interest, e.g., sulcal curves, on the 3 cardinal projections of the data. These curves then may be use to reconstruct surfaces representing the topological boundaries of cortical and sub-cortical regions of interest. The 3D features of the package include a SurfaceViewer and a full real-time VolumeRenderer. These allow the user to view the relative positions of different anatomical or functional regions which are not co-planar in any of the axial, sagittal or coronal 2D projection planes. The interactive part of LONI_Viz features a region drawing module used for manual delineation of regions of interest. A series of 2D contours describing the boundary of a region in projection planes (axial, sagittal or coronal) could be used to reconstruct the surface-representation of the 3D outer shell of the region. The latter could then be resliced in directions complementary to the drawing-direction and these complementary contours could be loaded in all tree cardinal views. In addition the surface object could be displayed using the SurfaceViewer. A pre-loading data crop and sub-sampling module allows the user to load and view practically data of any size. This is es…

CPODES numerical integrator
type: Resource
type: NamedIndividual
has db xref: nif-0000-23329
abbrev: CPODES
IAO_0000115: CPODES is a numerical integrator for solving multibody dynamics problems using coordinate projection. It is based on the CVODES integrator which is part of the DOE Sundials suite. It is a multistep integrator providing variable order Adams (up to 12th order) and BDF (up to 5th order) methods for non-stiff problems and BDF (up to 5th order) for stiff problems. It uses CVODES to advance the ODE, and then performs coordinate projection back to the constraint manifold to exactly solve the DAE. The projection is also incorporated back into the error test where it permits larger steps. Binaries of this software are bundled with other SimTK Core modules.

Syndicated Universities Preparatory Research Educational Program
type: Resource
type: NamedIndividual
has db xref: nif-0000-24046
synonym: SUPREP
IAO_0000115: SUPREP MODEL LEARNING is a standardized credit earning academic exchange program that enables a student from any third world countries or technologically deficient institutions around the world, to attend and earn credits from the best traditional recognized accredited institutions globally, in which the credits earned are transferred to the home institution or SUPREP agency for aggregation towards successful graduation. :The goal of this program is to facilitate bringing students from the third world to reputable undergraduate and graduate neuroscience programs. Additionally, this program also aims t o grant Third World Neuroscience students Academic exchange programs worldwide.

NIH/Merial Veterinary Scholars Program
type: Resource
type: NamedIndividual
has db xref: nif-0000-24392
synonym: NIH/Merck-Merial Summer Research Program
synonym: NIH/Merial Summer Research Program
IAO_0000115: Program designed to expose students in their first or second year of veterinary school to all phases of biomedical research. This includes development of research ideas, preparation of research proposals, performance of biomedical research, and presentation of research results in written and oral formats. Students perform full time biomedical research during months of June, July, and August, participate in weekly seminars, and present their work in oral, poster, and written presentations. Students also attend the National Merial Scholars Conference. Summer Research Program has existed at Penn Vet since 1990. The program is currently funded by Merial and by an NIH training grant. Other sources of support include funds from the office of the dean, the four departmental chairs and the Marie Lowe Cancer Center. Students present poster of their work at the conference. In September, students prepare a written manuscript of their work in the form of a research paper. The following March, all participating students submit their work to the Penn Veterinary Student Research Day. Non-Penn Vet students can receive up to an additional $500 for relocation costs and will be offered reasonably priced housing options for the summer. It is anticipated that 18-24 students will be funded each year.

Colour and Vision Research Laboratory
type: Resource
type: NamedIndividual
has db xref: nif-0000-24691
synonym: CVRL
IAO_0000115: The Colour & Vision Research laboratory and database are based at the Institute of Ophthalmology, which is part of University College London. The Institute and CVRL are both closely associated with Moorfields Eye Hospital. The Institute is next door to Moorfields Eye Hospital near Old Street tube station (see directions). At the Colour & Vision Research laboratory, we investigate normal and clinical human visual perception. Our research focuses on questions about colour perception, light and dark adaptation, night-time vision, and the temporal and spatial properties of vision. Our primary goal is to understand the nature of the mechanisms that underlie visual perception, and to understand how those mechanism malfunction in clinical cases. More details about our research can be found by looking at the publications of members of the laboratory. The CVRL database, first set up in 1995, provides an annotated library of downloadable standard data sets relevant to colour and vision research. The focus of this site is primarily scientific and technical, but some introductory background information is also provided. A consistent set of functions for modeling colour vision based on the Stockman & Sharpe cone fundamentals and on our more recent luminous efficiency measurements are summarized under the category CVRL functions. These functions are tabulated in 0.1, 1 and 5 nm steps and can be returned as csv, xml, or tabular data or as dynamic plots. The Stockman & Sharpe cone fundamentals are the basis of a CIE proposal for physiologically-relevant colour matching functions. These functions, which are indentical to the CVRL functions, are summarized under the category CIE 2007 functions. The CIE functions are also tabulated in 0.1, 1 and 5 nm steps, and can also be returned as csv, xml, or tabular data or as dynamic plots. Significant additions to the database are the individual colour matching measurements made by Stiles & Burch. These have been compiled and cross-checked wit…

Genomic Metadata for Infectious Agenets
type: Resource
type: NamedIndividual
has db xref: nif-0000-24989
synonym: Gemina
IAO_0000115: Gemina is a web-based system designed to identify infectious pathogens and their representative genomic sequences through selection of associated epidemiology metadata. Gemina supports the development of DNA signature-based assays for the detection of pathogens or sets of pathogen through the Insignia Signature Pipeline at the University of Maryland. Sponsors: This resource is supported by the US Department of Homeland Security Science and Technology Directorate. [W81XWH-05-2-005, NBCH2070002].

Computational Cancer Genomics Group
type: Resource
type: NamedIndividual
has db xref: nif-0000-25561
synonym: CCG
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Computational Cancer Genomics (CCG) group is dedicated to the development of analysis tools and databases relating molecular sequences and biological functions. Sponsors: This group is supported by the Swiss Institute of Bioinformatics (SIB).

UNAIDS
type: Resource
type: NamedIndividual
has db xref: nif-0000-30013
IAO_0000115: A partnership that leads and inspires the world in achieving universal access to HIV prevention, treatment, care and support. UNAIDS publishes a new Report on the global AIDS epidemic every two years. The Report draws upon and publishes the best available data from countries and provides an overview and commentary on the epidemic and the international response. UNAIDS fulfills its mission by: :- Uniting the efforts of the United Nations system, civil society, national governments, the private sector, global institutions and people living with and most affected by HIV; :- Speaking out in solidarity with the people most affected by HIV in defense of human dignity, human rights and gender equality; :- Mobilizing political, technical, scientific and financial resources and holding ourselves and others accountable for results; :- Empowering agents of change with strategic information and evidence to influence and ensure that resources are targeted where they deliver the greatest impact and bring about a prevention revolution; and :- Supporting inclusive country leadership for sustainable responses that are integral to and integrated with national health and development efforts. Sponsors: This resource is supported by: Advocacy partners; Civil society; Donors; Global Coalition on Women and AIDS; Global Fund to Fight AIDS TB and Malaria; People living with HIV; Private sector, and UN Family.

Top 50 Health 2.0 Blogs
type: Resource
type: NamedIndividual
has db xref: nif-0000-30026
IAO_0000115: Health 2.0 embraces the idea of bringing health care into the community of physicians, patients, and those in the health care industry together with technology and the Internet to provide the best possible health care environment.

Australian Wool Innovation Limited
type: Organization
type: NamedIndividual
has db xref: nif-0000-30047
synonym: AWI
IAO_0000115: Company focused on animal welfare and pest prevention in the wool industry.

Transgenic Animal Model Core
type: Resource
type: NamedIndividual
has db xref: nif-0000-30059
synonym: Transgenic Animal Model Core (TAMC)
abbrev: TAMC
IAO_0000115: A service for preparing genetically modified mice and rats for investigators at the University of Michigan. These mice models are typically used to study gene function, gene expression, gene regulation, and for the development of animal models of human disease and gene therapy reagents. TAMC provide access to their micromanipoulation and embryos stem cell workstations along with necessary reagents such as specialized plasmids, embryonic stem (ES) cell lines, FBS, and feeder cells certified for ES cell culture.

AtGenExpess - Weigel World
type: Resource
type: NamedIndividual
has db xref: nif-0000-30128
synonym: AtGenExpess
synonym: AtGenExpess Weigel World
synonym: AtGenExpress Visualization Tool
IAO_0000115: A visualization tool with microarray data and sample descriptions from the AtGenExpress project, which contains Affymetrix microarray data for Arabidopsis, a small flowering plant related to mustard and cabbage. This plant is used as a model organism in plant biology.

Biometric Research Branch: ArrayTools
type: Resource
type: NamedIndividual
has db xref: nif-0000-30199
synonym: BRB ArrayTools
IAO_0000115: A software package for the visualization and statistical analysis of DNA microarray gene expression data. The tools have been developed from the R statistical system, in C and fortran programs and Java applications. They are integrated into Excel as an add-in.

CELL- PREVEN Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-30316
synonym: CELL PREVEN
synonym: CELL PREVEN Project
IAO_0000115: An interactive computer system that utilizes cell phones and the Internet to collect real-time data about transmission rates of STDs, such as vaginosis among female sex workers, in Peru. This is tracked through the rates of precriptions of Metronidazole, an antibiotic used to treat bacterial infections of the vagina, stomach, skin, joints, and respiratory tract. Data from three communities is stored in an online database that can be accessed over secure Internet connection. This project has demonstrated that it is feasible to develop a public-health-surveillance system based on cell phones to collect data in real-time in Peru.

CryptoBase
type: Resource
type: NamedIndividual
has db xref: nif-0000-30395
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented July 19, 2016. This site is built and maintained by the Madhani Lab, Dept. of Biochemistry and Biophysics at the University of California, San Francisco

Distributed Computing Engine
type: Resource
type: NamedIndividual
has db xref: nif-0000-30413
synonym: DEngine
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 23,2022. Software designed to serve as a distributed computational framework to help perform mathematical simulations of muscle contraction. DEngine has a Windows PC, central controller PC and mathematical models that run as console applications on clients.

GlycoWorkbench
type: Resource
type: NamedIndividual
has db xref: OMICS_05691
IAO_0000115: A suite of software tools designed for the rapid drawing of glycan structures and for assisting the process of structure determination from mass spectrometry data.

FileMaker
type: Resource
type: NamedIndividual
has db xref: nif-0000-30436
IAO_0000115: A database software for managing, analyzing and sharing information across multiple devices and people, both online and offline.

Maitreya Dunham's Lab
type: Resource
type: NamedIndividual
has db xref: nif-0000-30476
synonym: The Dunham Lab
IAO_0000115: A portal for Maitreya Dunham's lab, which works on the genomic analysis of experimental evolution in yeast using microarrays and the chemostat. Research interests of the lab include experimental evolution of genetic networks in yeast, aneuploidy and copy number variation, comparative genomics, technology development and human genetics in yeast.

Understanding Human Disease Through Mouse Genetics
type: Resource
type: NamedIndividual
has db xref: nif-0000-30502
synonym: European Union Mouse Research for Public Health and Industrial Applications
abbrev: EUMORPHIA
IAO_0000115: A portal documenting a project for the development of novel approaches in phenotyping, mutagenesis and informatics to improve the characterization of mouse models for understanding human molecular physiology and pathology. EUMORPHIA has developed a new robust primary screening platform for determining the phenotype of mice: EMPReSS - European Mouse Phenotyping Resource for Standardised Screens. The project is also focused on training new young scientists by funding them to work in a variety of laboratories to gain a broader swathe of techniques. The project has also identified the need for more trained mouse pathologists. To address this, they are setting up training courses in pathology and working at a European level to establish more training.

Eppendorf
type: Commercial Organization
type: NamedIndividual
has db xref: nif-0000-30523
IAO_0000115: A commercial vendor for science equipment and life science consumables. This company offers customer support such as: taking/tracking orders, product installation and training, application support, calibration services, and general product maintenance and repair.

Epson
type: Organization
type: NamedIndividual
has db xref: nif-0000-30524
IAO_0000115: Commercial vendor of visualization software, factory automation equipment and electric components.

Functional Annotation of the Mammalian Genome
type: Resource
type: NamedIndividual
has db xref: nif-0000-30552
synonym: FANTOM
synonym: Functional Annotation of the Mammalian Genome (FANTOM)
IAO_0000115: International collaborative research project and database of annotated mammalian genome. Used to improve estimates of total number of genes and their alternative transcript isoforms in both human and mouse. Consortium to assign functional annotations to full length cDNAs that were collected during Mouse Encyclopedia Project at RIKEN.

FAS Center For Systems Biology
type: Organization
type: NamedIndividual
has db xref: nif-0000-30555
synonym: FAS Center
IAO_0000115: A group dedicated to combining a variety of experimental and theoretical approaches to find general principles that explain the structure, behavior and evolution of cells and organisms. The center hosts a variety of fellows and faculty from various backgrounds such as biology, physics, chemistry, mathematics, computer science and engineering.

G2P Knowledge Centre
type: Resource
type: NamedIndividual
has db xref: nif-0000-30605
synonym: GEN2PHEN Knowledge Centre
abbrev: GEN2PHEN
IAO_0000115: Portal of GEN2PHEN project, holistic approach to genotype-to-phenotype data. Aims to unify human and model organism genetic variation databases towards increasingly holistic views into Genotype-To-Phenotype (G2P) data, and to link this system into other biomedical knowledge sources via genome browser functionality.

IFPMA Clinical Trials Portal
type: Resource
type: NamedIndividual
has db xref: nif-0000-31391
synonym: International Federation of Pharmaceutical Manufacturers and Associations Clinical Trials Portal
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. IFPMA Clinical Trials Portal is brought to you by IFPMA on behalf of its Member Companies and Associations. IFPMA Clinical Trials Portal ensures: a free and easy-to-use interface for patients and health professionals alike to ongoing clinical trials, clinical trial results and complementary information on related issues; non-promotional and reliable information; industry's commitment to the transparency of clinical trials. * Search by Medical Condition and Drug Name * Language Interfaces (En, Es, Fr, De, Jp) * Glossary and Easy Explanation of Medical Expressions * Geographical Search

ROSTLAB
type: Organization
type: NamedIndividual
has db xref: nif-0000-31417
synonym: Rost Group
IAO_0000115: A lab organization which has bases in Munich, Germany and at Columbia University and focuses its research on protein structure and function using sequence and evolutionary information. They utilize machine learning and statistical methods to analyze genetic material and its gene products. Research goals of the lab involve using protein and DNA sequences along with evolutionary information to predict aspects of the proteins relevant to the advance of biomedical research.

Veterans Health Information Systems and Technology Architecture
type: Resource
type: NamedIndividual
has db xref: nif-0000-31445
synonym: VisTA
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A system of software applications that support patient care at Veterans Health Administration health care facilities. VISTA connects VHA facility workstations and PC's with nationally mandated and locally adapted software known as the Computerized Patient Record System (CPRS). Information is relevant to day-to-day operations for patients' medical and healthcare utilization histories such as data on demographics, episodes of care, medicines, practitioner information, diagnoses and procedures. All patients treated at VA Medical Centers are included in the files.

Community Health Sciences
type: Organization
type: NamedIndividual
has db xref: nif-0000-31446
synonym: School of Health Sciences
IAO_0000115: A school for education on community health sciences based out of the University of Nottingham. The school contains the divisions of epidemiology, public health, primary care, psychiatry, rehabilitation and aging. The common thread running through each of these divisions is that they all deal with communities, whether these be the entire populations of a region or country, or particular patient groups such as the mentally ill, people with disabilities, and elderly people.

Ronald M. Davis Tobacco Deposition and Trial Testimony Archive
type: Resource
type: NamedIndividual
has db xref: nif-0000-31469
synonym: Tobacco DATTA
IAO_0000115: A database of information from the Center for Tobacco Use Prevention and Research. Materials include depositions, trial testimony and opening and closing statements, expert reports, jury instructs, and verdicts. Some transcripts are rough copies and others may be marked as confidential although they no longer retain that status. This resource is in French.

SAGE GENIE
type: Resource
type: NamedIndividual
has db xref: nif-0000-31482
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 9, 2022. The SAGE Genie website provides highly intuitive, visual displays of human and mouse gene expression, based on a unique analytical process (Boon et al.) that reliably matches SAGE tags, 10 or 17 nucleotides in length, to known genes. Recently, with the construction and incorporation of a reference database of SNP-associated alternative tags into SAGE Genie (Silva et al.), the interpretation of tag to human gene mapping has been enhanced. Human SAGE Genie Tools The SAGE Anatomic Viewer visually displays the relative expression of a given gene in normal and malignant tissues of the human body. In addition, there is access to: o The Digital Northern, which shows the relative expression of the gene in each library. o The Ludwig Transcript (LT) Viewer, which visually represents a particular transcript with up to four possible virtual SAGE tag locations (starting from the 3' end) and locations of internally primed or alternatively polyadenylated transcripts. o Expanded access to brain, hES cells, and breast cell subtypes. * The SAGE Digital Gene Expression Displayer distinguishes significant differences in gene expression profiles between two pools of SAGE libraries. * The SAGE Experimental Viewer provides DGED results for pre-set pairs of libraries, one under control and the other under experimental conditions. * The SAGE Absolute Level Lister lists all SAGE libraries and links to the distribution of transcript expression levels in any given library. * The SAGE Library Finder tool searches for one or more tissue-specific libraries from the SAGE collection. * SAGE Genie Downloads provide files of genes, tags, datasets, mappings, and more. * SAGE Genomics Finder tool searches for genomics info for tags. * DKView tool for viewing Digital Karyotyping data. * DK Microbe tool searches for exact matches of 17 base-pair digital karyotyping tags in bacterial and viral genomes. * SAGE Tag Extraction tool to ex…

ECARUCA Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-31901
synonym: ECARUCA
IAO_0000115: A database of cytogenetic and clinical information on rare chromosomal disorders, including microdeletions and microduplications. The database is meant to be easily accessible for all participants, to improve patient care and collaboration between genetic centers, and collect the results of research and clinical features. The acronym ECARUCA stands for "European Cytogeneticists Association Register of Unbalanced Chromosome Aberrations".

Keyose
type: Resource
type: NamedIndividual
has db xref: nif-0000-31988
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 5, 2014. Keyose is a project designed and led by a family physician. We are not IT focused, but health-care focused. Technology is just a tool, not our purpose.

Sectional Atlas of Human Brain and Spinal Cord
type: Resource
type: NamedIndividual
has db xref: nif-0000-32420
abbrev: Neuroanatomy Lab Resource Appendices Sectional Atlas
IAO_0000115: Sectional atlas featuring sections of the spinal cord and brain for a neuroanatomy course offered by Temple University. Labels may be turned on and off.

Ensembl Metazoa
type: Resource
type: NamedIndividual
has db xref: nif-0000-33714
has db xref: r3d100011198
synonym: EnsemblMetazoa
IAO_0000115: Ensembl Genomes project produces genome databases for important species from across taxonomic range, using Ensembl software system. Five sites are now available, one of which is Ensembl Metazoa, which houses metazoan species.

aTag Generator
type: Resource
type: NamedIndividual
has db xref: nif-0000-37038
synonym: associated tags
synonym: associative tags
abbrev: aTag
abbrev: aTags
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 13, 2012. Snippets of HTML that capture the information that is most important in a machine-readable, interlinked format, making it easier to see the big picture. aTags work with any Web text and can store and connect any textual element that is highlighted in a browser. The structure of the embedded RDF/OWL is decidedly simple: a very short piece of human-readable text that is "tagged" with relevant ontological entities. An aTag generator can be easily added to any web browser and allows researchers to quickly generate aTags out of key statements from web pages, such as PubMed abstracts. The resulting aTags can be embedded anywhere on the web, for example on blogs, wikis, or biomedical databases. aTag demonstrates how the resulting statements that are distributed over the web can be searched, visualized and aggregated with Semantic Web / Linked Data tools, and discusses how aTags can be used to answer practically relevant biomedical questions even though their structure is very simple. aTags are based on Semantic Web standards and Linked Data practices. Specifically, they make use of RDFa, the SIOC vocabulary and various domain ontologies and taxonomies that are available in RDF/OWL format. The autocomplete functionality is based on Apache Solr. Reference: Simple, ontology-based representation of biomedical statements through fine-granular entity tagging and new web standards Matthias Samwald and Holger Stenzhorn. Bio-Ontologies 2009., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Online Education for the International Research Community: AboutIntroduction to Clinical Drug and Substance Abuse Research Methods
type: Resource
type: NamedIndividual
has db xref: nif-0000-37940
synonym: Neurobiology of Addiction Online Course
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on November 07, 2012. Decemeber 15, 2011 - Thank you for your interest in DrugAbuseResearchTraining.org. The site, courses, and resources are no longer available. Please send an email to inquiry (at) md-inc.com if you would like to be notified if the site or courses become available again. Introduction to Clinical Drug and Substance Abuse Research Methods is an online training program intended to introduce clinicians and substance abuse professionals to basic clinical research methods. The program is divided into four modules. Each module covers an entire topic and includes self-assessment questions, references, and online resources: * The Neurobiology of Drug Addiction * Biostatistics for Drug and Substance Abuse Research * Evaluating Drug and Substance Abuse Programs * Designing and Managing Drug and Substance Abuse Clinical Trials The learning objectives of this program are to help you: * Evaluate the benefits of alternative investigative approaches for answering important questions in drug abuse evaluation and treatment. * Define the proper levels of measurement and appropriate statistical methods for a clinical study. * Address common problems in data collection and analysis. * Anticipate key human subjects and ethical issues that arise in drug abuse studies. * Interpret findings from the drug abuse research literature and prepare a clinical research proposal. * Prepare research findings for internal distribution or publication in the peer reviewed literature. * Recognize drug addiction as a cyclical, chronic disease. * Understand and describe the brain circuits that are affected by addicting drugs, and explain to others the effects of major classes of addicting drugs on brain neurotransmitters. * Utilize new pharmacologic treatments to manage persons with drug addiction. Physicians can earn AMA PRA Category 1 Credit and purchase a high resolution printable electronic CME certificate(view sample); non-physicians…

CPCTR: Cooperative Prostate Cancer Tissue Resource
type: Resource
type: NamedIndividual
has db xref: nlx_143725
synonym: Cooperative Prostate Cancer Tissue Resource
abbrev: CPCTR
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Doumented on September 23,2022. The National Cancer Institute initially established the Cooperative Prostate Cancer Tissue Resource (CPCTR) to provide prostate cancer tissue samples with clinical annotation to researchers. The Resource provides access to formalin-fixed, paraffin-embedded primary prostate cancer tissue with associated clinical and follow-up data for research studies, particularly studies focused on translating basic research findings into clinical application. Fresh-frozen tissue is also available with limited clinical follow up information since these are more recent cases. The Resource database contains pathologic and clinical information linked to a large collection of prostate tissue specimens that is available for research. Researchers can determine whether the Resource has the tissues and patient data they need for their individual research studies. Consultation and interpretive services: Assistance is available from trained CPCTR pathologists. The CPCTR can provide consultative assistance in staining interpretation, and scoring, on a collaborative basis. Fresh Frozen and Paraffin Tissue: The resource has over 7,000 annotated cases (including 7,635 specimens and 38,399 annotated blocks). Tissue Microarrays (TMA): The CPCTR has slides from prostate cancer TMAs with associated clinical data. The information provided for each case on the arrays (derived from radical prostatectomy specimens) includes: age at diagnosis, race, PSA at diagnosis, tumor size, TNM stage, Gleason score and grade, and vital status and other variables.

ResearchRaven
type: Resource
type: NamedIndividual
has db xref: nlx_143808
IAO_0000115: A database of funding opportunities, professional conferences, calls for papers and other research-related materials. ResearchRaven is a public service provided by the Samaritan Health Services Center for Health Research and Quality.

Mind Research Network - COINS
type: Resource
type: NamedIndividual
has db xref: nlx_144067
synonym: Collaborative Informatics and Neuroimaging Suite
synonym: Collaborative Informatics Neuroimaging Suite
synonym: Mind Research Network - Collaborative Informatics and Neuroimaging Suite
abbrev: COINS
IAO_0000115: A web-based neuroimaging and neuropsychology software suite that offers versatile, automatable data upload/import/entry options, rapid and secure sharing of data among PIs, querying and export all data, real-time reporting, and HIPAA and IRB compliant study-management tools suitable to large institutions as well as smaller scale neuroscience and neuropsychology researchers. COINS manages over over 400 studies, more than 265,000 clinical neuropsychological assessments, and 26,000 MRI, EEG, and MEG scan sessions collected from 18,000 participants at over ten institutions on topics related to the brain and behavior. As neuroimaging research continues to grow, dynamic neuroinformatics systems are necessary to store, retrieve, mine and share the massive amounts of data. The Collaborative Informatics and Neuroimaging Suite (COINS) has been created to facilitate communication and cultivate a data community. This tool suite offers versatile data upload/import/entry options, rapid and secure sharing of data among PIs, querying of data types and assessments, real-time reporting, and study-management tools suitable to large institutions as well as smaller scale researchers. It manages studies and their data at the Mind Research Network, the Nathan Kline Institute, University of Colorado Boulder, the Olin Neuropsychiatry Research Center (at) Hartford Hospital, and others. COINS is dynamic and evolves as the neuroimaging field grows. COINS consists of the following collaboration-centric tools: * Subject and Study Management: MICIS (Medical Imaging Computer Information System) is a centralized PostgreSQL-based web application that implements best practices for participant enrollment and management. Research site administrators can easily create and manage studies, as well as generate reports useful for reporting to funding agencies. * Scan Data Collection: An automated DICOM receiver collects, archives, and imports imaging data into the file system and COINS, requiring no user in…

American Federation for Aging Research
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100005366
has db xref: grid.427612.4
has db xref: ISNI: 0000 0001 0395 8845
has db xref: nlx_144115
has db xref: Wikidata: Q4743745
abbrev: AFAR
IAO_0000115: A non-profit organization that supports the advance of healthy aging through biomedical research.

Yandell Lab Portal
type: Resource
type: NamedIndividual
has db xref: nlx_144364
IAO_0000115: Sequenced genomes contain a treasure trove of information about how genes function and evolve. Getting at this information, however, is challenging and requires novel approaches that combine computer science and experimental molecular biology. My lab works at the intersection of both domains, and research in our group can be summarized as follows: generate hypotheses concerning gene function and evolution by computational means, and then test these hypotheses at the bench. This is easier said than done, as serious barriers still exist to using sequenced genomes and their annotations as starting points for experimental work. Some of these barriers lie in the computational domain, others in the experimental. Though challenging, overcoming these barriers offers exciting training opportunities in both computer science and molecular genetics, especially for those seeking a future at the intersection of both fields. Ongoing projects in the lab are centered on genome annotation and comparative genomics; exploring the relationships between sequence variation and human disease; and high-throughput biological image analysis. Current software tools available: VAAST (the Variant Annotation, Analysis & Search Tool) is a probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST builds upon existing amino acid substitution (AAS) and aggregative approaches to variant prioritization, combining elements of both into a single unified likelihood-framework that allows users to identify damaged genes and deleterious variants with greater accuracy, and in an easy-to-use fashion. VAAST can score both coding and non-coding variants, evaluating the cumulative impact of both types of variants simultaneously. VAAST can identify rare variants causing rare genetic diseases, and it can also use both rare and common variants to identify genes responsible for common diseases. VAAST thus has a much greater scope of use than any exi…

Open Biosystems
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_144444
synonym: Open Biosystems - RNAi Gene Expression Antibodies
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. Open Biosystems offers products that span Genomics, RNAi and Antibodies. Building on the rapid sharing model that is at the core of the Human Genome Project, Open Biosystems collaborates with some of the most innovative life science investigators working today. We partner with them to bring to market new productsthey have often pioneered the new resources in their own lab, and we prepare it for widespread use and then provide access to the research community. Delivery of genetic content is our most recent technological breakthrough. Recently, we brought to market the Tranz-vector system, the safest human-based lentiviral delivery technology. Further supplementing our already strong line of RNA interference (RNAi) and complementary DNA (cDNA) products, this technology provides investigators with superior delivery capabilities for high-quality cellular screening. The combination or our unique Tranz-vector system and whole genome RNAi and cDNA content enables our customers to perform drug target validation on a large scale. With our genomics resources, Open Biosystems provides the content investigators utilize to unlock the functions of human genes and their relationships to normal and disease development. We offer the most complete gene library in the industry. This novel library consists of several full length cDNA and open reading frame collections. Most prominently among these is the Mammalian Gene Collection (MGC), the industry's gold standard gene catalog. The discovery of RNA interference has revolutionized the way investigators approach the studies of gene expression, regulation and interactions, particularly as it relates to drug development. Our collaboration with Drs. Greg Hannon (CSHL) and Steve Elledge (Harvard) has led the way in the evolution of the short hairpin RNA (shRNA) technologies to provide the life science community with whole genome resources for human, mouse and rat with a…

House of Mind
type: Resource
type: NamedIndividual
has db xref: nlx_144621
abbrev: House of MInd
IAO_0000115: Neuroscience/psych blog by a neuroscientist in training. I mostly review articles and try to synthesize what I deem important/interesting. Enjoy!

EMBL - Bork Group
type: Resource
type: NamedIndividual
has db xref: nlx_149173
synonym: Bork Group - Comparative Systems Analysis (EMBL)
IAO_0000115: The main focus of this Computational Biology group is to predict function and to gain insights into evolution by comparative analysis of complex molecular data. The group currently works on three different scales: * genes and proteins, * protein networks and cellular processes, and * phenotypes and environments. They require both tool development and applications. Some selected projects include comparative gene, genome and metagenome analysis, mapping interactions to proteins and pathways as well as the study of temporal and spatial protein network aspects. All are geared towards the bridging of genotype and phenotype through a better understanding of molecular and cellular processes. The services - resources & tools, developed by Bork Group, are mainly designed and maintained for research & academic purposes. Most of services are published and documented in one or more papers. All our tools can be completely customized and integrated into your existing framework. This service is provided by the company biobyte solutions GmbH. Please visit their tools and services pages for full details and more information. Standard commercial licenses for our tools are also available through biobyte solutions GmbH. The group is partially associated with Max Delbr��ck Center for Molecular Medicine (MDC), Berlin.

Google Project Hosting
type: Resource
type: NamedIndividual
has db xref: nlx_149266
synonym: Project Hosting on Google Code
IAO_0000115: Project Hosting on Google Code provides a free collaborative development environment for open source projects.

DIAN - Dominantly Inherited Alzheimer Network
type: Resource
type: NamedIndividual
has db xref: nlx_149316
synonym: Dominantly Inherited Alzheimer Network
synonym: Dominantly Inherited Alzheimer Network (DIAN)
abbrev: DIAN
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. An international research partnership of leading scientists determined to understand a rare form of Alzheimers disease that is caused by a gene mutation and to establish a research database and tissue repository to support research on Alzheimers disease by other investigators around the world. One goal of DIAN is to study possible brain changes that occur before Alzheimers disease is expressed in people who carry an Alzheimers disease mutation. Other family members without a mutation will serve as a comparison group. People in families in which a mutation has been identified will be tracked in order to detect physical or mental changes that might distinguish people who inherited the mutation from those who did not. DIAN currently involves eleven outstanding research institutions in the United States, United Kingdom, and Australia. John C. Morris, M.D., Friedman Distinguished Professor of Neurology at Washington University School of Medicine in St. Louis, is the principal investigator of the project., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Advanced Cognitive Training for Independent and Vital Elderly (ACTIVE)
type: Resource
type: NamedIndividual
has db xref: nlx_149439
synonym: ACTIVE Study
synonym: Advanced Cognitive Training for Independent and Vital Elderly
abbrev: ACTIVE
IAO_0000115: Data set from a randomized controlled trial of cognitive interventions designed to maintain functional independence in elders by improving basic mental abilities. Several features made ACTIVE unique in the field of cognitive interventions: (a) use of a multi-site, randomized, controlled, single-blind design; (b) intervention on a large, diverse sample; (c) use of common multi-site intervention protocols, (d) primary outcomes focused on long-term, cognitively demanding functioning as measured by performance-based tests of daily activities; and (e) an intent-to-treat analytical approach. The clinical trial ended with the second annual post-test in January 2002. A third annual post-test was completed in December 2003. The area population and recruitment strategies at the six field sites provided a study sample varying in racial, ethnic, gender, socioeconomic, and cognitive characteristics. At baseline, data were collected by telephone for eligibility screening, followed by three in-person assessment sessions, including two individual sessions and one group session, and a self-administered questionnaire. At post-tests, data were collected in-person in one individual session and one group session as well as by self-administered questionnaire. There were four major categories of measures: proximal outcomes (measures of cognitive abilities that were direct targets of training), primary outcomes (measures of everyday functioning, both self-report and performance), secondary outcomes (measures of health, mobility, quality of life, and service utilization), and covariates (chronic disease, physical characteristics, depressive symptoms, cognitive impairment, psychosocial variables, and demographics). Phase I of ACTIVE was a randomized controlled, single-blind trial utilizing a four-group design, including three treatment arms and a no-contact control group. Each treatment arm consisted of a 10-session intervention for one of three cognitive abilities memory, reasoning, and spe…

NBDC - National Bioscience Database Center
type: Resource
type: NamedIndividual
has db xref: nlx_151485
synonym: National Bioscience Database Center
synonym: National Bioscience Database Center (NBDC)
abbrev: NBDC
IAO_0000115: The National Bioscience Database Center (NBDC) intends to integrate all databases for life sciences in Japan, by linking each database with expediency to maximize convenience and make the entire system more user-friendly. We aim to focus our attention on the needs of the users of these databases who have all too often been neglected in the past, rather than the needs of the people tasked with the creation of databases. It is important to note that we will continue to honor the independent integrity of each database that will contribute to our endeavor, as we are fully aware that each database was originally crafted for specific purposes and divergent goals. Services: * Database Catalog - A catalog of life science related databases constructed in Japan that are also available in English. Information such as URL, status of the database site (active vs. inactive), database provider, type of data and subjects of the study are contained for each database record. * Life Science Database Cross Search - A service for simultaneous searching across scattered life-science databases, ranging from molecular data to patents and literature. * Life Science Database Archive - maintains and stores the datasets generated by life scientists in Japan in a long-term and stable state as national public goods. The Archive makes it easier for many people to search datasets by metadata in a unified format, and to access and download the datasets with clear terms of use. * Taxonomy Icon - A collection of icons (illustrations) of biological species that is free to use and distribute. There are more than 200 icons of various species including Bacteria, Fungi, Protista, Plantae and Animalia. * GenLibi (Gene Linker to bibliography) - an integrated database of human, mouse and rat genes that includes automatically integrated gene, protein, polymorphism, pathway, phenotype, ortholog/protein sequence information, and manually curated gene function and gene-related or co-occurred Disease/Phenotype an…

ZCre
type: Resource
type: NamedIndividual
has db xref: nlx_151618
IAO_0000115: ZCre is a consortium of researchers who have a shared interest in developing Cre/lox based tools for use in the zebrafish model organism. ZCre plans to generate 15 or more tissue specific ERT2CreERT2 driver lines to be expressed in either differentiated cell types or precursor/stem cells, as well as 20 or more lines based upon multilox technology. One set of multilox transgenes will allow long-term permanent labelling of individual cells for lineage tracing and other applications. Another set will allow perturbation of single pathways within individual cells (PathM lines). In order to make these lines ZCre has developed a three-way cloning system using Gateway technology (Invitrogen). Once constructs are made they will be deposited at Addgene.org. Transgenic lines will be available from ZCre or from regional stock centers as requested.

Longitudinal Employer-Household Dynamics
type: Resource
type: NamedIndividual
has db xref: nlx_151841
synonym: Longitudinal Employer-Household Dynamics (LEHD)
abbrev: LEHD
IAO_0000115: A dataset that combines federal and state administrative data on employers and employees with core Census Bureau censuses and surveys, while protecting the confidentiality of people and firms that provide the data. This data infrastructure facilitates longitudinal research applications in both the household / individual and firm / establishment dimensions. The specific research is targeted at filling an important gap in the available data on older workers by providing information on the demand side of the labor market. These datasets comprise Title 13 protected data from the Current Population Surveys, Surveys of Income and Program Participation, Surveys of Program Dynamics, American Community Surveys, the Business Register, and Economic Censuses and Surveys. With few exceptions, states have partnered with the Census Bureau to share data. As of December 2008, Connecticut, Massachusetts, New Hampshire and Puerto Rico have not signed a partnership agreement, while a partnership with the Virgin Islands is pending. LEHD's second method of developing employer-employee data relations through the use of federal tax data has been completed. LEHD has produced summary tables on accessions, separation, job creation, destruction and earnings by age and sex of worker by industry and geographic area. The data files consist of longitudinal datasets on all firms in each participating state (quarterly data, 1991- 2003), with information on age, sex, turnover, and skill level of the workforce as well as standard information on employment, payroll, sales and location. These data can be accessed for all available states from the Project Website. Data Availability: Research conducted on the LEHD data and other products developed under this proposal at the Census Bureau takes place under a set of rules and limitations that are considerably more constraining than those prevailing in typical research environments. If state data are requested, the successful peer-reviewed proposals must als…

Mexican Health and Aging Study
type: Resource
type: NamedIndividual
has db xref: nlx_151859
synonym: Mexican Health & Aging Study
synonym: Mexican Health and Aging Study (MHAS)
abbrev: MHAS
IAO_0000115: A dataset of a prospective panel study of health and aging in Mexico. The study was designed to ensure comparability with the U.S. Health and Retirement Study in many domains, and the NHANES III. The baseline survey in 2001 is nationally representative of the 13 million Mexicans born prior to 1951. The six Mexican states which are home to 40% of all migrants to the U.S. were over-sampled at a rate of 1.7:1. Spouse/partners of eligible respondents were interviewed also, even if the spouse was born after 1950. Completed interviews were obtained in 9,862 households, for a total of 15,186 individual interviews. All interviews were face-to-face, with average duration of 82 minutes. A direct interview (on the Basic questionnaire) was sought, and Proxy interviews were obtained when poor health or temporary absence precluded a direct interview. Questionnaire topics included the following: * HEALTH MEASURES: self-reports of conditions, symptoms, functional status, hygienic behaviors (e.g., smoking & drinking history), use/source/costs of health care services, depression, pain, reading and cognitive performance; * BACKGROUND: Childhood health and living conditions, education, ability to read/write and count, migration history, marital history; * FAMILY: rosters of all children (including deceased children); for each, demographic attributes, summary indicators of childhood and current health, education, current work status, migration. Parent and sibling migration experiences; * TRANSFERS: financial and time help given to and received by respondent from children, indexed to specific child; time and financial help to parent; * ECONOMIC: sources and amounts of income, including wages, pensions, and government subsidies; type and value of assets. All amount variables are bracketed in case of non-response. * HOUSING ENVIRONMENT: type, location, building materials, other indicators of quality, and ownership of consumer durables; * ANTHROPOMETRIC: for a 20% sub-sample, measured weigh…

OpenElectrophy
type: Resource
type: NamedIndividual
has db xref: nlx_151873
IAO_0000115: Software Python module for electrophysiology data analysis.

Bio-Synthesis
type: Organization
type: NamedIndividual
has db xref: nlx_152297
has db xref: SciEx_516
synonym: Bio-Synthesis Inc.
IAO_0000115: A commercial supplier of custom synthetic molecules. They specialize in peptides, oligonucleotides, bioconjugation, molecular biology services, proteins and specialty chemistry.

Vector Laboratories
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_152485
IAO_0000115: A private antibody-producing corporation in Burlingame, California with subsidiaries in UK and Canada.

Repository of neural and cognitive models
type: Resource
type: NamedIndividual
has db xref: nlx_152592
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A repository of models of neuronal networks maintained by the Nengo (http://nengo.org) project. Most but not all models use Nengo. Nengo is a graphical and scripting based software package for simulating large-scale neural systems.

BUSM Mass Spectrometry Resource
type: Resource
type: NamedIndividual
has db xref: nlx_152679
synonym: Boston University Mass Spectrometry Resource for Biology and Medicine
synonym: Boston University School of Medicine Mass Spectrometry Resource
synonym: Mass Spectrometry Resource for Biology and Medicine
abbrev: Mass Spectrometry Resource
IAO_0000115: Biomedical technology research center that conducts high-sensitivity structural determinations and analyses of biological compounds via mass spectrometry. The emphasis is on glycoconjugates, oligosaccharides and proteins.

MONARCH Initiative
type: Resource
type: NamedIndividual
has db xref: nlx_152525
has db xref: nlx_152748
has db xref: r3d100011594
has db xref: SCR_001373
synonym: MONARCH Disease Models View
synonym: MONARCH Integrated Disease Model
synonym: MONARCH Integrated Disease Models View
synonym: The MONARCH Initiative
abbrev: Monarch
IAO_0000115: Repository of information about model organisms, in vitro models, genes, pathways, gene expression, protein and genetic interactions, orthology, disease, phenotypes, publications, and authors, and ability to navigate multi-scale spatial and temporal phenotypes across in vivo and in vitro model systems in context of genetic and genomic data, using semantics and statistics. Discovery system provides basic and clinical science researchers, informaticists, and medical professionals with integrated interface and set of discovery tools to reveal genetic basis of disease, facilitate hypothesis generation, and identify novel candidate drug targets. Database that indexes authoritative information on experimental models of disease from MGI, RGD and ZFIN.

ADEGENET
type: Resource
type: NamedIndividual
has db xref: nlx_153996
has db xref: nlx_154580
has db xref: OMICS_11078
has db xref: SCR_007239
synonym: R/ADEGENET
IAO_0000115: Software package dedicated to the handling of molecular marker data for multivariate analysis. This package is related to ADE4, a R package for multivariate analysis, graphics, phylogeny and spatial analysis. (entry from Genetic Analysis Software)

2LD
type: Resource
type: NamedIndividual
has db xref: nlx_154006
IAO_0000115: Software program for calculating linkage disequilibrium (LD) measures between two polymorphic markers.

SQTL
type: Resource
type: NamedIndividual
has db xref: nlx_154032
synonym: Semiparametric QTL mapping in general pedigrees
IAO_0000115: Software application (entry from Genetic Analysis Software)

POLYMORPHISM
type: Resource
type: NamedIndividual
has db xref: nlx_154052
IAO_0000115: Software application for calculating the heterozygosity, PIC, and LIC values for polymorphic markers (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

EDAC
type: Resource
type: NamedIndividual
has db xref: nlx_154078
synonym: power calculator for Extremely Discordant And Concordant sibpairs
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016.

GENEHUNTER SAD
type: Resource
type: NamedIndividual
has db xref: nlx_154198
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 6th,2023. Software application with implementation of the Sad statistic, more robust to transmission ratio distortion in the context of allele sharing (entry from Genetic Analysis Software)

COMDS
type: Resource
type: NamedIndividual
has db xref: nlx_154255
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2022. Software application for combined segregation and linkage analysis, incorporating severity and diathesis. (entry from Genetic Analysis Software)

CHAPLIN
type: Resource
type: NamedIndividual
has db xref: nlx_154266
synonym: Case-control HAPLotype INference package
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.Software application for identifying specific haplotypes or haplotype features that are associated with disease using genotype data from a case-control study. (entry from Genetic Analysis Software)

CRIMAP
type: Resource
type: NamedIndividual
has db xref: nlx_154276
IAO_0000115: Software application for constructing multilocus linkage map (entry from Genetic Analysis Software)

DCHIP LINKAGE
type: Resource
type: NamedIndividual
has db xref: nlx_154280
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016.

FLOSS
type: Resource
type: NamedIndividual
has db xref: biotools:floss
has db xref: nlx_154319
synonym: FLexible Ordered SubSet analysis
IAO_0000115: Software application that performs ordered subset analysis using MERLIN's ouput .lod file created with the --perFamily option. Ordered subset analysis uses covariate information to identify a more homogenous subset of families for linkage analysis. The homogeneous subset of families does not need to be specified a priori, and the covariates can include environmental exposures, quantitative traits, or linkage scores at another locus in the genome. The evidence for linkage is evaluated with a permutation test. (entry from Genetic Analysis Software)

HAP 1
type: Resource
type: NamedIndividual
has db xref: nlx_154371
synonym: haplotype resolution using imperfect phylogeny
IAO_0000115: Software application (entry from Genetic Analysis Software)

HAPSCOPE
type: Resource
type: NamedIndividual
has db xref: nlx_154393
IAO_0000115: Software application that includes a comprehensive analysis pipeline and a sophisticated visualization tool for analyzing functionally annotated haplotypes. (entry from Genetic Analysis Software)

LDB/LDB+
type: Resource
type: NamedIndividual
has db xref: nlx_154413
synonym: Location DataBase
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application that integrate genetic linkage map and physical map (entry from Genetic Analysis Software)

LOCUSMAP
type: Resource
type: NamedIndividual
has db xref: biotools:locusmap
has db xref: nlx_154434
IAO_0000115: Software package designed for rapid linkage analysis and map construction of loci with a variety of inheritance modes. (entry from Genetic Analysis Software)

MRH
type: Resource
type: NamedIndividual
has db xref: nlx_154493
synonym: Minimum Recombinant Haplotype
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software)

PEDIGREE-VISUALIZER
type: Resource
type: NamedIndividual
has db xref: nlx_154521
IAO_0000115: Software application (entry from Genetic Analysis Software)

PEDPHASE
type: Resource
type: NamedIndividual
has db xref: nlx_154525
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE.Documented on August 23,2022. Software application for inferring haplotypes from genotypes on pedigree data (entry from Genetic Analysis Software)

QTL CAFE
type: Resource
type: NamedIndividual
has db xref: nlx_154563
IAO_0000115: Software application providing a user freiendly way to perform QTL analysis. The software currently allows 3 types of QTL analysis: (1) single marker ANOVA. (2) marker regression. (3) interval mapping by regression. (entry from Genetic Analysis Software)

RHMAPPER
type: Resource
type: NamedIndividual
has db xref: nlx_154576
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30, 2022. An interactive software program for radiation hybrid mapping (entry from Genetic Analysis Software)

SIMM
type: Resource
type: NamedIndividual
has db xref: nlx_154626
synonym: SimM
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 6th,2023. Gene dropping simulation software. The program is a gzip'ed tar archive and is designed to run under UNIX/Linux operating system.

SOLAR
type: Resource
type: NamedIndividual
has db xref: nlx_154653
synonym: Sequential Oligogenic Linkage Analysis Routines
IAO_0000115: A flexible and extensive software package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, and covariate screening. Operations are included for calculation of marker-specific or multipoint identity-by-descent (IBD) matrices in pedigrees of arbitrary size and complexity, and for linkage analysis of quantitative traits which may involve multiple loci (oligogenic analysis), dominance effects, and epistasis. (entry from Genetic Analysis Software)

CIFTI Connectivity File Format
type: Resource
type: NamedIndividual
has db xref: nlx_155527
synonym: Connectivity Informatics Technology Initiative Connectivity File Format
IAO_0000115: Standardizes file formats for the storage of connectivity data. These formats are developed by the Human Connectome Project and other interested parties. Use the MEDIAWIKI entry in the menu on the left for more information about the CIFTI file formats. Access the CIFTI discussion forum using the Forums entry in the menu on the left. Subscribe to the discussion forum and you will be informed about issues involving the CIFTI file formats via email.

3DSlicerLupusLesionModule
type: Resource
type: NamedIndividual
has db xref: nlx_155579
IAO_0000115: Slicer3 module to provide a capability for performing white matter lesion classification and summary.

BrainNetworkConstructionAnalysisPlatform
type: Resource
type: NamedIndividual
has db xref: nlx_155590
IAO_0000115: Construct and analyse brain network is a brain network visualization tool, which can help researchers to visualize construct and analyse resting state functional brain networks from different levels in a quick, easy and flexible way. Entrance parameter of construct and analyse brain network is export parameters of dparsf software.It would be greatly appreciated if you have any suggestions about the package or manual.

COMPARE
type: Resource
type: NamedIndividual
has db xref: nlx_155598
IAO_0000115: Generic classification tool for 3D images

Data Format Tools
type: Resource
type: NamedIndividual
has db xref: nlx_155608
abbrev: DFT
IAO_0000115: A loose collection of programs and configuration options that intend to make working with data more transparent to formats. Currently available is a basic specification for NIfTI-1 for the UNIX file command and proof of concept code for the concept of treating data as an abstract concept and instantiating physical instances on demand.

GesTr
type: Resource
type: NamedIndividual
has db xref: nlx_155637
IAO_0000115: A cross platform, open source gesture tracking program. You launch it from the web, and use it to streamline the way you communicate with the computer. It allows for a more natural method of issuing commands than with keyboard shortcuts or GUI buttons. GesTr supports simple XML files to customize recognized gestures and their corresponding actions. GesTr also has experimental support for the Wii Remote used with an infrared pen as an alternative input device.

I/OWA
type: Resource
type: NamedIndividual
has db xref: nlx_155643
synonym: I/OWA 3
synonym: Input / Output time aWare Architecture
synonym: Input/Output time-aWare Architecture
IAO_0000115: Software for real-time parametric statistical analysis of functional MRI (fMRI) data. The system that combines a general architecture for sampling and time-stamping relevant information channels in fMRI (image acquisition, stimulation, subject responses, cardiac and respiratory monitors, etc.) and an efficient approach to manipulating these data, featuring incremental subsecond multiple linear regression. The advantages of the system are the simplification of event timing and efficient and unified data formatting. Substantial parametric analysis can be performed and displayed in real-time. Immediate (replay) and delayed off-line analysis can also be performed with the same interface. The system provides a time-accounting infrastructure that readily supports standard and innovative approaches to fMRI.

MINC Example files
type: Resource
type: NamedIndividual
has db xref: nlx_155660
IAO_0000115: A reference MINC set of files that currently includes human head images only of standard modalities. The goal is to build a well curated collection of files that demonstrate the capabilities of MINC

cbiNifti: Matlab/Octave Nifti library
type: Resource
type: NamedIndividual
has db xref: nlx_155680
abbrev: cbiNifti
IAO_0000115: An I/O library for Matlab/Octave Matlab and Octave library for reading and writing Nifti-1 files. cbiNifti is intended to be a small, self-contained library that makes minimal assumptions about what Nifti files should look like and allow users easy access to the raw data. cbiNifti handles compressed file formats for reading and writing, using Unix pipes for compression and decompression. More information and code examples at: http://www.pc.rhul.ac.uk/staff/J.Larsson/software.html

BRAINSCut
type: Resource
type: NamedIndividual
has db xref: nlx_155699
IAO_0000115: A software package for segmentation of structures using automated neual networks. This is the reference implementation using NAMIC software development best practices and the Insight Toolkit of the paper Registration and machine learning-based automated segmentation of subcortical and cerebellar brain structures. (PMID: 17904870). The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3.

C-PAC
type: Resource
type: NamedIndividual
has db xref: nlx_155720
synonym: Configurable Pipeline for the Analysis of Connectomes
IAO_0000115: A configurable, open-source, Nipype-based, automated processing pipeline for resting state functional MRI (R-fMRI) data, for use by both novice and expert users. C-PAC was designed to bring the power, flexibility and elegance of the Nipype platform to users in a plug and play fashion?without requiring the ability to program. Using an easy to read, text-editable configuration file, C-PAC can rapidly orchestrate automated R-fMRI processing procedures, including: - quality assurance measurements - image preprocessing based upon user specified preferences - generation of functional connectivity maps (e.g., correlation analyses) - customizable extraction of time-series data - generation of local R-fMRI metrics (e.g., regional homogeneity, voxel-matched homotopic connectivity, fALFF/ALFF) C-PAC makes it possible to use a single configuration file to launch a factorial number of pipelines differing with respect to specific processing steps.

Connectir
type: Resource
type: NamedIndividual
has db xref: nlx_155729
IAO_0000115: An R-based package to conduct brain connectivity analyses with a focus on a novel approach to conducting Connectome-Wide Association Studies (CWAS) using functional connectivity.

DicomBrowser
type: Resource
type: NamedIndividual
has db xref: nlx_155743
IAO_0000115: A platform-independent desktop tool for inspecting DICOM header fields, editing DICOM header fields, viewing DICOM images, and transferring DICOM files to a DICOM receiver. DicomBrowser includes scriptable header editing to support various de-identification protocols. DicomBrowser is written in Java and uses ImageJ for image viewing and the dcm4che toolkit for much of its DICOM implementation.

Hitachi Optical Topography System
type: Resource
type: NamedIndividual
has db xref: nlx_155772
IAO_0000115: An instrumental supplier which provides researchers and clinicians with sophisticated All-in-One solutions in the field of neuroscience.

NeuroVigil
type: Organization
type: NamedIndividual
has db xref: nlx_15581
synonym: NeuroVigil: Revolutionizing Brain Analysis
IAO_0000115: Commercial company that produces simple EEG measurement devices compatible with phones.Develops proprietary non invasive brain monitors and advanced machine learning algorithms to detect constellation of biomarkers of pathologies in asymptomatic individuals, such as people with neurodegeneration, adverse drug side effects or brain cancer, and to ascertain intent including individuals who cannot otherwise communicate.

Net Station API
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_155824
synonym: Net Station Software for EEG Acquisition and Physician and Review
IAO_0000115: APIs for Net Station data files. APIs are available for C++, C#, and Java.

imcalc: SPM batch image calculator
type: Resource
type: NamedIndividual
has db xref: nlx_155854
synonym: SPM batch image calculator
synonym: SPM batch image calculator (imcalc)
abbrev: imcalc
IAO_0000115: A collection of functions with batch functionality for SPM: * user entered expression (one set of volumes); * binarize non-zero voxels; * binarize/threshold each image; * binarize non-zero voxels, sum, rebinarize; * voxelwise calculations on pairs (add sub mult div ... etc.); * flip sign of all non-zero voxels; * x-flip image along y = 0; * mask images to a template; * T-to-Z transform; * Winsorize (cap) extreme values; * Z-score transform of image relative to its global mean and SD; * write single voxels to a .nii; * create a cluster image; * split cluster image into constituent images; * write hemisphere masks from template; * homotopic calculations; * replace zeros with __; * pad image with extra voxels;

BWH Surgical Planning Laboratory
type: Organization
type: NamedIndividual
has db xref: nlx_156146
abbrev: BWH SPL
IAO_0000115: A laboratory dedicated to advancing health care through utilizing computation and imaging to new areas of medicine.

Children's Hospital Informatics Program
type: Organization
type: NamedIndividual
has db xref: nlx_156192
synonym: Harvard Children's Hospital Informatics Program
abbrev: CHIP
IAO_0000115: An applied research and education program at Children's Hospital in Boston. The program focuses on work done at the intersection of information science, health care and biomedical discovery. The field is inherently interdisciplinary, drawing on traditional biomedical disciplines, the science and technology of computing, data science, biostatistics, epidemiology, decision sciences, population health, omics, implementation science, and health care policy and management. This program's faculty are trained in medicine, data science, computer science, mathematics and epidemiology.

DF/HCC Health Communication Core
type: Resource
type: NamedIndividual
has db xref: nlx_156198
IAO_0000115: Core facility that provides the following services: Website development and hosting for research labs and studies requiring an online presence, interactive functionality, or site traffic tracking. The Health Communication Core offers a full range of creative communication services to support evidence-based recruitment and retention of study participants and intervention research. HCC serves researchers from diverse disciplines who need websites, logos, brochures, social media campaigns, publications, and interactive media targeted to the needs and preferences of specific audiences.

DF/HCC Specialized Histopathology Services Core
type: Resource
type: NamedIndividual
has db xref: nlx_156203
IAO_0000115: Core facility that provides the following services: Tissue trimming, cassetting, processing, and embedding, Cutting and staining of paraffin-embedded and cryostat sections, Immunohistochemistry for both routine and novel markers, In situ hybridization, using chromogenic or radioactive detection methods, Laser capture microdissection. Tissue analysis is critical to validation and evaluation of animal models of human cancer, and human cancer tissues serve as the operating system for translational research. The facility supports a wide spectrum of cancer-relevant research, from basic studies on pathogenic mechanisms in cancer to translational research focused on the development of new tests for biomarkers that stratify patients and direct therapy. The Specialized Histopathology (SHP) Core, was created in 2005 by consolidating five histopathology cores into a single unit with two performance sites: Longwood, Directed by Jon Aster and based at the Brigham and Women?s Hospital and MGH, Directed by Anat Stemmer-Rachamimov and based at Massachusetts General Hospital East in Charlestown. The SHP Core provides professional and technical research pathology services to DF/HCC investigators working in diverse organisms (e.g., rodents, fish, and monkeys) or human tissues. The Core also assists in experimental design and the development and interpretation of tests and their results. As of July 2012, the Longwood site offers CLIA Certified services.

Dartmouth College Clinical Pharmacology Shared Resource Core Facility
type: Resource
type: NamedIndividual
has db xref: ABRF_1715
has db xref: nlx_156223
synonym: Dartmouth College DCC Clinical Pharmacology Shared Resource
synonym: DCC Clinical Pharmacology Shared Resource
IAO_0000115: Supports Dartmouth Cancer Center investigators in design, performance, data analysis, and interpretation of pharmacology objectives in preclinical, clinical and epidemiological studies.

Dartmouth Geospatial Shared Resource
type: Resource
type: NamedIndividual
has db xref: nlx_156227
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A resource to develop shared resources for the implementation of geospatial analysis for cancer research at Dartmouth. Their goal is to provide expert consultation and collaboration for research projects of NCCC members in behavior, epidemiology, and health services research. The GeoSpatial Resource also strives to educate members of the community in different aspects of geospatial analysis by providing courses through TDI and at Dartmouth College.

Dartmouth College Optical Cellular Imaging Core Facility
type: Resource
type: NamedIndividual
has db xref: nlx_156232
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2026. Core facility that provides the following services: Optical cellular imaging, Microscopy training. A Norris Cotton Cancer Center Shared Resource Facility. The Optical Cellular Imaging Shared Resource strives to provide reliable and affordable access to point scanning confocal microscopy, conventional bright field and fluorescence light microscopy, and image analysis resources. The facility provides individual and group training for operation of the light microscopes. Training is intended to provide an understanding of the basic light microscopy and digital imaging principles involved. Training for our microscope use and imaging consultation is open to all members of Dartmouth College, DMS, DHMC, and outside users.

FAMU Drug Discovery Core Facility
type: Organization
type: NamedIndividual
has db xref: nlx_156247
synonym: Florida Agricultural and Mechanical University Drug Discovery Core Facility
IAO_0000115: A core facility at the Florida Agricultural and Mechanical University.

FAMU Flow cytometry laboratory
type: Organization
type: NamedIndividual
has db xref: nlx_156248
synonym: Flow Cytometry facility at Florida A&M University
IAO_0000115: A laboratory equipped with laser-based flow cytometric instruments, the main one being the Becton Dickinson two-laser FACScalibur analyzer. This facility provides a resource for analytical and preparative studies of cells using flow cytometry to the FAMU biomedical researchers. This facility offers FACS acquisition and analysis for detecting cell surface or intracellular proteins, measuring apoptosis, cell cycle, cellular physiology that have both biomedical and clinical applications.

jmzIdentML API
type: Resource
type: NamedIndividual
has db xref: OMICS_03339
IAO_0000115: A Java application programming interface (API) for the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) mzIdentML standard for peptide and protein identification data.

HMS NERCE FACSCalibur Flow Cytometer Resource
type: Resource
type: NamedIndividual
has db xref: nlx_156273
IAO_0000115: Core facility that provides the following services: Flow cytometry assay service, Data management system. The BD FACSCalibur system combines unique dual-laser technology, an automated sample loader option, and powerful software to provide the high throughput necessary to meet productivity requirements of clinical laboratories. The modularity and innovative technology designed into the BD FACSCalibur system also offers investigators the performance and flexibility required for a variety of research applications. Please note that since the NERCE program will end in February 2014, our ability to support new requests for services is limited.

Harvard HSCI iPS Cell Core Facility
type: Organization
type: NamedIndividual
has db xref: nlx_156318
IAO_0000115: A lab facility that aims to accelerate research in the stem cell field by facilitating the derivation and distribution of induced pluripotent stem cell lines. Disease-specific pluripotent stem cell lines can provide the opportunity to study the mechanisms of disease and develop treatments. The core facility serves as a repository for iPS cells produced by HSCI scientists.

Harvard NeuroDiscovery Center - Biomarker Study
type: Resource
type: NamedIndividual
has db xref: nlx_156319
abbrev: HNDC Biomarker Study
IAO_0000115: Core facility that provides the following services: Sample processing/storage. The Harvard NeuroDiscovery Center Biomarker Study aims to discover and validate biomarkers for neurodegenerative diseases.

Harvard Partners HealthCare Center for Personalized Genetic Medicine Bioinformatics Core Facility
type: Resource
type: NamedIndividual
has db xref: nlx_156324
synonym: bioinformatics
synonym: PCPGM
synonym: The Partners HealthCare Center for Personalized Genetic Medicine
IAO_0000115: Core to provide gene expression data analysis service. Activities range from the provision of services to fully collaborative grant funded investigations.

Hunter NMR Spectroscopy Facility
type: Organization
type: NamedIndividual
has db xref: nlx_156342
IAO_0000115: A service facility with four main spectrometers. The facility consists of four NMR instruments: a JEOL GX-400, a Varian Inova 500, a Bruker Avance 500 equipped with a 13C-1H cryoprobe, and a Bruker Avance III 600 MHz spectrometer equipped with a cryoprobe. These spectrometers are utilized by scientists from Hunter College, as well as from the entire CUNY community. The large variety of available probes allows detection of virtually any MR-active nuclide. Data analysis is performed either at the spectrometer workstation with vendor software or off-line with third party software packages.

JSU Environmental Toxicology Core Lab
type: Organization
type: NamedIndividual
has db xref: nlx_156361
synonym: Jackson State University Environmental Toxicology Lab
IAO_0000115: A research laboratory and facility which supports research on environmental toxicology at Jackson State University.

MGH Center for Morphometric Analysis
type: Organization
type: NamedIndividual
has db xref: nlx_156387
IAO_0000115: A center dedicated to developing and applying morphometric methods to biomedical imaging data such as high-resolution MRI. The lab uses automated and semi-automated software such that MRI brain images are segmented into anatomical regions of interest. Projects in both basic and applied brain research include research on strokes and tumors; medical image processing research includes shape analysis of anatomical brain regions and measurement and analysis of brain volumes.

MGH Vector Development and Production Core Facility
type: Organization
type: NamedIndividual
has db xref: nlx_156398
IAO_0000115: A lab facility that provides viral vectors with custom-designed promoters and reporter genes and capacity for gene regulation. Services include DNA packaging and purification and titering and allocation of viral vectors.

MSU Magnetic Resonance Core Laboratory
type: Organization
type: NamedIndividual
has db xref: nlx_156410
IAO_0000115: A lab facility at Montana State University dedicated to utilizing MRI technologies to research applications of magnetic resonance microscopy (MRM) methods in the study of transport phenomena and material characterization. Research areas of this lab include: ceramics and foams, colloidal suspensions, biofilms, porous media, gels, and techniques and equipment.

Penn Diabetes Research Center Mouse Phenotyping Physiology and Metabolism Core
type: Resource
type: NamedIndividual
has db xref: nlx_156493
IAO_0000115: Core which provides researchers with resources for performing metabolic studies in mice. It also provides services, innovative techniques, and helpful consultation to both experienced and novice investigators with regards to metabolic questions.

Penn Research Instrumentation Shop
type: Organization
type: NamedIndividual
has db xref: nlx_156500
IAO_0000115: A nonprofit machine shop at the University of Pennsylvania, Perelman School of Medicine. It aims to assist university faculty in the design and construction of both laboratory and clinical instrumentation. The shop's staff include both mechanical and optical specialists that have experience collaborating with scientists to design the custom clinical research instrumentation they needed.

Penn Small Animal Imaging Facility: PET/SPECT/CT Sub-Core
type: Resource
type: NamedIndividual
has db xref: nlx_156504
IAO_0000115: Core facility that provides the following services: PET/SPECT/CT image analysis.

Penn Translational Biomarker Core
type: Resource
type: NamedIndividual
has db xref: nlx_156508
IAO_0000115: Core facility that provides the following services: Biomarker quantification by mass spectrometry. This core provides sophisticated analytical services based on liquid chromatography-mass spectrometry.

UH Manoa Insect Museum
type: Organization
type: NamedIndividual
has db xref: nlx_156570
IAO_0000115: A museum and center for insect identification and systematic research. The museum has workspace equipment, resources for taxonomic analysis and researchers from different laboratories that collaborate.

UTEP BSL 3 Laboratory
type: Organization
type: NamedIndividual
has db xref: nlx_156616
IAO_0000115: A lab and program dedicated to developing diagnostic tests, vaccines and biomarkers of infectious agents that are prevalent in the El Paso, Ciudad Juarez and McAllen Texas border communities. The BSL 3 lab's research interests include the West Nile virus and Myobacterium tuberculosis.

UTSA Engineering Core
type: Organization
type: NamedIndividual
has db xref: nlx_156625
synonym: University of Texas at San Antonio Engineering Core
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 13,2025. Core facility located at the University of Texas at San Antonio.

Vanderbilt Flow Cytometry Core Laboratory
type: Resource
type: NamedIndividual
has db xref: nlx_156656
IAO_0000115: Core facility that provides the following services: FACS AriaCell Sorting, LSRII-Analytical Cytometry, AutoMacs-Magnetic Sorting, EasyCyte-Cell Counting/Viability. We enjoy state-of-the-art digital instrumentation maintained at the highest standards we can attain. This quality control allows researchers to sort cells at high efficiency and purity under the proper conditions or to run analytical experiments with as many as 17 different fluorochromes simultaneously. We are dedicated to providing the best service and training possible to ensure the best results attainable for our research scientists and physicians. Please investigate the pages of this website to address your scheduling needs and questions relating to flow cytometry research, methods and fees

Vanderbilt Diabetes Research and Training Center Islet Procurement and Analysis Core
type: Resource
type: NamedIndividual
has db xref: nlx_156666
abbrev: VU IPA Core
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 13,2025.Core facility that provides access to isolated pancreatic islets from normal and diabetic models and performs islet functional analysis. The IPA Core also provides solutions for high-resolution whole slide imaging and access to image analysis tools for quantitative assessment of pancreatic islet morphology.

Vanderbilt X-Ray Photoelectron Spectroscopy Lab
type: Resource
type: NamedIndividual
has db xref: nlx_156680
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 13,2025.Lab with access to the PHI Versaprobe, a surface-sensitive analytical tool for identifying elemental composition and local bonding environment.

Wyss Institute Imaging Core
type: Organization
type: NamedIndividual
has db xref: nlx_156690
IAO_0000115: A core facility with access to imaging equipment and analysis software such as wide-field light microscopy, Total Internal Reflection Fluorescence microscopy (TIRF), confocal microscopy, Atomic Force Microscopy (AFM), Transmission Electron Microscopy (TEM), small animal imaging, spectroscopy, and flow cytometry.

XULA Materials Research - Shared Instrumentation Facilities
type: Organization
type: NamedIndividual
has db xref: nlx_156696
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 13,2025. Network of shared instrumentation facilities across Xavier University's research community.

CDC Toxprofiles
type: Resource
type: NamedIndividual
has db xref: nlx_156852
IAO_0000115: A database of information about contaminants found at hazardous waste sites. The toxicological profiles are cataloged by chemical with the NTIS order number.

ZooBank
type: Organization
type: NamedIndividual
has db xref: nlx_156872
IAO_0000115: A database of scientific names in zoology. ZooBank is an online, open-access, community-generated registry for zoological nomenclature. It serves as a service to taxonomists, biologists, and the global diversity informatics community. It is the Official Register of the International Commission on Zoological Nomenclature (ICZN).

SoftBerry
type: Resource
type: NamedIndividual
has db xref: nlx_156881
synonym: Linux SoftBerry
synonym: Soft berry
IAO_0000115: Developer of software tools for genomic research focused on computational methods of high throughput biomedical data analysis, including software to support next generation sequencing technologies, transcriptome analysis with RNASeq data, SNP detection and selection of disease specific SNP subsets. Provides custom genome annotation services.

Spike2 Software
type: Resource
type: NamedIndividual
has db xref: nlx_156886
has db xref: rid_000090
synonym: Spike2
synonym: Spike 2 software Cambridge Electronic Device
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 23,2022. A data acquisition and analysis software package for electrophysiology data. Spike2 software offers multi-channel continuous data acquisition and analysis with a multitude of options. This offers flexible usage from a simple chart recorder to complex applications requiring stimulus generation, data capture, scrolling or triggered displays, control of external equipment, and custom analysis. Spike2 software can be used in many fields such as electrophysiology, neurophysiology, cardiovascular and respiratory studies, sports science and pharmacology.

DANS
type: Organization
type: NamedIndividual
has db xref: DOI:10.17026
has db xref: grid.500519.8
has db xref: ISNI: 0000 0001 2179 2789
has db xref: nlx_156902
has db xref: Wikidata: Q13570995
synonym: Data Archiving and Networked Services
synonym: EASY
IAO_0000115: Netherlands institute for permanent access to digital research resources. DANS encourages researchers to make their digital research data findable, accessible, interoperable and reusable. It does this by providing expert advice and certified services.

DHS Program
type: Organization
type: NamedIndividual
has db xref: nlx_156927
synonym: The Demographic and Health Surveys Program
IAO_0000115: A program that provides technical assistance for surveys that aim to advance global understanding of health and population trends in developing countries. The DHS program collects, analyzes, and disseminates accurate and representative data on population, health, HIV, and nutrition through more than 300 surveys in over 90 countries.

Amphibian Taxonomy Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157317
abbrev: ATO
IAO_0000115: A taxonomy of Amphibia

Anatomic Pathology Lexicon
type: Resource
type: NamedIndividual
has db xref: nlx_157318
abbrev: PATHLEX
IAO_0000115: A comprehensive lexicon - a unified language of anatomic pathology terms - for standardized indexing and retrieval of anatomic pathology information resources.

HIV ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157422
abbrev: HIV
IAO_0000115: Ontology that encompasses all knowledge about HIV

International Classification of Primary Care - 2 PLUS
type: Resource
type: NamedIndividual
has db xref: nlx_157454
abbrev: ICPC2P
IAO_0000115: Ontology of the international classification of primary care -2 PLUS

Mathematical Modelling Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157467
abbrev: MAMO
IAO_0000115: Ontology that is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features.

Nursing Interventions Classification
type: Resource
type: NamedIndividual
has db xref: nlx_157512
abbrev: NIC
IAO_0000115: Ontology of nursing interventions classification.

Phylogenetic Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157550
abbrev: PHYLONT
IAO_0000115: Ontology for Phylogenetic Analysis

Alaska Climate Research Center
type: Resource
type: NamedIndividual
has db xref: nlx_157755
IAO_0000115: Archive of digital climate records, climate statistics, and monthly weather summaries on Alaska and the polar regions.

Frontier Scientific Chemical Supplier
type: Organization
type: NamedIndividual
has db xref: grid.504592.f
has db xref: nlx_157824
IAO_0000115: A commercial vendor of chemicals that provides custom synthesis of a wide variety of organic compounds. Frontier Scientific has capabilities for custom work in organoborons, organotins, porphyrins, silanes, halogenations, catalysts and cross couplings using Suzuki, Stille, and Kumada processes.

hivebench
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_158032
IAO_0000115: A commercial software laboratory notebook.

Makray Family Foundation
type: Organization
type: NamedIndividual
has db xref: nlx_158459
IAO_0000115: Non-profit charitable organization that benefits philanthropy, voluntarism and grantmaking foundations, focusing specifically on private independent foundations programs. (http://non-profit-organizations.findthebest.com/l/558154/Makray-Family-Foundation)

BC Fisheries Living Gene Bank
type: Resource
type: NamedIndividual
has db xref: nlx_17177
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. An ichtyological gene bank with data from fisheries in British Columbia, Canada.

Coreva Human Milk Bank
type: Organization
type: NamedIndividual
has db xref: nlx_28858
IAO_0000115: Resource is currently not in service, documented July 29, 2016.

PCR Blog
type: Resource
type: NamedIndividual
has db xref: nlx_38687
IAO_0000115: A blog that contains reviews and information on PCR methods, applications and technology. Topics include tips and advice, troubleshooting, optimization and up-to-date information on the polymerase chain reaction.

Taburit Umbilical Cord Blood Bank
type: Resource
type: NamedIndividual
has db xref: nlx_38777
synonym: Tamburit
IAO_0000115: A blood bank that operates as the marketing arm for the family cord blood banking operations of Sheba Medical Center. It is the largest medical center in the Middle East with a 24/7 call center to answer questions. The center provides collection kits, supervises the collection process, and transports the collected blood to the Sheba Cord Blood Bank.

Babel's Dawn
type: Organization
type: NamedIndividual
has db xref: nlx_39156
IAO_0000115: A blog about the origins of speech by Edmund Blair Bolles. The topics include book recommendations, commentary on linguistic theories, and other informational articles. Babel's Dawn is a book by Bolles that discusses the natural history of the origins of speech.

NeuroBase
type: Resource
type: NamedIndividual
has db xref: nlx_44174
IAO_0000115: A database of gene transcription in neurons derived from Next Gen sequencing. Transcriptomes hosted on this database were designed and constructed at the University of Florida.

Hanalyzer
type: Resource
type: NamedIndividual
has db xref: nlx_48287
synonym: Hanalyzer: A 3R System
IAO_0000115: An open-source data integration system designed to assist biologists in explaining the results observed in genome-scale experiments as well as generating new hypotheses. It combines information extraction techniques, semantic data integration, and reasoning and facilitates network visualization. The Hanalyzer source code and binaries are available for download.

K Bar Livestock
type: Organization
type: NamedIndividual
has db xref: nlx_52158
synonym: K Bar Livestock LLC
synonym: K-Bar Livestock
IAO_0000115: A business that supplies livestock organisms and equipment to biomedical researchers and teachers. Examples of services include livestock such as sheep, goats, swine, and calves; materials such as blood, isolated tissue, feed, hay, equipment; and timed pregnancies and pre-delivery laboratory tests.

60-Second Mind
type: Organization
type: NamedIndividual
has db xref: nlx_52233
IAO_0000115: A podcast of neuroscience news in minute-intervals from the Scientific American. New episodes become available every Saturday.

Australia Breast Cancer Tissue Bank
type: Organization
type: NamedIndividual
has db xref: nlx_54620
abbrev: ABCTB
IAO_0000115: A tissue bank which houses and supplies cancerous tissue for use by the research community. Along with tissue, the bank collects clinical history, lifestyle factors, breast pathology, treatment information, and follow up information.

Latvia Biobank
type: Organization
type: NamedIndividual
has db xref: nlx_55758
abbrev: VIGDB
IAO_0000115: A tissue donation bank based in Latvia. This resource is in Latvian.

JISC Blog
type: Resource
type: NamedIndividual
has db xref: nlx_57936
IAO_0000115: A blog of up-to-the-minute insights into the innovative use of technology in further and higher education.

ENA Sequence Version Archive
type: Resource
type: NamedIndividual
has db xref: nlx_59165
synonym: EMBL-SVA
synonym: Sequence Version Archive
abbrev: SVA
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 23,2022. The ENA Sequence Version Archive is a repository of all entries which have ever appeared in EMBL-Bank Sequence Database. You can browse the archive or use the batch retrieval form.

PhenoBank
type: Resource
type: NamedIndividual
has db xref: nlx_73232
IAO_0000115: A database that provides primary data from two high-content screens that profile the set of ~900 essential C. elegans genes (~5% of the genome) required for embryo production and/or events during the first two embryonic divisions. Phenobank houses the movies, scored defects, and phenotypic classification data for the embryo-filming and gonad morphology screens.

Research Information Network
type: Organization
type: NamedIndividual
has db xref: nlx_77489
IAO_0000115: A network resource that aims to enhance and broaden understanding of how researchers in the UK create and use information resources. The network provides services of all kinds to support the development of effective policies and practices for researchers, institutions, funders, information professionals and everyone who is involved in the information landscape.

Nothing's Shocking
type: Organization
type: NamedIndividual
has db xref: nlx_80372
IAO_0000115: A neuroscience blog written by Noah Gray.

Bio-Job.org
type: Resource
type: NamedIndividual
has db xref: nlx_81563
IAO_0000115: Bio-Job.org is a sister site to PROTOCOL-ONLINE.ORG and offers free job posting to not-for-profit employers such as universities, governments, research institutions/organizations. Currently industrial job listing is also free. * Employer's Services: Post a Job, Manage Jobs Posts, View Resumes * Jobseeker: Announce your availability and submit your resume to hundreds of Employers that visit this site. Employers can contact you directly as soon as a suitable position becomes available. Why is this site created: It's never been an easy job to recruit qualified people for employer or PI who runs a lab--Not only have you to pay a fee for job listing that could be as high as hundreds of dollars, you have to go through all the hassle of setting up an account, dealing with your account manager and making the payment. In an era when science is free, genome data is free, publications are free, and why is job posting not free? With this belief in mind, we created this site to allow free job posting for academia. What types of jobs can be posted here: Jobs in any scientific discipline and biotech jobs can be posted.

Broad Minded
type: Organization
type: NamedIndividual
has db xref: nlx_88552
synonym: Broad Blog
synonym: Broad Minded blog
IAO_0000115: A blog that serves as a forum for disseminating the science, culture, and life of the Broad Institute. Broad Minded provides content that comes from the collaboration of the Broad community.

Taizhou Biobank
type: Organization
type: NamedIndividual
has db xref: nlx_88700
IAO_0000115: THIS RESOURCE IS NOT IN SERVICE, documented August 9, 2016. A genetic biobank in Taizhou, China which plans to collect five million samples in 10 years.

Medscape Education - Medscape CME/CE
type: Organization
type: NamedIndividual
has db xref: nlx_91735
synonym: Medscape CME/CE
synonym: Medscape Education Medscape CME/CE
synonym: MedscapeCME
IAO_0000115: A portal with listings of continuing medical education opportunities such as radiology, pediatrics, and HIV/AIDS specializations.

SpinalGraft Technologies LLC
type: Organization
type: NamedIndividual
has db xref: nlx_92159
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 02, 2016.

BrainPains
type: Organization
type: NamedIndividual
has db xref: nlx_94026
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 28, 2016.

Korean National Tissue Bank
type: Organization
type: NamedIndividual
has db xref: nlx_97045
IAO_0000115: A national tissue bank that provides management for database purposes, on-line ordering, guidelines, educational programs, policy making and certification of resources.

Banco de datos de biodiversidad del Ecuador
type: Resource
type: NamedIndividual
has db xref: nlx_98270
IAO_0000115: A searchable database of biology-related data based in Ecuador.

SciRoKo
type: Resource
type: NamedIndividual
has db xref: OMICS_00113
IAO_0000115: Comparative genomics software that assists in whole genome microsatellite search and investigation. The command line version is called SciRoKoCo. The perl script DesignPrimer can be used to design PCR primer pairs for the SciRoKo output.

HapCompass
type: Resource
type: NamedIndividual
has db xref: OMICS_00197
IAO_0000115: Software that utilizes a fast cycle basis algorithm for the accurate haplotype assembly of sequence data. It is able to create pairwise SNP phasings.

Functional Biosciences
type: Organization
type: NamedIndividual
has db xref: SciEx_9422
synonym: Functional Biosciences Inc.
IAO_0000115: A service that provides low cost DNA sequencing. They utilize microfluidic technology.

Macquarie University Labs and Facilities
type: Organization
type: NamedIndividual
has db xref: SciEx_9680
synonym: Macquarie University Labs Facilities
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. Set of facilities based out of Macquarie University in New South Wales. Some facilities provide services such as proteome analysis or resources of various academic departments like engineering, biological sciences, and geography.

Macquarie University NMR Facility
type: Organization
type: NamedIndividual
has db xref: SciEx_9684
synonym: Macquarie NMR Facility
synonym: Macquarie University Department of Chemistry and Biomolecular Sciences NMR Facility
synonym: MQ NMR Facility
IAO_0000115: A facility that houses NMR spectroscopy services. It has a state-of-the-art facility including 400 and 600 MHz NMR spectrometers, the latter with a cryoprobe. All 1D and 2D NMR experiments are performed as per customer requests. They also offer a consultative service and spectral interpretation.

A.T.Still University; Arizona; USA
type: Organization
type: NamedIndividual
has db xref: grid.251612.3
has db xref: ISNI:0000 0004 0383 094X
has db xref: nlx_34827
has db xref: Wikidata:Q4647420
synonym: A.T. Still University
abbrev: ATSU
IAO_0000115: A university which provides programs in medical postgraduate studies as well as graduated health sciences.

Aalto University; Espoo; Finland
type: Organization
type: NamedIndividual
has db xref: nlx_155549
synonym: Aalto University
synonym: Aalto-universitetet
synonym: Aalto-yliopisto
IAO_0000115: The unification of three major universities in Finland - the Helsinki University of Technology, Helsinki School of Economics and the University of Art and Design Helsinki.

Aarhus University; Aarhus; Denmark
type: Organization
type: NamedIndividual
has db xref: nlx_156945
synonym: Aarhus Universitet
synonym: Aarhus University
synonym: University of Aarhus
abbrev: AU
IAO_0000115: A public university in Denmark that offers degrees at the undergraduate and graduate level in fields such as engineering, nanotechnology, medicine and modern languages.

Aberystwyth University; Wales; United Kingdom
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100000315
has db xref: grid.8186.7
has db xref: ISNI:121682483
has db xref: nlx_149415
has db xref: Wikidata:Q319761
synonym: Prifysgol Aberystwyth
synonym: Prifysgol Aberystwyth University
IAO_0000115: A public research university located in Wales, United Kingdom. The university offers degrees at the undergraduate and postgraduate level in fields from physics and earth sciences to creative writing and international politics.

Academia Sinica; Taipei; Taiwan
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100001869
has db xref: grid.28665.3f
has db xref: ISNI:0000 0001 2287 1366
has db xref: nlx_89460
has db xref: Wikidata:Q337266
IAO_0000115: The national academy of Taiwan that supports research activities in a wide variety of disciplines, ranging from mathematical and physical sciences, to life sciences, and to humanities and social sciences. The institution plays a particularly important role in the academic field of Chinese Studies.

Australian Research Council
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100000923
has db xref: grid.413452.5
has db xref: ISNI: 0000 0004 0611 9213
has db xref: nlx_156882
has db xref: Wikidata: Q4824612
synonym: ARC
IAO_0000115: An Australian government agency that allocates research funding to academics and researchers at Australian universities. The mission of the council is to deliver policy and programs that advance Australian research, spur innovation and benefit the community.

Austrian Academy of Sciences; Vienna; Austria
type: Organization
type: NamedIndividual
has db xref: nlx_99930
IAO_0000115: A national academy in Austria that promotes the sciences and humanities, especially in research. Resource is in German.

August Pi i Sunyer Biomedical Research Institute; Barcelona; Spain
type: Organization
type: NamedIndividual
has db xref: nlx_158267
synonym: August Pi i Sunyer Biomedical Research Institute
synonym: Institut d''Investigacions Biomediques August Pi i Sunyer
synonym: Institut d''Investigacions Biomèdiques August Pi i Sunyer
synonym: Institut d''Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)
abbrev: IDIBAPS
IAO_0000115: A biomedical research center in Barcelona. The institute focuses on encouraging translational research, innovation and technological progress, and the development of programs that address diseases with high morbidity and mortality.

Austrian Agency for Health and Food Safety
type: Organization
type: NamedIndividual
has db xref: grid.414107.7
has db xref: ISNI: 0000 0001 2224 6253
has db xref: nlx_157916
synonym: Austrian Agency for Health and Food Safety (AGES)
abbrev: AGES
IAO_0000115: A company based in Austria that supports the management of federal agencies relating to public health, animal health, food safety, medical and drug safety, food security and consumer protection. They provide professional and scientific expertise.

Biomedical University Campus of Rome; Rome; Italy
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100003765
has db xref: grid.9657.d
has db xref: ISNI:0000 0004 1757 5329
has db xref: nlx_158520
has db xref: Wikidata:Q1440288
synonym: Bio-medical University Campus of Rome
synonym: Biomedical University Campus of Rome
synonym: Biomedical University of Rome
synonym: Universita Campus Bio Medico di Roma
synonym: Universita Campus Bio-Medico
synonym: University Campus Bio-Medical of Rome
synonym: University Campus Bio-Medico of Rome
synonym: Universit� Campus Bio-Medico
synonym: Universit� Campus Bio-Medico di Roma
abbrev: Campus Bio-Medico
IAO_0000115: A university in Rome that confers degrees in medicine, nursing, dieticians, the science of alimentation, and biomedical engineering.

Brown University; Rhode Island; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100006418
has db xref: grid.40263.33
has db xref: ISNI:0000 0004 1936 9094
has db xref: nlx_78147
has db xref: Wikidata:Q49114
synonym: Brown
IAO_0000115: A private, Ivy League research university in Rhode Island, USA. The university offers degrees at the undergraduate and graduate level in a wide variety of fields.

Catholic University of the Sacred Heart; Milan; Italy
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100005743
has db xref: grid.8142.f
has db xref: ISNI:0000 0001 0941 3192
has db xref: nlx_158321
has db xref: Wikidata:Q229022
synonym: Catholic University of the Sacred Heart
synonym: Universita Cattolica
synonym: Universita Cattolica del Sacro Cuore
synonym: Universit� Cattolica
synonym: Universit� Cattolica del Sacro Cuore
abbrev: UCSC
IAO_0000115: An Italian private research university that offers undergraduate, graduate and postdoctoral level degrees in both Italian and English.

Curie Institute; Paris; France
type: Organization
type: NamedIndividual
has db xref: nlx_156709
synonym: Curie Institute
synonym: Institut Curie
IAO_0000115: A private, non-profit foundation that operates a research center on biophysics, cell biology and oncology. The institute, located in Paris, France, is also home to a hospital that specializes in the treatment of cancer.

Ecole Normale Superieure; Paris; France
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100007649
has db xref: grid.5607.4
has db xref: ISNI: 121105547
has db xref: nlx_73418
has db xref: Wikidata: Q83259
synonym: Ecole Normale Superieure
synonym: �cole Normale Sup�rieure
abbrev: ENS
IAO_0000115: A higher education institute for advanced undergraduate and graduate studies in France. The institute has fourteen teaching and research departments that span the humanities and sciences.

Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland
type: Organization
type: NamedIndividual
has db xref: nlx_151927
synonym: Ecole Polytechnique Federale de Lausanne
synonym: Ecole polytechnique fédérale de Lausanne
synonym: Federal Polytechnic School of Lausanne
synonym: École Polytechnique Fédérale de Lausanne
abbrev: EPFL
IAO_0000115: A research institute in Lausanne, Switzerland that specializes in the physical sciences and engineering.

ETH Zurich; Zurich; Switzerland
type: Organization
type: NamedIndividual
has db xref: nlx_143698
synonym: Eidgenossische Technische Hochschule Zurich
synonym: Eidgenössische Technische Hochschule Zürich
synonym: ETH Zurich
synonym: ETH Zürich
synonym: Swiss Federal Institute of Technology Zurich
abbrev: ETH
IAO_0000115: Public institute of technology in Zurich, Switzerland that specializes in science, technology, mathematics and management. École Polytechnique Fédérale de Lausanne is its sister university.

European Food Safety Authority
type: Organization
type: NamedIndividual
has db xref: grid.483440.f
has db xref: ISNI: 0000 0004 1792 4701
has db xref: nlx_157920
has db xref: Wikidata: Q516521
abbrev: EFSA
IAO_0000115: A government granting agency which consults with partnered programs through national authorities and food safety agencies. EFSA organizes its annual and multi-annual work program according to priorities agreed with the European Commission and other partners, taking into account available resources. EFSA staff may also produce scientific outputs on behalf of the agency, such as peer reviews of the assessment of active substances in pesticides, or responses to urgent requests for advice. EFSA staff also monitor and analyze information and data on biological hazards, chemical contaminants, food consumption and emerging risks.

Franklin and Marshall College; Pennsylvania; USA
type: Organization
type: NamedIndividual
has db xref: grid.256069.e.
has db xref: nlx_36085
has db xref: Wikidata:Q664881
synonym: F and M
synonym: FandM
synonym: Franklin and Marshall
IAO_0000115: A private, co-educational liberal arts college in Lancaster, Pennsylvania.

Fudan University; Shanghai; China
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100003347
has db xref: grid.8547.e
has db xref: ISNI:0000 0001 0125 2443
has db xref: nlx_86135
has db xref: Wikidata:Q495015
IAO_0000115: A public university in Shanghai, China that confers undergraduate and graduate degrees.

Genome Canada
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100008762
has db xref: grid.440163.4
has db xref: ISNI: 0000 0001 0352 8618
has db xref: nlx_151964
has db xref: Wikidata: Q3123000
IAO_0000115: Genome Canada is a non-profit organization that is funded by the Government of Canada. The organization funds large-scale science and technology to fuel innovation regarding genomics in multiple sectors such as health, agriculture and agri-food, forestry, fisheries and aquaculture, environment, energy and mining. They create partnerships at the program and research project levels.

Greek General Secretariat of Research and Technology
type: Organization
type: NamedIndividual
has db xref: nlx_151781
synonym: General Secretariat for Research and Technology (GSRT)
abbrev: GSRT
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 15,2025. Greek government funding agency for scientific research institutes for advanced ΙΤ systems and networks. The agency promotes the transfer and dissemination of advanced technologies throughout the country's productive sector through funding. This organization focuses on sectors important for the the improvement of the national economy by establishing new institutes and technological centers important for the development of the Greek economy.

Indian Council of Medical Research; New Delhi; India
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100001411
has db xref: grid.19096.37
has db xref: ISNI: 0000 0004 1767 225X
has db xref: nlx_151509
has db xref: Wikidata: Q291019
abbrev: ICMR
IAO_0000115: A government-funded council for the promotion and coordination of biomedical research in India. The council focuses on specific diseases such as HIV/AIDS, tuberculosis, and leprosy in addition to national health priorities including the management of communicable diseases, fertility control, and mental health research.

Indian Institute of Science; Bangalore; India
type: Organization
type: NamedIndividual
has db xref: nlx_73023
synonym: Indian Institute of Science
abbrev: IISc
IAO_0000115: A public research university for science and higher education in India. The university has six main divisions, including the biological sciences, chemical sciences, electrical sciences, mechanical sciences, physical and mathematical sciences, and interdisciplinary research.

Institute of Statistical Mathematics; Tokyo; Japan
type: Resource
type: NamedIndividual
has db xref: nlx_149272
synonym: Institute of Statistical Mathematics
abbrev: ISM
IAO_0000115: The Institute of Statistical Mathematics (ISM) is a national research institute in Tokyo, Japan that conducts studies relating to theory and application of statistics and data science. IMS focuses on data-centric science, which includes fields of engineering involving massive data, statistical science, computer science, machine learning, and data mining.

International Institute of Molecular and Cell Biology; Warsaw; Poland
type: Organization
type: NamedIndividual
has db xref: grid.419362.b
has db xref: nlx_156957
synonym: International Institute of Molecular and Cell Biology
synonym: International Institute of Molecular and Cell Biology (IIMCB)
abbrev: IIMCB
IAO_0000115: International Institute of Molecular and Cell Biology creates partnerships with research centers within and outside Poland. This organization provides a base of administration, management of finances and resources, sharing space and equipment, grant writing and grant management procedures, etc. They organize workshops, training courses, conferences and other scientific events for researchers of various specialties and nationalities. Additionally, this organization commercializes results to provide biotechnological solutions with regards to the global economy and global research services deals.

Iowa State University; Iowa; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100009227
has db xref: grid.34421.30
has db xref: ISNI:0000 0004 1936 7312
has db xref: nlx_75450
has db xref: Wikidata:Q1136919
synonym: Iowa State University
synonym: Iowa State University (ISU)
abbrev: ISU
IAO_0000115: Iowa State University (ISU) is an undergraduate, graduate and research institute. ISU has 100 majors and upwards of 800 student organizations.

Johns Hopkins University School of Medicine; Baltimore, Maryland; USA
type: Organization
type: NamedIndividual
has db xref: GRID: grid.469474.c
has db xref: ISNI: 0000 0000 8617 4175
has db xref: nlx_76328
has db xref: Wikidata: Q50363516
synonym: Johns Hopkins Medicine
synonym: Johns Hopkins University School of Medicine
synonym: Johns Hopkins University School of Medicine (JHM)
abbrev: JHM
IAO_0000115: Johns Hopkins University School of Medicine is a medical graduate institution that provides physician, clinical fellowship and residency programs.

Jozef Stefan Institute; Ljubljana; Slovenia
type: Resource
type: NamedIndividual
has db xref: nlx_153883
synonym: Institut Joef Stefan
synonym: Jozef Stefan Institute
abbrev: IJS
abbrev: JSI
IAO_0000115: A scientific research institute that is involved with a broad spectrum of basic and applied research. Some of the areas they focus on include production and control technologies, communication and computer technology, and energy utilization and environmental science. They also engage in collaborations to develop medical equipment and new diagnostic methods into clinical medicine.

Liverpool John Moores University; Liverpool; United Kingdom
type: Organization
type: NamedIndividual
has db xref: nlx_158057
synonym: Liverpool John Moores University
synonym: Liverpool John Moores University (LJMU)
abbrev: LJMU
IAO_0000115: Liverpool John Moores University provides undergraduate, masters, and doctorate programs.

Loma Linda University; California; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100008891
has db xref: grid.43582.38
has db xref: ISNI:0000 0000 9852 649X
has db xref: nlx_86012
has db xref: Wikidata:Q1057447
synonym: Loma Linda University (LLU)
abbrev: LLU
IAO_0000115: Loma Linda University (LLU) is a Seventh-day Adventist educational health-sciences institution comprised of eight schools. Programs such as Allied Health Professions, Dentistry, Medicine, Nursing, Pharmacy, Public Health, Religion and Science and Technology are offered by the school. Curricula offered range from certificates of completion and associate in science degrees to doctor of philosophy and professional doctoral degrees. LLU also offers distance education.

Massachusetts Institute of Technology; Massachusetts; USA;
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100006919
has db xref: grid.116068.8
has db xref: ISNI: 0000 0001 2341 2786
has db xref: nlx_32884
has db xref: SCR_016675
has db xref: Wikidata: Q49108
synonym: Massachusetts Institute of Technology (MIT)
synonym: Massachusetts Institute of Technology; Cambridge; USA;
synonym: MIT; Cambridge; Massachusetts; United States
abbrev: MIT
IAO_0000115: Independent, coeducational, privately endowed university, organized into five schools: architecture and planning; engineering; humanities, arts, and social sciences; management; and science.

Max Planck Institute for Marine Microbiology; Bremen; Germany
type: Organization
type: NamedIndividual
has db xref: grid.419529.2
has db xref: ISNI: 0000 0004 0491 3210
has db xref: nlx_81711
has db xref: Wikidata: Q876880
synonym: max planck institut fur marine mikrobiologie
synonym: Max Planck Institute for Marine Microbiology
abbrev: MPI
IAO_0000115: The Max Planck Institute for Marine Microbiology is an international university that offers the PhD programme International Max-Planck Research School (IMPRS) of Marine Microbiology (Marmic) together with the Alfred Wegener Institute for Polar and Marine Research, the University of Bremen and Jacobs University Bremen. Currently, the institute consists of four departments with several associated research groups: Microbiology, Biogeochemistry, Molecular Ecology, and Symbiosis.

Montana State University
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100009501
has db xref: grid.41891.35
has db xref: ISNI:0000 0001 2156 6108
has db xref: nlx_53872
has db xref: Wikidata:Q1861687
synonym: Montana State
synonym: Montana State University (MSU)
abbrev: MSU
IAO_0000115: Montana State University is a university institute has programs for undergraduate, master's and doctoral degrees. There are 54 master's degree options, 37 doctoral degree options including one specialist program, and 14 certificate options.

National Cheng Kung University; Tainan; Taiwan
type: Organization
type: NamedIndividual
has db xref: nlx_34096
synonym: Guoli Chenggong Daxue
synonym: National Cheng Kung University
synonym: National Cheng Kung University (NCKU)
synonym: NCKU
IAO_0000115: National Cheng Kung University is a research-led comprehensive university in Tainan, Taiwan that has undergraduate, master's, and doctoral degree programs. This university has fields of: science, engineering, medicine, management, planning and design.

National Institute of Health Sciences; Tokyo; Japan
type: Organization
type: NamedIndividual
has db xref: nlx_157927
synonym: National Institute of Health Sciences
synonym: National Institute of Health Sciences (Japan)
synonym: National Institute of Health Sciences - Japan
abbrev: NIHS
IAO_0000115: Japanese national institute that conducts testing, research, and studies toward the proper evaluation of the quality, safety, and efficacy of pharmaceutical products, foods, and numerous chemicals in the living environment. Its major responsibilities involve extensive testing and research to ensure the quality, efficacy, and safety of chemical substances (including pharmaceuticals and food) that are closely related to people's lives.

National Institute on Chemical Dependency
type: Resource
type: NamedIndividual
has db xref: nlx_143601
abbrev: NICD
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 19, 2016.

National Taiwan University; Taipei; Taiwan
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100006477
has db xref: grid.19188.39
has db xref: ISNI:0000 0004 0546 0241
has db xref: nlx_65230
has db xref: Wikidata:Q32746
abbrev: NTU
IAO_0000115: A national research university in Taipei, Taiwan. The university confers degrees at the undergraduate and graduate level bio-resources and agriculture, electrical engineering and computer science, engineering, law, liberal arts, management, medicine, public health, and the social sciences.

National University of Singapore; Singapore; Singapore
type: Organization
type: NamedIndividual
has db xref: nlx_67014
synonym: National University of Singapore
abbrev: NUS
IAO_0000115: A public university located in Singapore that has a wide range of faculties and schools, including arts, business, computing, and dentistry.

Nihon University; Tokyo; Japan
type: Organization
type: NamedIndividual
has db xref: nlx_152063
synonym: Nihon University
IAO_0000115: A private research university in Tokyo, Japan that has undergraduate and graduate degree programs in a wide variety of fields, including in law, humanities, economics, and industrial technology.

NIH Office of Research on Women's Health; Bethesda; Maryland
type: Organization
type: NamedIndividual
has db xref: nlx_152796
synonym: NIH Office of Research on Women's Health
synonym: NIH Office of Research on Womens Health
abbrev: NIH ORWH
abbrev: ORWH
IAO_0000115: The Office of Research on Women's Health (ORWH) is part of the Office of the Director of NIH. ORWH works in partnership with the 27 NIH Institutes and Centers to ensure that women’s health research is part of the scientific framework at the NIH and throughout the scientific community.

NIH Office of Research Services
type: Organization
type: NamedIndividual
has db xref: nlx_inv_1005067
synonym: Office of Research Services
synonym: Office of Research Services - Serving the NIH Community
abbrev: ORS
IAO_0000115: The Office of Research Services (ORS) provides support to the NIH research mission by planning, directing and delivering scientific and regulatory activities, public safety, security, and services for the NIH community.

Netherlands Organization for Scientific Research
type: Organization
type: NamedIndividual
has db xref: nlx_151487
abbrev: NWO
IAO_0000115: Netherlands Organization for Scientific Research (NWO) is a research institute and regional funding source in the Netherlands.

Ontario Ministry of Research and Innovation; Ontario; Canada
type: Organization
type: NamedIndividual
has db xref: nlx_157929
synonym: Ontario Ministry of Research and Innovation
abbrev: ORFAB
IAO_0000115: Ministry that supports research, commercialization and innovation taking place across Ontario through a range of programs and services like the Ontario Research Fund, Innovation Demonstration Fund and Ontario Venture Capital Fund.

Pasteur Institute of Lille; Lille; France
type: Organization
type: NamedIndividual
has db xref: grid.8970.6
has db xref: ISNI: 0000 0001 2159 9858
has db xref: nlx_158125
has db xref: Wikidata: Q3151788
synonym: Institut Pasteur de Lille
synonym: Pasteur Institute of Lille
synonym: Pasteur Lille
synonym: Pasteur-Lille
IAO_0000115: Pasteur Institute of Lille is an international research institute in Lille, France focused on bettering human health by detecting risk factors in degenerative diseases.

Pontifical Catholic University of Argentina; Buenos Aires; Argentina
type: Organization
type: NamedIndividual
has db xref: grid.412525.5
has db xref: ISNI:0000 0001 2097 3932
has db xref: nlx_143718
has db xref: Wikidata:Q973767
synonym: Pontifical Catholic University of Argentina
synonym: Pontificia Universidad Catolica Argentina
abbrev: UCA
IAO_0000115: Pontifical Catholic University of Argentina is a part time MBA program university accredited by the London-based Association of MBAs (AMBA). It is located in Argentina with campuses in the cities of Buenos Aires, Santa Fe, Rosario, Parana, Mendoza and Pergamino.

Royal Institute of Technology; Stockholm; Sweden
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100004270
has db xref: grid.5037.1
has db xref: ISNI: 121581746
has db xref: nlx_48999
has db xref: Wikidata: Q854280
synonym: Royal Institute of Technology
IAO_0000115: Royal Institute of Technology is a university in Stockholm, Sweden that has undergraduate, master's, and doctoral degree programs.

Temple University; Pennsylvania; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100005806
has db xref: grid.264727.2
has db xref: ISNI:0000 0001 2248 3398
has db xref: nlx_32415
has db xref: Wikidata:Q1420239
synonym: Temple University
IAO_0000115: Temple University is a university institute in Pennsylvania, USA that provides undergraduate, graduate and professional degree programs.

Tufts University; Massachusetts; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100008090
has db xref: grid.429997.8
has db xref: ISNI:0000 0004 1936 7531
has db xref: nlx_38314
has db xref: Wikidata:Q49120
synonym: Tufts
synonym: Tufts University
IAO_0000115: Private research university in Medford and Somerville, Massachusetts, United States, with additional facilities in Boston and Grafton, as well as Talloires, France. Provides undergraduate, graduate, and professional degree programs.

Tufts University School of Medicine; Massachusetts; USA
type: Organization
type: NamedIndividual
has db xref: nlx_157971
synonym: Tufts University School of Medicine
abbrev: TUSM
IAO_0000115: University in Massachusetts, USA that provides medical, physical assistant, master's, and health science degree programs.

University of Cambridge; Cambridge; United Kingdom
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100000735
has db xref: grid.5335.0
has db xref: ISNI:121885934
has db xref: nlx_31670
has db xref: Wikidata:Q35794
synonym: University of Cambridge
IAO_0000115: Public research university in Cambridge, United Kingdom. Founded in 1209 is second oldest university in English speaking world.

University of Dundee; Scotland; United Kingdom
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100008890
has db xref: grid.8241.f
has db xref: ISNI:0000 0004 0397 2876
has db xref: nlx_76402
has db xref: Wikidata:Q1249005
synonym: University of Dundee
IAO_0000115: University in Scotland, UK that provides undergraduate and doctoral degree programs.

University of Hawaii; Hawaii; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100008782
has db xref: grid.162346.4
has db xref: ISNI:0000 0001 1482 1895
has db xref: nlx_88254
has db xref: Wikidata:Q217439
synonym: University of Hawaii
abbrev: UH
IAO_0000115: University in Hawaii that provides undergraduate, master's, doctorate, and professional degree programs. Campuses are located in Manoa and in Hilo.

University of Melbourne; Victoria; Australia
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100001782
has db xref: grid.1008.9
has db xref: ISNI:0000 0001 2179 088X
has db xref: nlx_20770
has db xref: Wikidata:Q319078
synonym: University of Melbourne
IAO_0000115: University in Victoria, Australia that provides undergraduate and graduate degree programs.

University of San Diego; California; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100010285
has db xref: grid.267102.0
has db xref: ISNI:104485736
has db xref: nlx_49162
has db xref: Wikidata:Q262663
synonym: University of San Diego
abbrev: USD
IAO_0000115: Private university in San Diego, California that provides undergraduate, master's, doctoral, and professional degree programs.

University of Surrey; Surrey; United Kingdom
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100003513
has db xref: grid.5475.3
has db xref: ISNI:0000 0004 0407 4824
has db xref: nlx_157977
has db xref: Wikidata:Q546976
synonym: University of Surrey
IAO_0000115: Public university in Surrey, UK that provides undergraduate, master's, doctoral, professional, and research degree programs.

University of Ulster; Ulster; Northern Ireland
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100001632
has db xref: grid.12641.30
has db xref: ISNI:105519715
has db xref: nlx_26417
has db xref: Wikidata:Q2096524
synonym: University of Ulster
IAO_0000115: Public university in Ulster, Northern Ireland that provides undergraduate, post graduate and post research degree programs.

University of Utah; Utah; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100007747
has db xref: grid.223827.e
has db xref: ISNI:0000 0001 2193 0096
has db xref: nlx_26775
has db xref: Wikidata:Q168515
synonym: University of Utah
IAO_0000115: Public university in Utah, USA that provides undergraduate, master's, post graduate, graduate, and professional degree programs.

JBrowse
type: Resource
type: NamedIndividual
has db xref: OMICS_00918
IAO_0000115: A high-performance visualization tool for interactive exploration of large, integrated genomic datasets written primarily in JavaScript. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

DSRC
type: Resource
type: NamedIndividual
has db xref: biotools:dsrc
has db xref: OMICS_00955
synonym: DNA Sequence Reads Compression
synonym: DNA Sequence Reads Compression (DSRC)
IAO_0000115: An application designed for compression of data files containing reads from DNA sequencing in FASTQ format. Its main features include multithreaded compression of FASTQ output, python and C++ libraries, and support for lossy IDs compression.

fastqz
type: Resource
type: NamedIndividual
has db xref: biotools:fastqz
has db xref: OMICS_00956
IAO_0000115: Source code used to compress FASTQ files. FASTQ is DNA sequencing machine output.

GDC
type: Resource
type: NamedIndividual
has db xref: OMICS_00958
synonym: GDC 2
synonym: Genome Differential Compressor
synonym: Genome Differential Compressor (GDC)
IAO_0000115: A C++ application designed for compression of genome collections from the same species.

GRS
type: Resource
type: NamedIndividual
has db xref: OMICS_00960
IAO_0000115: A compression tool for efficient storage of Genome Re-Sequencing data. GRS processes genome sequence data without use of reference SNPs and other variants. It can also automatically rebuild the individual genome sequence data using the reference genome sequence.

PREFAB
type: Resource
type: NamedIndividual
has db xref: OMICS_00984
synonym: PREFAB - Protein Reference Alignment Benchmark
synonym: Protein Reference Alignment Benchmark
IAO_0000115: Downloadable data designed for testing multiple sequence alignment methods.

BLASTP
type: Resource
type: NamedIndividual
has db xref: OMICS_00991
synonym: blastp suite
synonym: Standard Protein BLAST
IAO_0000115: Data analysis service whose programs search protein databases using a protein query. The algorithms used include blastp, psi-blast, phi-blast, and delta-blast.

Google Compute Engine
type: Resource
type: NamedIndividual
has db xref: OMICS_01204
abbrev: Compute Engine
IAO_0000115: An infrastructure as a service that lets you run your large-scale computing workloads on Linux virtual machines hosted on Google's infrastructure.

SplitSeek
type: Resource
type: NamedIndividual
has db xref: biotools:splitseek
has db xref: OMICS_01253
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented September 20, 2016. A program for de novo prediction of splice junctions in RNA-seq data.

ASC
type: Resource
type: NamedIndividual
has db xref: biotools:sqn
has db xref: OMICS_01298
IAO_0000115: Borrows information across sequences to establish prior distribution of sample variation, so that biological variation can be accounted for even when replicates are not available.

NPEBseq
type: Resource
type: NamedIndividual
has db xref: OMICS_01312
IAO_0000115: A method for non-parametric, empirical Bayesian-based analysis of RNA-seq count data.

FUSIM
type: Resource
type: NamedIndividual
has db xref: OMICS_01366
synonym: FUsion SIMulator
synonym: Fusion Simulator
IAO_0000115: A software tool for simulating fusion transcripts from a reference genome.

Geoffs Bio-Directories
type: Resource
type: NamedIndividual
has db xref: OMICS_01704
synonym: Geoff's Bio Directories
synonym: grouthbio
IAO_0000115: A comprehensive listing of companies and organizations involved with genomics and molecular biology. There are lists for genome software and services, genome institutions and supplies, and general institutions.

Phred
type: Resource
type: NamedIndividual
has db xref: OMICS_01809
IAO_0000115: A base calling program for DNA sequence traces.

MassGenomics
type: Resource
type: NamedIndividual
has db xref: OMICS_01830
synonym: MassGenomics - Medical genomics in the post-genome era
IAO_0000115: Blog discussing next-generation sequencing and medical genomics in the post-genome era. Most posts are in-depth reviews of recent research publications or editorials.

Illuminator
type: Resource
type: NamedIndividual
has db xref: biotools:illuminator
has db xref: OMICS_02165
IAO_0000115: A sequence alignment program for the output from Illumina GA-II clonal sequencers. It uses an algorithm that indexes the reference sequence as a series of 8-mers and then matches the genomic reads to the 8-mer index, in a mutation-tolerant way permitting identification of single-nucleotide substitutions and indels.

RPCI Gene Targeting and Transgenic Shared Resource
type: Resource
type: NamedIndividual
has db xref: SciEx_10094
synonym: Roswell Park Cancer Institute Gene Targeting and Transgenic Facility
synonym: Roswell Park Cancer Institute Gene Targeting and Transgenic Shared Resource
synonym: RPCI Gene Targeting and Transgenic Facility
IAO_0000115: Facility which provides researchers with transgenic mouse technologies, methods, and animal models. Knockout mice, transgenic mice, and mice on multiple strain backgrounds are provided.

Reveal Biosciences
type: Commercial Organization
type: NamedIndividual
has db xref: SciEx_10233
synonym: Reveal Biosciences LLC
IAO_0000115: Contract research organization (CRO) that specializes in advanced tissue technologies. It offers services in histology, immunohistochemistry, digital pathology, and image analysis.

University of Oxford Labs and Facilities
type: Resource
type: NamedIndividual
has db xref: SciEx_10257
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. An independent portal that lists the labs and facilities at the University of Oxford.

Translational Research Laboratory
type: Organization
type: NamedIndividual
has db xref: SciEx_10351
synonym: Peter MacCallum Cancer Centre - Cancer Therapeutics Program
IAO_0000115: Cancer research laboratory at the Peter MacCallum Cancer Centre which investigates biomarkers identification, compounds for activity as anti-cancer drugs, and small molecule targeted therapies.

DTU Multi-Assay Core
type: Resource
type: NamedIndividual
has db xref: SciEx_10437
synonym: DTU Multi Assay Core
synonym: DTU Multi-Assay Core (DMAC)
abbrev: DMAC
IAO_0000115: Facility for performing and analyzing high-throughput biological assays. The facility provides advice and research service with a range of high-throughput assays. Analysis of microarrays, sequencing, QPCR, and flow cytometry are provided.

PersMed
type: Commercial Organization
type: NamedIndividual
has db xref: SciEx_10589
synonym: PersMed sro
IAO_0000115: Life science consultancy and analysis service company. Analysis services include microarray analysis, next generation sequencing, experiment design, and biostatistics. Consultancy centers around experimental design in approaches involving large sets of patient-derived data.

ACGT Inc.
type: Commercial Organization
type: NamedIndividual
has db xref: SciEx_10623
abbrev: ACGT
IAO_0000115: Company which provides a suite of molecular biology and genomic services, including DNA sequencing by Sanger and Next Generation Sequencing. All services are offered at a research, GLP or clinical grade levels.

WCMC Optical Microscopy Core Facility
type: Resource
type: NamedIndividual
has db xref: SciEx_10836
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 14,2024. Core facility whose resources and services include confocal microscopy, wide field fluorescence microscopy, histology services, and phosphorimaging, among others. It also provides consultation on project design and image visualization and analysis.

Indiana University Labs and Facilities
type: Resource
type: NamedIndividual
has db xref: SciEx_10924
synonym: IU Labs and Facilities
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented September 15, 2016. A portal which lists and provides access to the labs and facilities at Indiana University.

Sanford-Burnham Medical Research Institute Labs and Facilities
type: Resource
type: NamedIndividual
has db xref: SciEx_11229
synonym: Sanford Burnham Medical Research Institute Labs and Facilities
IAO_0000115: A portal which lists the various labs and facilities that are part of the Sanford-Burnham Medical Research Institute.

Washington University School of Medicine Genome Technology Access Center Core Facility
type: Resource
type: NamedIndividual
has db xref: ABRF_279
has db xref: SciEx_32
has db xref: SCR_018204
has db xref: SCR_018300
synonym: Genome Technology Access Center
synonym: McDonnell Genome Institute Genome Technology Access Center
synonym: Washington University in St. Louis Genome Technology Access Center
synonym: Washington University in St. Louis McDonnell Genome Institute Genome Technology Access Center
synonym: Washington University in St. Louis School of Medicine Genome Technology Access Center Core Facility
synonym: Washington University McDonnell Genome Institute Genome Technology Access Center
synonym: Washington University School of Medicine GTAC
synonym: Washington University School of Medicine GTAC Core Facility
abbrev: GTAC
abbrev: WUSTL GTAC
IAO_0000115: Genome Access Technology Center at the McDonnell Genome Institute offers comprehensive next generation sequencing, microarray, PCR and Bioinformatic services. In addition to generating high quality genomic, transcriptomic, and proteomic data, performs data analysis and provides technological support to users. Full service facility, from hypothesis to publication. Offers advanced analysis of microarray data. Provides free initial consultation to discuss project and offers several tiers of analysis packages to best suit your needs. NGS equipment includes NovaSeqs, Seqwell II, Oxford. Microarray expression and genotyping - all platforms.

Harvard FAS Bauer Core Laboratory
type: Resource
type: NamedIndividual
has db xref: SciEx_11636
synonym: Bauer Core Laboratory (FAS)
synonym: Harvard Bauer Core Laboratory
synonym: Harvard Bauer Core Laboratory (FAS)
synonym: Harvard University Bauer Core Laboratory
synonym: Harvard University Bauer Core Laboratory (FAS)
abbrev: Bauer Laboratory
IAO_0000115: Core facility that provides the following services: Liquid handling, Long read sequencing, Cell sorting service, Cell analysis service, Imaging systems service, Microarrays service, Sequencing service, Genotyping service, Fragment analysis, Solexa DNA sequencing service, Solexa gene expression service, Solexa small RNA service, Solexa ChIP-Seq service, Real-time quantitative PCR service, Protein-molecule interaction service, Library replication service, Nucleic acid isolation service, Nucleic acid shearing service, DNA, RNA and protein sample analysis service. Their goal is to advance research efforts in the life sciences that cannot readily be accomplished in the traditional academic laboratory because of a need for expensive instrumentation or automation, scientific or organizational infrastructure, or multidisciplinary expertise. To promote cutting-edge research and to foster scientific collaborations, we make our extensive laboratory and computational resources available to scientists at Harvard. Our technical staff provide expertise and hands-on training in protocols and the use of instrumentation for a nominal fee. Researchers can sign up to use the instrumentation through an on-line scheduling system and conduct their experiments independently.

P212121
type: Commercial Organization
type: NamedIndividual
has db xref: SciEx_11644
synonym: P212121 LLC
IAO_0000115: Chemical supplier that both curates and sells laboratory supplies and reagents.

Pathology Diagnostics
type: Commercial Organization
type: NamedIndividual
has db xref: SciEx_11698
synonym: Pathology Diagnostics Ltd
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented September 15, 2016. Pathology Diagnostics Ltd is an independent GCLP accredited histopathology research organisation delivering tissue, laboratory, and diagnostics services to industry Research and Development scientists engaged in drug and biomarker development.

Universite de Sherbrooke Labs and Facilities
type: Resource
type: NamedIndividual
has db xref: SciEx_11939
synonym: University of Sherbrooke Labs & Facilities
synonym: University of Sherbrooke Labs and Facilities
abbrev: Universite de Sherbrooke Labs & Facilities
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 19,2024. Portal, Core facility

Renovo Neural
type: Commercial Organization
type: NamedIndividual
has db xref: SciEx_12107
synonym: Renovo
synonym: Renovo Neural Inc
IAO_0000115: A specialized preclinical research organization that provides services for biological research and development on neural therapies. Renovo offers preclinical assays and 3D-electron microscopy services that provide routine and customized solutions for basic science, preclinical and clinical research, and drug development.

AZ Core Labs
type: Organization
type: NamedIndividual
has db xref: SciEx_12874
synonym: Arizona Bioindustry Association Core Labs
IAO_0000115: A core facility which provides fee-based sample imaging and analysis using analytical and microscopy equipment to technology incubator clients, university researchers, and industry.

PNA Bio
type: Commercial Organization
type: NamedIndividual
has db xref: SciEx_13409
synonym: PNA Bio Inc
IAO_0000115: A company which provides peptide nucleic acid products for use in research. It also provides engineered nuclease services to laboratories.

North Carolina State University Labs and Facilities
type: Resource
type: NamedIndividual
has db xref: SciEx_1402
synonym: NCSU Labs and Facilities
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 15,2024. Online portal for the labs and facilities at North Carolina State University. Resources include a plant transformation lab, analytical instrumentation facility, and nuclear services center.

State University of New York at Buffalo Labs and Facilities
type: Resource
type: NamedIndividual
has db xref: SciEx_1511
synonym: Facilities
synonym: Labs
synonym: State University of New York
synonym: SUNY
synonym: university at Buffalo
abbrev: SUNY Buffalo Labs & Facilities
abbrev: SUNY Buffalo Labs and Facilities
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 23,2024. Portal listing the labs and facilities at SUNY at Buffalo.

Miami University Labs and Facilities
type: Resource
type: NamedIndividual
has db xref: SciEx_1655
synonym: Miami University Labs & Facilities
IAO_0000115: A portal listing Miami University's labs and facilities which include the Center for Bioinformatics and Functional Genomics. The CBFG is the onsite core molecular biology and bioinformatics resource at Miami University that focuess mainly on DNA and protein analysis as well as expertise in robotics liquid handling.

Texas A and M University Labs and Facilities
type: Resource
type: NamedIndividual
has db xref: SciEx_1949
synonym: Texas A&M University Labs & Facilities
abbrev: TAMU Labs & Facilities
abbrev: TAMU Labs and Facilities
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 22,2024. Portal listing the Texas A and M University's labs and facilities, which include the TAMU Protein Chemistry Lab and the TIGM Transgenic Core.

University of Utah Labs and Facilities
type: Resource
type: NamedIndividual
has db xref: SciEx_1964
synonym: Utah Labs & Facilities
synonym: UUtah Labs and Facilities
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. Labs and facilities of the University of Utah, which include: Microarray and Genomic Analysis Core Facility, Flow Cytometry Core Facility, Mutation Generation and Detection Facility, and the Transgenic and Gene Targeting Core.

MS Bioworks
type: Commercial Organization
type: NamedIndividual
has db xref: SciEx_4856
synonym: MS Bioworks - Protein Mass Spectrometry Services
IAO_0000115: A protein mass spectrometry service provider that delivers data to industrial and government organizations as well as academic institutions. Protein services include protein identification, mapping, profiling, and mass measurement. Post-translational modification services include PTM profiling, phospho-screening, and glyco-screening. Quantitative proteomics services include workflows for label free, TMT, SILAC, and PRM. MS Bioworks also provides immunoprecipitated protein analysis and custom analysis.

GVK Biosciences Labs and Facilities
type: Resource
type: NamedIndividual
has db xref: SciEx_4904
synonym: GVK Biosciences Labs & Facilities
IAO_0000115: A contract research organization based in India that provides services including Clinical Development, Contract Manufacturing and Informatics.

Ottawa Hospital Research Institute Labs and Facilities
type: Resource
type: NamedIndividual
has db xref: SciEx_4969
synonym: Facilities
synonym: OHRI
synonym: Ottawa Hospital
synonym: Research Institute Labs
abbrev: OHRI Labs & Facilities
abbrev: OHRI Labs and Facilities
IAO_0000115: Portal to research facilities and services within the Ottawa Hospital Research Institute. Facilities and services include access to their bioinformatics facility, flow cytometry facility, human pluripotent stem cell facility, and their clinical research lab.

Louisiana State University Labs and Facilities
type: Organization
type: NamedIndividual
has db xref: SciEx_5112
synonym: Louisiana State University Labs & Facilities
synonym: LSU Labs & Facilities
synonym: LSU Labs and Facilities
IAO_0000115: Portal for Louisiana State University labs and facilities which include the AgCenter Biotechnology Laboratory, a core facility that provides basic and applied research expertise to support researchers in the LSU system as well as those in other academic institutions and industry. The ABL consists of three units: the Protein Facility, the Plant Transformation Facility and the Animal Cell Culture Facility.

Donald Danforth Plant Science Center Bioanalytical Chemistry Facility
type: Resource
type: NamedIndividual
has db xref: ABRF_194
has db xref: SciEx_522
synonym: Danforth Center Ionomics
synonym: Danforth Center Mass Spectrometry Facility
synonym: Danforth Center Proteomics and Mass Spectrometry Facility
synonym: Danforth Center Proteomics Facility
synonym: Donald Danforth Plant Science Center Proteomics and Mass Spectrometry Facility
synonym: Proteomics and Mass Spectrometry Facility
IAO_0000115: Facility provides tools for high quality plant and biological sample analysis in proteomics, mass spectrometry, metabolomics, ionomics, and related analytical fields. It works with academic and commercial institutions and has established collaborations with many principle investigators.

UAlbany Proteomics Core Facility
type: Resource
type: NamedIndividual
has db xref: SciEx_537
synonym: UAlbany CFG Proteomics Core Facility
synonym: University at Albany Center for Functional Genomics Proteomics Core Facility
synonym: University at Albany CFG Proteomics Core Facility
IAO_0000115: A core facility that provides services in the identification of individual proteins, characterization of entire protein complexes or biosimilars, and global analysis to discover changes in the proteomes of different samples. The core also specializes in the development of custom assays for quantitation of specific molecules in complex clinical samples.

Show of Hands
type: Resource
type: NamedIndividual
has db xref: SciEx_565
synonym: Show of Hands Mobile Polling
IAO_0000115: A mobile application for real-time mobile polling on topics that include politics, ethics, pop culture, sports, health, and humor. Poll results can be filtered by gender, political party, age, or income range. The app is available for iPhone, iPad, Android devices, and Kindle Fire.

EZ BioResearch
type: Commercial Organization
type: NamedIndividual
has db xref: SciEx_571
synonym: EZ BioResearch LLC
IAO_0000115: A biotechnology company that develops, manufactures and distributes molecular biology tool kits and laboratory consumable products. Services include DNA and RNA microarrays, PCR and transgenic genotyping, and DNA/RNA analysis and quality control.

Duke Model System Genomics
type: Resource
type: NamedIndividual
has db xref: SciEx_586
synonym: Duke University Model System Genomics
IAO_0000115: Portal to the Duke University Model Systems Genomics facility equipped to perform molecular genetic research in Drosophilia. Equipment includes stereo microscopes for fly pushing and microdissection, a compound microscope and a microscope equipped to view GFP and RFP as well as two inverted microscopes for embryo injections.

ECRbase
type: Resource
type: NamedIndividual
has db xref: nif-0000-02785
IAO_0000115: ECRbase is the Database of Evolutionary Conserved Regions (ECRs), Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes created using ECR Browser alignments. Currently there are over 26 million ECRs available in the ECRbase that correspond to regions extracted from pairwise comparisons of all the available species.

UNC Metabolomics Laboratory
type: Resource
type: NamedIndividual
has db xref: SciEx_598
synonym: UNC School of Medicine Metabolomics Laboratory
synonym: University of North Carolina at Chapel Hill School of Medicine Metabolomics Laboratory
IAO_0000115: Laboratory equipped for metabolite profiling from a wide range of biological samples. Equipment includes high-throughput robotic systems for the analysis of large sample sets. Data analysis software, both commercial and home built, is also available for discovery of biomarkers, metabolic signatures of disease, toxicity or other biological outcomes.

University of Colorado at Boulder Labs and Facilities
type: Resource
type: NamedIndividual
has db xref: SciEx_850
synonym: CU Boulder Labs & Facilities
synonym: CU Boulder Labs and Facilities
synonym: University of Colorado at Boulder Labs & Facilities
IAO_0000115: A portal for the core labs and facilities at the University of Colorado at Boulder.

University of Minnesota Histology and Immunohistochemistry Laboratory
type: Resource
type: NamedIndividual
has db xref: SciEx_8914
synonym: University of Minnesota - Twin Cities Histology and Immunohistochemistry (IHC) Laboratory
synonym: University of Minnesota - Twin Cities Histology and Immunohistochemistry Laboratory
synonym: University of Minnesota Histology and Immunohistochemistry (IHC) Laboratory
IAO_0000115: Lab based at the University of Minnesota that provides histology services, including frozen sectioning, tissue grossing, fixation, and sectioning, optimization and performance of immunohistochemistry (IHC).

University of Illinois College of Medicine; Illinois; USA
type: Organization
type: NamedIndividual
has db xref: nlx_40705
synonym: UIC College of Medicine
synonym: University of Illinois at Chicago College of Medicine
synonym: University of Illinois at Chicago College of Medicine; Illinois; USA
synonym: University of Illinois College of Medicine at Chicago
IAO_0000115: The medical school division of the University of Illinois with four separate campuses. The school focuses on excellence in research, education and clinical work, diversity and innovation, and collaboration.

Northwestern University Feinberg School of Medicine; Illinois; USA
type: Organization
type: NamedIndividual
has db xref: nlx_41572
synonym: Northwestern University Feinberg School of Medicine
synonym: Northwestern University FSM
synonym: Northwestern University Medical School
abbrev: FSM
IAO_0000115: Medical school of Northwestern University which focuses on research initiatives, clinical affiliates, and global outlook.

Princeton University; New Jersey; USA
type: Organization
type: NamedIndividual
has db xref: nlx_16293
synonym: Princeton University
IAO_0000115: A private Ivy League research university based in New Jersey that confers undergraduate and graduate degrees in the humanities, social sciences, natural sciences, and engineering. It offers professional degrees in international affairs, engineering and applied science, architecture, and finance

U.S. Department of Education
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100000138
has db xref: grid.419881.d
has db xref: ISNI: 0000 0001 2176 2483
has db xref: nlx_143871
has db xref: Wikidata: Q861556
synonym: ED.gov
synonym: United States Department of Education
abbrev: ED
IAO_0000115: The United States federal government Department of Education, which oversees policies on federal financial aid for education, collecting data and disseminating research, and working to promote key educational discussions and equal access to education.

Virginia Commonwealth University School of Medicine; Virginia; USA
type: NamedIndividual
has db xref: nlx_64661
synonym: VCU School of Medicine
abbrev: VCU SOM
IAO_0000115: Medical school division of Virginia Commonwealth University.

University of Kentucky; Kentucky; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100007472
has db xref: grid.266539.d
has db xref: ISNI:0000 0004 1936 8438
has db xref: nlx_89604
has db xref: Wikidata:Q1360303
synonym: University of Kentucky
abbrev: UKY
IAO_0000115: A public co-educational university in Lexington, Kentucky that offers undergraduate, graduate and postgraduate degree programs in a variety of fields such as nursing, the arts, law and medicine.

SERVA
type: Commercial Organization
type: NamedIndividual
has db xref: nif-0000-31492
IAO_0000115: Commercial supplier for biochemical reagents for manufacturing, development and distribution of products.

University at Buffalo School of Medicine and Biomedical Sciences; New York; USA
type: Organization
type: NamedIndividual
has db xref: nlx_35230
synonym: UB School of Medicine and Biomedical Sciences
synonym: University at Buffalo School of Medicine and Biomedical Sciences
synonym: University at Buffalo SMBS
abbrev: UB SMBS
IAO_0000115: Public university medical school located in Buffalo, New York.

RIKEN
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100006264
has db xref: grid.7597.c
has db xref: ISNI: 94465255
has db xref: nlx_143906
has db xref: Wikidata: Q50295658
IAO_0000115: An independent administrative institution dedicated to comprehensive research in science and technology and the dissemination of scientific research and technological developments to the public. RIKEN works in a range of fields, including physics, chemistry, medical science, biology, and engineering, covering the entire range from basic research to practical application.

RettBASE: IRSF MECP2 Variation Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-00156
synonym: RettBase
IAO_0000115: Database constructed by merging mutation and polymorphism data from the published literature pertaining to Rett syndrome and related clinical disorders, and by incorporating unpublished mutation and polymorphism data that have been submitted directly. RettBase is updated on a very frequent basis manually by curators to ensure the validity of the data submitted., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

BAC
type: Resource
type: NamedIndividual
has db xref: OMICS_00801
IAO_0000115: R software package that uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments.

targetscan.Hs.eg.db
type: Resource
type: NamedIndividual
has db xref: OMICS_00790
IAO_0000115: R software that predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA.

RmiR
type: Resource
type: NamedIndividual
has db xref: OMICS_00789
IAO_0000115: R package that contains functions to merge microRNA and respective targets using different databases.

MmPalateMiRNA
type: Resource
type: NamedIndividual
has db xref: OMICS_00788
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software R package written for analysis of murine palate miRNA two-color expression data.

Starr
type: Resource
type: NamedIndividual
has db xref: OMICS_00811
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software R package for the analysis of ChIP-chip data and Affymetrix tiling arrays. It provides functions for data import, quality assessment, and data visualization. The software provides tools for the efficient mapping of genomic sequences.

bsseq
type: Resource
type: NamedIndividual
has db xref: biotools:bsseq
has db xref: OMICS_01847
synonym: bsseq - Analyze manage and store bisulfite sequencing data
IAO_0000115: R package with tools for analyzing and visualizing bisulfite sequencing data.

Qvalue
type: Resource
type: NamedIndividual
has db xref: OMICS_00624
IAO_0000115: R package that takes a list of p-values resulting from the simultaneous testing of hypotheses and estimates their q-values. It is designed to measure the proportion of false positives when a test is significant. The software is capable of generating plots for visualization. It can be applied to problems in genomics, brain imaging, astrophysics, and data mining.

University of Oklahoma; Oklahoma; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100007926
has db xref: grid.266900.b
has db xref: ISNI:0000 0004 0447 0018
has db xref: nlx_27458
has db xref: Wikidata:Q640652
synonym: University of Oklahoma
abbrev: OU
IAO_0000115: A coeducational public research university located in Oklahoma, USA. The institution confers undergraduate and graduate degrees in fields such as law, medicine, aviation, energy management, history of science, and Native American studies.

University of Adelaide; Adelaide; Australia
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100001786
has db xref: grid.1010.0
has db xref: ISNI:0000 0004 1936 7304
has db xref: nlx_73637
has db xref: Wikidata:Q15574
IAO_0000115: Public research university in Adelaide, South Australia. It is known for its focus on research and emphasis on moving towards commercialization of research.

ExomePeak
type: Resource
type: NamedIndividual
has db xref: OMICS_00570
abbrev: exomePeak
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software package developed for the analysis of affinity-based epitranscriptome shortgun sequencing data from MeRIP-seq (maA-seq). It was built on the basis of the exomePeak MATLAB package with new functions for differential analysis of two experimental conditions to unveil the dynamics in post-transcriptional regulation of the RNA methylome. The exomePeak R-package accepts and statistically supports multiple biological replicates, internally removes PCR artifacts and multi-mapping reads, outputs exome-based binding sites (RNA methylation sites) and detects differential post-transcriptional RNA modification sites between two experimental conditions in term of percentage rather the absolute amount.

Medical College of Wisconsin; Wisconsin; USA
type: Organization
type: NamedIndividual
has db xref: Crossref Funder ID 100008980
has db xref: GRID grid.30760.32
has db xref: ISNI 0000 0001 2111 8460
has db xref: nlx_30873
has db xref: Wikidata Q6806307
synonym: Medical College of Wisconsin
abbrev: MCW
IAO_0000115: Private and freestanding medical school and graduate school of sciences in Milwaukee, Wisconsin. The institution offers medical degrees as well as masters and PhD-level studies in areas such as biochemistry, cell biology, and community and public health.

National Center for Health Statistics
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100005262
has db xref: grid.416789.5
has db xref: ISNI: 0000 0001 1958 5959
has db xref: nlx_151844
has db xref: Wikidata: Q3336854
abbrev: NCHS
IAO_0000115: Center dedicated to providing statistical information to guide policies to improve the health of the American people. An affiliate of the Center for Disease Control and Prevention.

Athens Research and Technology
type: Organization
type: NamedIndividual
has db xref: grid.423006.3
has db xref: nlx_152285
has db xref: Wikidata: Q30284050
synonym: Athens Research and Technology Inc.
IAO_0000115: Commercial supplier of bioproducts for studies of inflammation, autoimmune disease, cancer, coronary disease, Alzheimer's Disease and more. These include antibodies, enzymes, coagulation factors, and assay kits.

Corner Cube Environment
type: Resource
type: NamedIndividual
has db xref: nif-0000-00282
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. DOCUMENTED NOVEMBER 17, 2016: This program was removed on 03/18/15 and is not being monitored.A software visualization package for the symbolic display of functional neuroimaging datasets in an anatomical context. Written in IDL.

University of Florida College of Medicine Neuroscience
type: Organization
type: NamedIndividual
has db xref: nif-0000-02172
synonym: UFL
IAO_0000115: A department at the University of Florida's College of Medicine that offers programs of study on neural function and how it changes with injury and disease. The institution's research ranges from fundamental discovery to clinical application. These neuroscience programs are offered at the undergraduate, graduate, postdoctoral and resident level.

BRAINSCortex
type: Resource
type: NamedIndividual
has db xref: nlx_155698
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. A suite of tools to generate the cortical surface of the brain. The surface is generated in the middle of grey matter and can be used to measure surface features including cortical depth and curvature.

NextGenSeq(at)nature.com
type: Resource
type: NamedIndividual
has db xref: OMICS_01742
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. A collection of latest articles published by Nature Publishing Group about the current state of next generation sequencing technologies.

Howard University; Washington D.C.
type: Organization
type: NamedIndividual
has db xref: nlx_152178
synonym: Howard
synonym: Howard U
synonym: Howard University
abbrev: HU
IAO_0000115: A federally chartered, private, coeducational, nonsectarian, historically black university in Washington, D.C. Howard University has graduate schools in many fields, including business, nursing, engineering, and medicine.

Japan Society for the Promotion of Science
type: Resource
type: NamedIndividual
has db xref: nlx_151882
abbrev: JSPS
IAO_0000115: Research and outreach organization dedicated to promoting science, research and education. The society has four main objectives, including building international cooperative networks, enhancing education and research at universities, building evidence-based science-promotion systems and creating diverse world level knowledge.

Australian National University; Acton; Australia
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100000995
has db xref: grid.1001.0
has db xref: ISNI:0000 0001 2180 7477
has db xref: nlx_23045
has db xref: Wikidata:Q127990
synonym: Australian National University
abbrev: ANU
IAO_0000115: A national research university in Canberra, Australia. It offers undergraduate and graduate degrees in fields such as law, medicine, business, arts and the social sciences.

AutoAssemblyD
type: Resource
type: NamedIndividual
has db xref: biotools:autoassemblyd
has db xref: OMICS_00874
IAO_0000115: Software which performs local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers.

Monash University; Melbourne; Australia
type: Organization
type: NamedIndividual
has db xref: nlx_77388
synonym: Monash
synonym: Monash University
IAO_0000115: Public research university based in Melbourne, Australia. The institution is divided into ten faculties, including art design and architecture, engineering, information technology, and medicine, nursing, and health sciences.

Viral Immunology Center
type: Resource
type: NamedIndividual
has db xref: nif-0000-24367
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. The National B Virus Resource Center is located in the Viral Immunology Center of Georgia State Universitys Department of Biology. Their laboratory is studying viruses that directly affect the central nervous system of infected hosts. Current projects in the laboratory are focused on the molecular biology of human and nonhuman primate alphaherpesviruses and the diseases they cause, immune response characterization, antiviral strategies, including drug discovery and high-throughput drug screening within unique, high containment laboratory suites. They are also actively engaged in the study of unique reoviruses that have the capacity to infect the central nervous systems of non human primates, langur viruses, and a newly isolated mangaby herpesvirus. Alphaherpesviruses target the central nervous system of susceptible hosts, and subsequently establish latent infections generally without severely damaging the host. There may be an initial acute phase when the virus successfully replicates in peripheral tissue of the host. This replication, when it occurs, induces a series of specific immune functions that can serve as markers of infection. We use these markers to design, develop and implement diagnostic assays that will be useful during the management of clinical disease. Each herpesvirus coexists peacefully with the natural host in which it has co-evolved, but when the viruses for any reason find themselves no longer in the natural host, the usual host:parasite relationship may change dramatically. In some closely related hosts the virus can replicate and, in some cases, pathogenesis of the infection is radically more severe than that which occurs in the natural host. For example, this can be seen when New World monkeys are infected with humans herpesviruses, e.g., HSV-1 or HSV-2, or when humans are infected with B virus from a macaque, a member of the Old World monkey family. Their studies focus on t…

CUDA-EC
type: Resource
type: NamedIndividual
has db xref: biotools:cuda-ec
has db xref: OMICS_01100
synonym: Compute Unified Device Architecture
IAO_0000115: A fast parallel error correction tool for short reads.

rGADEM
type: Resource
type: NamedIndividual
has db xref: OMICS_00491
IAO_0000115: R package with tools for de novo motif discovery in large-scale genomic sequence data.

qips
type: Resource
type: NamedIndividual
has db xref: OMICS_00457
IAO_0000115: A software package for analyzing ChIP-seq (Chromatin ImmunoPrecipitation on sequencing) data that finds enriched regions of arbitrary lengths and is therefore especially suited for analyzing ChIP-seq of histone marks or polymerase.

PICS
type: Resource
type: NamedIndividual
has db xref: OMICS_00455
synonym: Probabilistic inference of ChIP-seq
IAO_0000115: R package with tools that use probabilistic inference of ChIP-Seq. It follows an empirical Bayes mixture model approach.

Jmosaics
type: Resource
type: NamedIndividual
has db xref: OMICS_00445
IAO_0000115: R software that detects enriched regions of ChIP-seq data sets jointly.

Acris Antibodies
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_152250
synonym: Acris Antibodies GmbH
synonym: Acris Antibodies Inc.
IAO_0000115: Commercial supplier of biomaterials such as antibodies, antigens, lysates, and various assay kits.

McGill Global Health Resource Guide
type: Resource
type: NamedIndividual
has db xref: nlx_29904
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 15,2025. Wiki of resources useful for researchers and clinicians interested in global health. All McGill faculty, clinicians, researchers, staff and students are encouraged to use and add to these resources. If members of the research community would like to contribute to this resource, but are not a member of the McGill community, the McGill community is available for contact. An account will be created for users.

HWESTRATA
type: Resource
type: NamedIndividual
has db xref: nlx_154405
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application that calculates an exact stratified test for HWE for diallelic markers, such as single nucleotide polymorphisms (SNPs), and an exact test for homogeneity of Hardy Weinberg disequilbrium. In addition, exact tests for HWE are calculated for each stratum. (entry from Genetic Analysis Software)

Proteomics Research Center for Integrative Biology
type: Resource
type: NamedIndividual
has db xref: nlx_152684
synonym: Proteomics Research Resource for Integrative Biology
abbrev: Proteomics Resource for Integrative Biology
IAO_0000115: Biomedical technology research center that develops and integrates new proteomic technologies for collaborative and service studies, disseminating the new technologies and training scientists in their use.

Catholic University of Leuven; Flemish Brabant; Belgium
type: Organization
type: NamedIndividual
has db xref: nlx_149306
synonym: Catholic University of Leuven
synonym: Katholieke Universiteit Leuven
synonym: KU Leuven
synonym: University of Leuven
IAO_0000115: An independent, Catholic university in Belgium. The institution is Dutch-speaking but also offers several English programs.

SparseAssembler
type: Resource
type: NamedIndividual
has db xref: OMICS_00032
IAO_0000115: Software for memory-efficient genome assembly. It utilizes sparse k-mer.

SeaGIS
type: Commercial Organization
type: NamedIndividual
has db xref: nif-0000-31888
IAO_0000115: Commercial company that specializes in measurement science software, hardware and services. Their software products include a range of photogrammetric camera calibration, measurement and event logging software. Their hardware products include calibration cubes and underwater camera housings. Services include design, construction and calibration of vision measurement systems, software development and GIS consulting.

BreakFusion
type: Resource
type: NamedIndividual
has db xref: OMICS_01342
IAO_0000115: Software package written in Perl and C++ that provides a computational pipeline for identifying gene fusions from RNA-seq data.

ParticleCall
type: Resource
type: NamedIndividual
has db xref: OMICS_01154
IAO_0000115: A base-calling algorithm for Illumina DNA sequencing.

DSGseq
type: Resource
type: NamedIndividual
has db xref: OMICS_01331
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 15,2025. R software program for identifying differentially spliced genes from two groups of RNA-seq samples. It reads the count file and outputs the differences in the relative abundance of the isoforms of each gene in the annotation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

R453Plus1Toolbox
type: Resource
type: NamedIndividual
has db xref: OMICS_01354
IAO_0000115: R software toolbox of functions for the analysis of data generated by Roche's 454 sequencing platform. Additional functions are included for quality assurance, annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. A pipeline for the detection of structural variants is provided.

SynView
type: Resource
type: NamedIndividual
has db xref: OMICS_00947
IAO_0000115: A software tool for comparative visualization of genomes. It is based in the GBrowse frameworks and integrates with the annotation features.

ShortFuse
type: Resource
type: NamedIndividual
has db xref: biotools:shortfuse
has db xref: OMICS_01355
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A software package with tools for identifying fusion transcripts from RNA-Seq data. It is written in C++, and has dependencies on packages from Python 2.

Academy Biomedical Company
type: Organization
type: NamedIndividual
has db xref: nlx_152249
synonym: Academy Bio-Medical Company
synonym: Academy Biomedical Company Inc.
IAO_0000115: Commercial antibody supply company that focuses on providing antibodies for research in cardiovascular and atherosclerosis.

Phospho.ELM
type: Resource
type: NamedIndividual
has db xref: biotools:phosphoelm
has db xref: nif-0000-03278
IAO_0000115: Database of experimentally verified phosphorylation sites in eukaryotic proteins. Entries are manually curated with links to literature references, information about structure, interaction partners and sub-cellular compartment tissues, and sequences from the UniProt database.

North Dakota State University; North Dakota; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100007518
has db xref: grid.261055.5
has db xref: ISNI:0000 0001 2293 4611
has db xref: nlx_71768
has db xref: Wikidata:Q2000624
synonym: North Dakota State University
abbrev: NDSU
IAO_0000115: Public research university in North Dakota, USA. It is a land-grant university that focuses on agriculture and the applied sciences. In addition, it offers undergraduate and graduate degrees in a wide variety of areas including engineering, science and mathematics, health professions, business, and agriculture and food systems studies.

NIH Worker Training Program
type: Resource
type: NamedIndividual
has db xref: nlx_inv_1005149
abbrev: WT
abbrev: WTP
IAO_0000115: A set of National Institutes of Health-funded programs for worker's training. Programs include the Hazardous Materials Worker Health and Safety Training and the HAZMAT Training at DOE Nuclear Weapons Complex training program. There are also Small Business Innovation Research (SBIR) Grants that fund research projects that further the development of e-learning products that support health and safety training of emergency responders, community and citizen engagement and the long-term health effects of environmental disasters.

Mouse Brain Library
type: Resource
type: NamedIndividual
has db xref: nif-0000-00030
synonym: MBL - Mouse Brain Library
synonym: The Mouse Brain Library
abbrev: MBL
IAO_0000115: Collection of high resolution images and databases of brains from many genetically characterized strains of mice with aim to systematically map and characterize genes that modulate architecture of mammalian CNS. Includes detailed information on genomes of many strains of mice. Consists of images from approximately 800 brains and numerical data from just over 8000 mice. You can search MBL by strain, age, sex, body or brain weight. Images of slide collection are available at series of resolutions. Apple's QuickTime Plugin is required to view available MBL Movies.

Human Genetics Laboratory: WFS1 Gene Mutation and Polymorphism Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-10276
synonym: WFS1
IAO_0000115: This web site lists the disease causing mutations and polymorphisms found in the Wolfram syndrome (WFS1) gene. Sponsors: This resource is supported by the University of Michigan at Ann Arbor.

Speech Perception
type: Resource
type: NamedIndividual
has db xref: nlx_145380
IAO_0000115: An entry of the Cognitive Atlas which defines the term speech perception.

Ministry of Education of China
type: Organization
type: NamedIndividual
has db xref: nlx_151426
synonym: Chinese Ministry of Education
synonym: Ministry of Education of the People''s Republic of China
synonym: Ministry of Eduction of PRC
IAO_0000115: A governmental ministry that works on education reform, program development, and regulation and supervision of China's education system.

TDT-PC
type: Resource
type: NamedIndividual
has db xref: biotools:tdt_power_calculator
has db xref: nlx_154677
synonym: TDT Power Calculator
synonym: Transmission Disequilibrium Test Power Calculator
IAO_0000115: Software program to compute the statistical power of the Transmission/Disequilibrium Test (TDT) analytically, based on the most accurate asymptotic algorithms up to date, and is applicable in very general situations, where different parental disease status, multiple children, mixed family type and recombination events are considered. Routine algorithms for Monte Carlo simulations with significant improvements are also implemented in this program. (entry from Genetic Analysis Software)

Cancer Gene Index
type: Resource
type: NamedIndividual
has db xref: OMICS_01575
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on November 17, 2016. A database of genes that have been experimentally associated with human cancer diseases and/or pharmacological compounds, the evidence of these associations, and relevant annotations on the data.

FluView: A Weekly Influenza Surveillance Report
type: Resource
type: NamedIndividual
has db xref: nif-0000-30241
synonym: FluView
IAO_0000115: This page contains the Influenza Surveillance Report during 2008-2009 Influenza Season Week 15, ending April 18, 2009.

jmzML
type: Resource
type: NamedIndividual
has db xref: biotools:jmzml
has db xref: OMICS_03340
IAO_0000115: A Java application programming interface (API) for the Proteomics Standards Initiative mzML data standard.

Kyoto Encyclopedia of Genes and Genomes Expression Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-21234
has db xref: r3d100011570
abbrev: KEGG Expression Database
IAO_0000115: Database for mapping gene expression profiles to pathways and genomes. Repository of microarray gene expression profile data for Synechocystis PCC6803 (syn), Bacillus subtilis (bsu), Escherichia coli W3110 (ecj), Anabaena PCC7120 (ana), and other species contributed by the Japanese research community.

CASVM
type: Resource
type: NamedIndividual
has db xref: OMICS_01671
synonym: Server for SVM Prediction of Caspase Substrates Cleavage Sites
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented December 12, 2016. CASVM is a web server for predicting caspase cleavage sites on protein sequences based on the SVM algorithms. It can also be used for predicting non-canonical caspase substrate cleavage sites. The server has a relational database containing experimentally verified caspase substrates retrievable using accession IDs, keywords or sequence similarity.

Birdseed
type: Resource
type: NamedIndividual
has db xref: OMICS_00704
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.SNP genotyping algorithm that runs on the Affymetrix 500K, SNP5.0, and SNP6.0 platforms. This software runs a clustering algorithm and generally should be run on a sample at least 50 times. It utilizes an Expectation-Maximization (EM) algorithm to produce genotypes and confidence scores for every individual at every SNP.

EQTL EXPLORER
type: Resource
type: NamedIndividual
has db xref: nlx_154018
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. An eQTL visualization tool that allows users to mine and understand data from a repository of genetical genomics experiments (entry from Genetic Analysis Software)

Orthologous and Paralogous Transcripts in Clades
type: Resource
type: NamedIndividual
has db xref: nif-0000-03222
synonym: OPTIC
IAO_0000115: Database and portal for the analysis of complete genomes in several clades. It includes orthologous and paralogous transcripts in clades for flies, nematodes, amniota, and yeasts. Users can browse and download the data within the database.

Marshall University; West Virginia; USA
type: Organization
type: NamedIndividual
has db xref: grid.259676.9
has db xref: ISNI: 0000 0001 2214 9920
has db xref: nlx_68123
has db xref: Wikidata: Q1379613
IAO_0000115: Coeducational public research university in West Virginia. Its undergraduate colleges include business, education, arts and media, health professions, information technology, liberal arts, and science. Its graduate colleges include schools of medicine and pharmacy.

GAS2
type: Resource
type: NamedIndividual
has db xref: nlx_154323
synonym: statistical significance in Genomewide Association Studies in 2-stage
IAO_0000115: Software application for evaluating Statistical Significance in Two-Stage Genomewide Association Studies (entry from Genetic Analysis Software)

LDMET
type: Resource
type: NamedIndividual
has db xref: nlx_154027
IAO_0000115: Software application (entry from Genetic Analysis Software)

LAMBDAA
type: Resource
type: NamedIndividual
has db xref: nlx_154421
IAO_0000115: Software application (entry from Genetic Analysis Software)

NewEast Biosciences
type: Organization
type: NamedIndividual
has db xref: nlx_152421
IAO_0000115: Commercial supplier which provides antibodies, assay kits, biomarkers, and proteins.

MitoScience
type: Organization
type: NamedIndividual
has db xref: nlx_152413
synonym: MitoScience LLC
IAO_0000115: Commercial supplier and developer of mitochondrial antibodies and mitochondrial assays. The company focuses on supporting critical research areas in cancer, neurodegeneration and metabolic disorders.

IBL-America
type: Organization
type: NamedIndividual
has db xref: nlx_152380
synonym: IBL
synonym: IBL - America
synonym: IBL - America (Immuno-Biological Laboratories)
synonym: IBL America
synonym: IBL International GmbH
IAO_0000115: A commercial biomaterial supply resource for laboratory reagent assays. IBL-American provides resources to further research and clinical testing in various areas including autoimmunity, endocrinology, infectious disease, oncology and neuroscience among others.

IBA GmbH
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_152379
IAO_0000115: A commercial company that provides a range of services from nucleic acid custom services to products and services for cloning, transfection, recombinant protein production and cell isolation.

Hytest
type: Organization
type: NamedIndividual
has db xref: grid.417767.4
has db xref: nlx_152378
has db xref: Wikidata: Q5952196
synonym: HyTest Ltd.
IAO_0000115: A commercial antibody supplier that specializes in high-quality monoclonal antibodies and antigens for the diagnostic industry.

BioLegend
type: Organization
type: NamedIndividual
has db xref: nlx_152302
IAO_0000115: Commercial antibody supplier and developer for biomedical research. These products are compatible with use in flow cytometry and mass cytometry, immunoprecipitation and chip, western blotting, immunofluorescence microscopy, and quantitative multiplexing.

BioCytex
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_152301
IAO_0000115: A French biotech company that specializes in the development of standardized flow cytometry kits in the field of haemostasis. It became part of the Stago group in 1994.

Aves Labs
type: Organization
type: NamedIndividual
has db xref: nlx_152287
IAO_0000115: An antibody supplier that specializes in high-affinity custom chicken antibody production, providing clients with chicken IgY and other immunoreagents for biomedical research and antibody manufacturing.

Atlas Antibodies
type: Organization
type: NamedIndividual
has db xref: nlx_152286
IAO_0000115: An antibody supply company that provides reagents targeting all human proteins. Atlas Antibodies develops reagents and antibodies for mass-spectrometry-based quantitative proteomics as well. Their production and development is based on the Human Protein Atlas (HPA) project, which released a complete tissue-based map of human protein expression using antibodies.

Visualization and Analysis of Networks containing Experimental Data (VANTED)
type: Resource
type: NamedIndividual
has db xref: biotools:vanted
has db xref: nif-0000-00373
synonym: VANTED v2
synonym: Visualization and Analysis of Networks containing Experimental Data
abbrev: VANTED
IAO_0000115: Software tool for extendable network visualization and analysis for the life sciences. It is Java-based and allows users to create, edit and map data onto existing or new networks. Experimental datasets can be visualized on network elements as graphical charts to show time series data or data of different treatments, as well as environmental conditions in the context of the underlying biological processes. Users can utilize built-in statistical algorithms to evaluate mapped data.

Abazyme
type: Organization
type: NamedIndividual
has db xref: nlx_152242
IAO_0000115: Commercial antibody supplier that provides reagents such as immunoassay kits, antibodies, and proteins as well as custom services such as antigen preparation, sequencing and engineering.

Diffusing Tensor Imaging in Java
type: Resource
type: NamedIndividual
has db xref: nif-0000-00320
synonym: Diffusing Tensor Imaging in Java (JDTI)
synonym: Diffusion Tensor Imaging
synonym: Java Diffusion Tensor Imaging
abbrev: JDTI
IAO_0000115: Software tool used to analyze diffusion tensor imaging. It produces three different diffusion-related images: the apparent diffusion coefficient map, a measurement of the general tendency of water protons to diffuse in the underlying voxel; the fractional anisotropy map, a measurement of whether water proton diffusion is equal in all directions or whether diffusion proceeds preferentially in certain directions; and directional map, a color map of the primary direction of diffusion.

Phoenix Pharmaceuticals
type: Organization
type: NamedIndividual
has db xref: nlx_152429
synonym: Phoenix Pharmaceuticals Inc.
IAO_0000115: Commercial antibody supplier that specializes in peptide-related products for research in obesity, cardiovascular disease, and diabetes.

BloodExpress
type: Resource
type: NamedIndividual
has db xref: nif-0000-02615
synonym: Blood Express
IAO_0000115: A database of gene expression in mouse haematopoiesis, integrating 271 individual microarray experiments derived from 15 distinct studies done on most characterized mouse blood cell types. Gene expression information has been discretized to absent/present/unknown calls. It supports gene-centric searches to find out where a gene of interest is expressed, and what other genes follow the same (or a similar) pattern of expression. It also supports cell-centric searches to find out what genes are expressed in specific cell types/studies and not others.

NeuroMouse Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-11000
abbrev: NeuroMouse
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 17, 2023.Toolbook(tm) based, interactive graphical database which provides structural, molecular, and genetic information on the adult murine nervous system; and its relevance to human neurobiology. This resource is primarily designed as a platform for users to interact, each sharing knowledge on their own area of expertise, which is compiled to a master database. This hypertext atlas presently comprises more than 1000 pages and is designed to provide a flexible integrated resource for the description and discussion of all forms mammalian neurologic data. Version 4.0 of the NeuroMouse program extends the program's basic framework to include a number of areas in modern molecular neurobiology. This system provides an integrated resource for the characterization and description of mammalian neurological data. Major divisions include: Neural Atlas, Molecular Atlas, Genetics/Surgical Lesion Atlas. Neuromouse has been integrated into our strain-specific three dimensional MRI and surgical atlases of the murine CNS. Database contents: Neural Atlas: - Rotational representation of the murine brain. - Neural structures: visual and alphabetic point and click index of neural structures, pathways and systems. - Brain atlas:photographic serial sections in the coronal, sagittal, and horizontal planes (average plate distance - 300 um). Physical brain distances are also provided as are meta-index grids to allow rapid movement between different planes and regions. # Catalog of primary and immortalized neural cells indexed to relevant neural structures. Molecular Atlas: - Index of neurotransmitters: Acetylcholine, GABA, Glutamate, Aspartate, Glycine, Dopamine, Norepinephrine, Epinephrine, Serotonin (synthesis, distribution, degradation, molecular modules, receptors, subunits, agonists, antagonists, gene structure, localization, physical properties and transgenics are indicated for each item). - Index of neurotrophins / neuro…

Reaper - Demultiplexing trimming and filtering sequencing data
type: Resource
type: NamedIndividual
has db xref: biotools:reaper
has db xref: OMICS_02157
abbrev: Reaper
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. Software program for demultiplexing, trimming and filtering short read sequencing data.

Magnetic Resonance Microscopy of Mouse Embryo Specimens
type: Resource
type: NamedIndividual
has db xref: nif-0000-11003
synonym: MRI Embryos
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 14, 2013. A multidimensional, digital atlas based on magnetic resonance images of normal mouse embryos from 9.5 days after conception (E9) to the newborn (P0). The images include surface views and cross-sectional views from the transverse, coronal, and sagittal planes for each embryo. Several movies have also been included to demonstrate growth of the embryos and to present a variety of visualization tools available for studying and documenting embryonic anatomy. These images are organized as a reference for educators and researchers who want to understand better the embryological anatomy of their own specimens and to understand how their images relate to the whole embryo at many stages of development.

GimmeMotifs
type: Resource
type: NamedIndividual
has db xref: biotools:gimmemotifs
has db xref: OMICS_02150
synonym: GimmeMotifs: a systematic de novo motif prediction pipeline
IAO_0000115: Software that provides a de novo motif prediction pipeline, especially suited for ChIP-seq datasets. It incorporates several existing motif prediction algorithms in an ensemble method to predict motifs and clusters these motifs using the WIC similarity scoring metric., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

BodyMap-Xs
type: Resource
type: NamedIndividual
has db xref: nif-0000-02617
synonym: BodyMap
synonym: BodyMap- human and mouse gene expression database
synonym: BodyMap-cross species
synonym: BodyMap-Xs(cross species)
synonym: BodyMap-Xs: anatomical and taxonomical breakdown of animal EST
synonym: BodyMap: human and mouse gene expression database
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. A taxonomical and anatomical database of latest cross species animal EST data, clustered by UniGene and inter connected by Inparanoid. Users can search by Unigene, RefSeq, or Entrez Gene ID, or search for Gene Name or Tissue type. Data is also sortable and viewable based on qualities of normal, Neoplastic, or other. The last data import appears to be from 2008

Intramodal Registration Software
type: Resource
type: NamedIndividual
has db xref: nif-0000-00318
IAO_0000115: Software that implements a set of C routines for robust, high-quality registration of two volumes, aligning according to a least-squares criterion which is well-suited to intramodal registration tasks. Programming skills are required to attach the ANSI-C routine to whichever system users have. It is available on Unix, Macintosh, and PC.

Insight Segmentation and Registration Toolkit
type: Resource
type: NamedIndividual
has db xref: nif-0000-00319
synonym: Insight Toolkit
synonym: National Library of Medicine Insight Segmentation and Registration Toolkit (ITK)
abbrev: ITK
IAO_0000115: Open source, cross platform library that provides developers with extensive suite of software tools for image analysis. Developed through extreme programming methodologies, ITK builds on proven, spatially oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.

Earlier versus Later Levodopa Therapy in Parkinson Disease
type: Resource
type: NamedIndividual
has db xref: nif-0000-11249
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This site has a dataset from the ELLDOPA study: a multicenter, placebo-controlled, randomized, dose-ranging, double-blind clinical trial of 361 early, mild Parkinson's disease (PD) subjects, not requiring symptomatic medications with a duration from time of diagnosis less than 2 years. A NINDS funded study. The multicenter, placebo-controlled, randomized, dose-ranging, double-blind clinical trial, called the Earlier versus Later Levodopa Therapy in Parkinson Disease (ELLDOPA) study was run by the Parkinson Study Group and sponsored by the National Institute of Neurological Disorders and Stroke (NINDS). The subjects (n=361) were enrolled between September 1998 and August 2001 at 33 sites in the United States and 5 sites in Canada. Despite the known benefit of levodopa in reducing the symptoms of Parkinsons disease, concern has been expressed that its use might hasten neurodegeneration. This study assessed the effect of levodopa on the rate of progression of Parkinsons disease.The primary analysis assessed the doseresponse relationship between the assigned doses and the worsening of parkinsonism, as indicated by the changes in the total score on the UPDRS between the baseline visit and week 42. Washout of study drug occurred during weeks 40-42.

skewer
type: Resource
type: NamedIndividual
has db xref: biotools:skewer
has db xref: OMICS_02106
synonym: skewer - A fast and sensitive adapter trimmer for illumina paired-end sequences
IAO_0000115: Software program for adapter trimming that is specially designed for processing Illumina paired-end sequences.

CISCRP- The Center for Information and Study on Clinical Research Participation
type: Resource
type: NamedIndividual
has db xref: nif-0000-11642
synonym: CISCRP
IAO_0000115: CISCRP is a resource for information on participation in, understanding of, and resources for clinical research participants and scientists. The mission of the Center is to educate, inform and empower patients, the public, medical and research professionals, the media and policymakers about clinical research participation and what it means to be an active participant in the clinical research process, promote greater awareness and understanding of clinical research participation and the role that it plays in public health, facilitate more effective collaboration among all members of the clinical research enterprise, and provide resources for the research community to better understand the study volunteer. To that end, the Center has developed a broad national awareness and education initiative in order to better inform the public at large about clinical study information. Furthermore, on its website, the Center offers program and event information related to clinical trials, an information center with facts, figures, informational resources, and FAQs for both patients and researchers, and a mailing list of clinical trial information. :The Center also maintains its own search engine website, : :searchclinicaltrials.org : : :, for those looking for further clinical trial information. The Center for Information and Study on Clinical Research Participation is located in Dedham, MA. :NIF thanks the : :Parkinson's Disease Foundation : : :for their referral of this resource to us.

NET-PD (Neuroprotection Exploratory Trials in PD): Futility Study I
type: Resource
type: NamedIndividual
has db xref: nif-0000-11251
synonym: FS-1
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This site has a dataset from a multicenter, double-blind, futility study of minocycline and creatine in subjects with early untreated Parkinson's Disease (PD) or FS-I (Futility Study I). There were 65 subjects/treatment arm with 195 total randomized subjects from approximately 42 sites in the US and Canada. A NINDS funded study. A Multicenter, Double-Blind, Futility Study of Minocycline and Creatine in subjects with early untreated Parkinson's Disease (PD) (FS-1).The primary objective of the study was to assess the impact of minocycline and creatine on the progression of PD in order to assess whether it was non-futile to proceed with further study of these agents. The progression of PD was measured by the change in total UPDRS score between the baseline visit and month 12 or the time of sufficient disability to require symptomatic therapy (last visit before subject goes on dopaminergic therapy), whichever occurs first. The additional follow-up of subjects until 18 months addressed the secondary objectives. The FS-1 study was conducted by the NINDS funded Neuroprotection Exploratory Trials in PD (NET-PD).

NET-PD (Neuroprotection Exploratory Trials in PD): Futility Study II
type: Resource
type: NamedIndividual
has db xref: nif-0000-11252
synonym: FS-TOO
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This site has a dataset from a multicenter, double-blind, pilot study of CoQ10 and GPI 1485 in subjects with early untreated Parkinson's Disease (PD) or FS-TOO (Futility Study II). There were 65 subjects/treatment arm with 195 total randomized subjects from approximately 42 sites in the US and Canada. A NINDS funded study. Multicenter, double-blind, pilot study of outpatients with early, untreated PD. De novo subjects were equally randomized to one of the three study arms: (1) active CoQ10 and placebo for GPI 1485, (2) active GPI 1485 and placebo for CoQ10 and (3) placebo for CoQ10 and GPI 1485. Subjects remained on blinded study drug for 12 months. The primary comparison of each drug was to historical control data, but a placebo group was included in order to ascertain concurrent control rates. The FS-TOO study was conducted by the NINDS funded Neuroprotection Exploratory Trials in PD (NET-PD).

flowWorkspace
type: Resource
type: NamedIndividual
has db xref: OMICS_05616
synonym: flowWorkspace - Import flowJo Workspaces into BioConductor and replicate flowJo gating with flowCore
IAO_0000115: Software package that facilitates comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.

khmer
type: Resource
type: NamedIndividual
has db xref: biotools:khmer
has db xref: OMICS_02560
has db xref: SciRes_000166
synonym: khmer - k-mer counting & filtering FTW
synonym: khmer - k-mer counting and filtering FTW
synonym: khmer project
synonym: khmer: k-mer counting filtering and graph traversal FTW
IAO_0000115: Software library and suite of command line tools for working with DNA sequence that takes a k-mer-centric approach to sequence analysis. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform.

massiR
type: Resource
type: NamedIndividual
has db xref: biotools:massir
has db xref: OMICS_03638
synonym: massiR: MicroArray Sample Sex Identifier
synonym: MicroArray Sample Sex Identifier
IAO_0000115: Software that predicts the sex of samples in gene expression microarray datasets.

CenterWatch
type: Resource
type: NamedIndividual
has db xref: nif-0000-11641
IAO_0000115: CenterWatch is an online resource for news, directories, analysis, and proprietary market research for clinical research professionals and patients. For patients, CenterWatch is committed to providing information on clinical trials, specific drugs, as well as other essential health and educational resources. On this website, patients can search clinical trials, receive e-mail notifications about specific clinical trials, review results from completed clinical trials, search drug information, learn about volunteering for a clinical trial, read an overview of the clinical trials process and find other health and educational resources. For researchers, CenterWatch offers a wide range of tools and resources to improve patient and investigator recruitment, remain current with industry trends and business practices, and strengthen organizational procedures. CenterWatch also offers information on grant opportunities, and a variety of educational books and publications. Researchers can provide the public with information about their clinical trials by using the Clinical Trials Listing Serviceprovided through CenterWatch, or look up more specific information on medicines and equipment using Drug and Device Pipeline News. Overall, the mission of CenterWatch is to be the leading source of news, directories, analysis, and proprietary market research for clinical research professionals and patients. It is located in Boston, MA. :NIF thanks the :Parkinson's Disease Foundation : :for their referral of this resource to us.

Transposon Insertion Finder
type: Resource
type: NamedIndividual
has db xref: OMICS_03508
abbrev: TIF
IAO_0000115: A search program to detect insertions of transposable element from short reads of next generation sequencer.

LONI Debabeler
type: Resource
type: NamedIndividual
has db xref: nif-0000-00321
abbrev: Debabeler
IAO_0000115: Software to manage the conversion of imaging data from one file format and convention to another. It consists of a graphical user interface to visually program the translations, and a data translation engine to read, sort and translate the input files, and write the output files to disk. The data translation engine: (1) Reads metadata from a set of image files on disk to identify the source that produced each file; (2) Groups the image files into user-defined collections using image metadata values; (3) Translates each image file collection by reading metadata and pixel data and mapping the data into the appropriate output file format through a programmable set of connected modules. The Debabeler uses the Java Image I/O Plugin Architecture to read and write a wide variety of common medical image file formats, including ANALYZE, MINC, and most variations of DICOM.

LONI Pipeline Processing Environment
type: Resource
type: NamedIndividual
has db xref: nif-0000-00322
synonym: LONI Pipeline Environment
abbrev: LONI Pipeline
IAO_0000115: A free workflow application primarily aimed at neuroimaging researchers that allows users to easily describe their executables in a graphical user interface (ie. create a module) and connect them together to create complex analyses all without having to code a single line in a scripting language. The Pipeline Client runs on your PC/Mac/Linux computer upon which you can create sophisticated processing workflows using a variety of commonly available executable tools (e.g. FSL, AIR, FreeSurfer, AFNI, Diffusion Toolkit, etc). The Distributed Pipeline Server can be installed on your Linux cluster and you can submit processing jobs directly to your own compute systems. Once you����??ve created a module for use in the LONI Pipeline, you can save it into your personal library and reuse it in other workflows you create by simply dragging and dropping it in. Because the LONI Pipeline is written in Java, you can work in whatever operating system suits you best. If there are tools that you need that can only work on another operating system, you can install a Pipeline server on that computer and connect from your client to do processing and analysis remotely.

BSDPF
type: Resource
type: NamedIndividual
has db xref: nif-0000-11645
synonym: Bachmann-Strauss Dystonia & Parkinson Foundation
synonym: The Bachmann-Strauss Dystonia and Parkinson Foundation
synonym: The Bachmann-Strauss Dystonia and Parkinson Foundation Inc.
IAO_0000115: A nonprofit organization whose goal is to find better treatments and cures for the movement disorders dystonia and Parkinson's disease. Funding opportunities are available through the collaborative research program between BSDPF and the Michael J. Fox Foundation.

International Essential Tremor Foundation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100008447
has db xref: grid.480535.f
has db xref: ISNI: 0000 0004 5903 8599
has db xref: nif-0000-11649
abbrev: IETF
IAO_0000115: The IETF is an international nonprofit organization whose mission is to provide global educational information, services and support to those affected by essential tremor (ET) and to health care providers, while promoting and funding ET research. Services provided by the IETF include mailing or emailing a free information packet about ET upon request, maintaining an up-to-date listing of physicians specializing in ET, and assisting in forming and maintaining ET support groups. In addition, the IETF conducts several free educational events in cities across the United States every year, and an annual awareness campaign that runs in conjunction with the organization's largest fundraising activity, Tulips for Tremors. Every year, the IETF also funds basic research into the cause(s) of ET. Small grants are awarded to established scientists whose primary interest is tremor disorders. The IETF funds this program in the hope that these scientists will collect sufficient published data to help them qualify for future federal funding that will lead to better treatments and a cure. IETF members receive two copies a year of the member magazine, Tremor Talk and three copies of the research newsletter, The Scoop on Tremor. Articles in both publications are written for the non-medically trained person and discuss recent advances in research, coping techniques and topics of general interest to those with ET. Medical and research articles are written by physicians and researchers who work with patients with ET and/or study ET in laboratories. The International Essential Tremor Foundation is based in Lenexa, Kansas.

Shimmer
type: Resource
type: NamedIndividual
has db xref: OMICS_03612
IAO_0000115: Software package that detects somatic single-nucleotide variants using statistical hypothesis testing with multiple testing correction. It uses Fisher's exact test along with multiple testing correction (Benjamini-Hochberg) to find significant differences between allele composition with a specified false discovery rate.

Bleeding History Phenotype Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157338
abbrev: BHO
IAO_0000115: An application ontology devoted to the standardized recording of phenotypic data related to hemorrhagic disorders.

GenVision
type: Commercial Organization
type: NamedIndividual
has db xref: OMICS_02135
synonym: DNASTAR GenVision
synonym: GenVision - Software for Publication-Quality Illustrations
IAO_0000115: A genomic visualization application to support easy generation of publication quality graphics and maps. It produces high quality images of annotated genomes but it can also be customized to accentuate specific areas of interest, such as comparing gene functionality, illustrating gene expression levels, and visualizing the coverage in an assembled contig.

icyou Health Videos
type: Resource
type: NamedIndividual
has db xref: nif-0000-11652
synonym: icyou
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 18, 2016. icyou is an internet resource of health-related video clips submitted by users. Health topics covered in videos can range anywhere from infectious diseases to fitness and exercise, with videos generally being shorter than 10 minutes in length. Videos also contain information on treatment and procedures, medical fields, and health politics and policy. These videos may or may not be authored by licensed medical personnel. All videos are searchable, and users can also choose to upload their own healthcare-related videos. In addition to gathering healthcare video from the best sources on the Web and beyond, icyou.com can call on its own award-winning health reporting team to cover the latest issues and trends. Through its parent company Benefitfocus, icyou.com has full access to the Benefitfocus Media Studio, a state-of-the-art HD facility located in Charleston, South Carolina. This studio is the only one of its kind devoted solely to creating healthcare-oriented video content. In it, the Benefitfocus Media team creates up-to-the-minute reports, tutorials, features and more that help illuminate its users about the complexities of the many facets of healthcare.

DiMO
type: Resource
type: NamedIndividual
has db xref: OMICS_02190
synonym: DiMO: Discriminative Motif Optimizer
synonym: Discriminative Motif Optimizer
IAO_0000115: Software for discriminative motif optimization based on perceptron training. It takes a seed motif along with a positive and a negative database and improves the motif based on a discriminative strategy. They use the area under receiver-operating characteristic curve (AUC) as a measure of discriminating power of motifs and a strategy based on perceptron training that maximizes AUC rapidly in a discriminative manner.

MetaPhyl
type: Resource
type: NamedIndividual
has db xref: OMICS_02189
IAO_0000115: Software implementing a supervised classification method for metagenomic samples that takes advantage of the natural structure of microbial community data encoded by phylogenetic trees.

WiggleTools
type: Resource
type: NamedIndividual
has db xref: OMICS_02188
IAO_0000115: A multithreaded software library that computes statistics on large numbers of datasets, generating statistical summaries within minutes with limited memory requirements, whether on the whole genome or on selected regions.

EMI
type: Resource
type: NamedIndividual
has db xref: OMICS_02186
synonym: Efficient Multiple-IBD
IAO_0000115: Clustering software which uses pairwise identity-by-descent (IBD) segments to infer multiple-haplotype IBD clusters. It expands clusters from seed haplotypes by adding qualified neighbors and extends clusters across sliding windows in the genome.

SplicePlot
type: Resource
type: NamedIndividual
has db xref: biotools:spliceplot
has db xref: OMICS_02185
synonym: SplicePlot: a tool for visualizing alternative splicing
IAO_0000115: A software tool for visualizing alternative splicing and the effects of splicing quantitative trait loci (sQTLs) from RNA-seq data. It provides a simple command line interface for drawing sashimi plots, hive plots, and structure plots of alternative splicing events from .bam, .gtf, and .vcf files.

CrossMap
type: Resource
type: NamedIndividual
has db xref: OMICS_02184
IAO_0000115: A software program for convenient conversion of genome coordinates (or annotation files) between different assemblies. It supports most commonly used file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF. It is designed to liftover genome coordinates between assemblies. It?s not a program for aligning sequences to reference genome. CrossMap is not recommend for converting genome coordinates between species.

GraphIBD
type: Resource
type: NamedIndividual
has db xref: OMICS_02183
IAO_0000115: Identity-by-descent (IBD) association testing software for genome-wide association study analysis. It requires an IBD detection method such as Beagle FastIBD to run first. GraphIBD then builds upon the IBD information to test if the IBD segments show association to the traits.

rbsurv
type: Resource
type: NamedIndividual
has db xref: BioTools:rbsurv
has db xref: biotools:rbsurv
has db xref: OMICS_02088
synonym: rbsurv - Robust likelihood-based survival modeling with microarray data
IAO_0000115: Software package that selects genes associated with survival.

Skylign
type: Resource
type: NamedIndividual
has db xref: biotools:skylign
has db xref: OMICS_02182
synonym: Skylign - Interactive logos for alignments and profile HMMs
IAO_0000115: A tool for creating logos representing both sequence alignments and profile hidden Markov models. The interactive logos enable scrolling, zooming, and inspection of underlying values. Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequences and by combining observed counts with informed priors. It also simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position.

HMMvar
type: Resource
type: NamedIndividual
has db xref: OMICS_02181
IAO_0000115: Software applying a quantitative prediction method to predict the effect of genetic variation using hidden Markov models.

tbvar
type: Resource
type: NamedIndividual
has db xref: OMICS_02180
IAO_0000115: Database of the variome of Mycobacterium tuberculosis (Mtb) comprising of over 29,000 single nucleotide variations created from re-analyzed data sets corresponding to over 400 isolates of Mtb. Using a systematic computational pipeline, potential functional variants and drug-resistance associated variants have been annotated. The database has an option to annotate variants from clinical re-sequencing of Mtb.

STRViper
type: Resource
type: NamedIndividual
has db xref: OMICS_02177
synonym: Short Tandem Repeat Variation Indentification from Paired-End Reads
synonym: STRViper: Short Tandem Repeat Variation Indentification from Paired-End Reads
IAO_0000115: Software tool for detection of short tandem repeat (STR) variations from paired-end next generation sequencing data. It makes variant calls based on deviations in sequence fragment sizes, allowing the analysis of repeats of size up to fragment length. This stratergy also helps avoiding false calls resulting from errors arised from sequencing of repeat DNA.

Breakway
type: Resource
type: NamedIndividual
has db xref: OMICS_02176
synonym: Breakway: Identify Structural Variations in Genomic Data
IAO_0000115: A suite of software programs that take aligned genomic data and report structural variation breakpoints. Features include: * Takes in BAM formatted input, the current standard for genomic alignments. * Compatible with standard output from major alignment algorithms such as BFAST, BWA, MAQ, et cetera. * Capable of analyzing data from any major platform--Solexa, SOLiD, 454, et cetera. * Empirically identifies structural variation breakpoints. * Highly specific analysis generates very few false positives. * Includes a suite of downstream tools for annotating identified breakpoints and reducing false positives.

Genometa
type: Resource
type: NamedIndividual
has db xref: biotools:genometa
has db xref: OMICS_02175
synonym: Genometa - Rapid analysis of metagenomic short reads
IAO_0000115: A Java based bioinformatics program which allows rapid analysis of metagenomic short read datasets. Millions of short reads can be accurately analysed within minutes and visualised in the browser component. A large database of diverse bacteria and archaea has been constructed as a reference sequence. The approach is based upon the established open source visualisation tool IGB and supported by the rapid alignment program bowtie. The Picard toolset for SAM files is also made use of.

CATCHprofiles
type: Resource
type: NamedIndividual
has db xref: OMICS_02171
synonym: CATCH - Unsupervised clustering of ChIP profiles
IAO_0000115: Software tool for exploring patterns in Chromatin Immuno Precipitation (ChIP) profiling data. The CATCH algorithm performs a hierachical clustering of the profile patterns with an exhaustive alignment at each step. The algorithm has a user-friendly graphical interface that makes it easy to browse results.

ActionPotential.com
type: Resource
type: NamedIndividual
has db xref: nif-0000-07740
synonym: actionpotential
synonym: Dr. Donald Doherty''s Blog ActionPotential.com
synonym: Dr. Donald Doherty''s Blog: ActionPotential.com
IAO_0000115: Blog on neuroscience related topics by Dr. Donald Doherty. Donald Doherty, Ph.D., is a neuroscientist, software engineer, and entrepreneur with twenty-five years of experience delivering information technology based products in the health care and life sciences. During 2001, Donald founded and lead Brainstage Research, Inc. where he designed and built a Web platform that included a search engine, components to transform data into life science simulations, and a number of Semantic Web technologies. Brainstage Research, Inc. was sold in 2007 and reincorporated as Brainstage, Inc. Donald served as Chief Science Officer of Brainstage, Inc. where he continued to lead the development of its software platform until January 2010. Donald received his doctorate in Neuroscience from the University of California at Irvine.

VAAL
type: Resource
type: NamedIndividual
has db xref: biotools:vaal
has db xref: OMICS_02170
IAO_0000115: A polymorphism discovery algorithm for short reads. To run it, you provide reads (and quality scores) from a "sample genome" as input, along with a vector sequence to trim from the reads, and a reference sequence for a related genome to compare to. VAAL produces as output a an assembly for the sample genome, together with a mask showing which bases are "trusted". It then deduces from that a list of differences between the sample and related genomes. Alternatively, it can be provided as input read data for two sample genomes, together with a reference sequence for a related genome. In this case, VAAL produces assemblies for each of the sample genomes, and compares them to each other, thereby deducing a list of differences between them. VAAL has been tested on bacteria, using single lanes of 36 bp unpaired reads from the Illumina platform. Note: This software package is no longer supported and information on this page is provided for archival purposes only.

SLOPE
type: Resource
type: NamedIndividual
has db xref: biotools:slope
has db xref: OMICS_02169
IAO_0000115: Software that consists of two command-line utilities, slope_align (which finds the best split-read alignments to the reference genome) and slope_cluster (which clusters and outputs the alignments)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

BreakSeq
type: Resource
type: NamedIndividual
has db xref: biotools:breakseq
has db xref: OMICS_02168
synonym: Breakpoint Library and BreakSeq
IAO_0000115: Software for scanning reads from short-read sequenced genomes against a human breakpoint library to accurately identify structural variants (SVs). The library of breakpoints at nucleotide resolution were assembled from collating and standardizing ~2,000 published structural variants (SVs). For each breakpoint, its ancestral state (through comparison to primate genomes) was inferred and its mechanism of formation (e.g., nonallelic homologous recombination, NAHR).

Third Reviewer
type: Resource
type: NamedIndividual
has db xref: nif-0000-07741
synonym: The Third Reviewer
synonym: ThirdReviewer
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 11, 2017. The Third Reviewer is a forum for scientists to share opinions about recently published research. Currently both microbiology and neuroscience papers in different journals are included. Third Reviewer allows anonymous commenting and provides a centralized location for commentary on papers from 11 major neuroscience venues.

Anchored Assembly
type: Commercial Organization
type: NamedIndividual
has db xref: OMICS_02167
IAO_0000115: Analysis pipeline that accurately detects and maps variations that are often missed by standard analysis algorithms. It uses direct de novo read overlap assembly to accurately detect and characterize SNPs (single nucleotide polymorphisms), indels, and SVs (structural variations). The pipeline uses existing Illumina HiSeq data and does not require additional library preparation. The algorithm is optimized for projects with at least 20x coverage per chromosome set (i.e. 40x for diploid).

Bionimbus
type: Resource
type: NamedIndividual
has db xref: biotools:bionimbus
has db xref: OMICS_02160
IAO_0000115: A cloud-based infrastructure for managing, analyzing and sharing genomics datasets.

I Do Imaging
type: Resource
type: NamedIndividual
has db xref: nlx_15230
synonym: I Do Imaging - Free Medical Software
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Web-based portal and database aggregate of free and open source software for medical imaging. The programs are categorized and placed in a searchable database.

ChIPMunk
type: Resource
type: NamedIndividual
has db xref: biotools:chipmunk
has db xref: OMICS_02140
IAO_0000115: DNA motif discovery software adapted for ChIP-Seq data. It is an iterative algorithm that combines greedy optimization with bootstrapping and uses coverage profiles as motif positional preferences. It does not require truncation of long DNA segments and it is practical for processing up to tens of thousands of data sequences

RDPipeline
type: Resource
type: NamedIndividual
has db xref: OMICS_02158
synonym: RDP Amplicon Sequence Pipeline
synonym: RDP Pipeline
IAO_0000115: Software to simplify the processing of large rRNA sequence libraries (including single-strand and paired-end reads) obtained through high-throughput sequencing technology. Tools for assembly, quality filtering, taxonomy based analysis and taxonomy independent analysis tools, and tools to convert the data to formats suitable for common ecological and statistical packages are available. For extremely large datasets, command line tools are available.

Peking University; Beijing; China
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100007937
has db xref: grid.11135.37
has db xref: ISNI:0000 0001 2256 9319
has db xref: nlx_76213
has db xref: Wikidata:Q16952
synonym: PKU
IAO_0000115: Chinese research university in Beijing, China that offers undergraduate and graduate degree programs in pure and applied sciences, social sciences and humanities, and sciences of management and education.

PeakAnalyzer
type: Resource
type: NamedIndividual
has db xref: biotools:peakanalyzer
has db xref: OMICS_02156
IAO_0000115: A set of standalone software programs for the automated processing of any genomic loci, with an emphasis on datasets consisting of ChIP-derived signal peaks. The software is able to identify individual binding / modification sites from enrichment loci, retrieve peak region sequences for motif discovery, and integrate experimental data with different classes of annotated elements throughout the genome. PeakAnalyzer requires a peak file and a feature annotation file in BED or GTF format. Complete annotation files for the current builds of the human (HG19) and mouse (MM9) genomes are provided with the software distribution.

DicomWorks
type: Resource
type: NamedIndividual
has db xref: nif-0000-00288
IAO_0000115: Software to help users work with DICOM files by organizing, managing and analyzing them. Key features: * a smart DICOM viewer with 4 panel display, annotations, arrows, multimodality synchronization, etc... * an export wizard to the most common picture or movie file formats * an export wizard to Microsoft PowerPoint * the most simple and compatible DICOM CD-ROM reader * the most simple and smart DICOM CD-ROM WRITER * an archiving solution with lossless compression of the data * a DICOM creation module to dicomize images from any image source (even video capture) * e-mail or FTP import end export functions (teleradiology) * 16 native localized versions

SomaticCall
type: Resource
type: NamedIndividual
has db xref: OMICS_02155
IAO_0000115: Software program that finds single-base differences (substitutions) between sequence data from tumor and matched normal samples. It is designed to be highly stringent, so as to achieve a low false positive rate. It takes as input a BAM file for each sample, and produces as output a list of differences (somatic mutations). Note: This software package is no longer supported and information on this page is provided for archival purposes only.

Baa.pl
type: Resource
type: NamedIndividual
has db xref: OMICS_02154
IAO_0000115: Software tool to evaluate de novo genome assemblies with RNA transcripts.

VirusHunter
type: Resource
type: NamedIndividual
has db xref: biotools:virushunter
has db xref: OMICS_02153
IAO_0000115: A fully automated and modular software package for mining sequence data to identify sequences of microbial origin. The pipeline was optimized for analysis of data generated by the Roche/454 next-generation sequencing platform but can be applied to longer sequences (Sanger sequencing data or assembled contigs) as well. Microbial sequences are identified on the basis of BLAST alignments and the taxonomic classification of the reference sequence(s) to which a read is aligned. Viruses are the focal point of VirusHunter as released, but it can be easily modified to generate parallel outputs for bacterial or parasitic species. To date, VirusHunter has been applied to thousands of specimens, including human, animal and environmental samples, resulting in the detection of many known and novel viruses.

seq2HLA
type: Resource
type: NamedIndividual
has db xref: OMICS_02152
synonym: seq2HLA - HLA typing from RNA-Seq sequence reads
IAO_0000115: Software for obtaining an individualXs HLA class I and II type and expression using standard NGS (Next-generation sequencing) RNA-Seq data. It comprises mapping RNA-Seq reads against a reference database of HLA alleles, determining and reporting HLA type, confidence score and locus-specific expression level.

MUMmerGPU
type: Resource
type: NamedIndividual
has db xref: OMICS_02151
synonym: High-throughput sequence alignment using Graphics Processing Units
IAO_0000115: Software tool as high throughput DNA sequence alignment program that runs on nVidia G80-class GPUs. Aligns sequences in parallel on video card to accelerate widely used serial CPU program MUMmer.

GeneMeta
type: Resource
type: NamedIndividual
has db xref: OMICS_02120
synonym: GeneMeta - MetaAnalysis for High Throughput Experiments
IAO_0000115: Software package providing a collection of meta-analysis tools for analysing high throughput experimental data.

GenoMiner
type: Resource
type: NamedIndividual
has db xref: OMICS_02149
synonym: GenoMiner: Genome Analyzer
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A next generation sequencing data analysis computer for biologists with or without IT background. It has an easy to-use graphical interface to analyze sequencing data in with only 15 clicks. A range of standard, add-on and custom applications help analyze and visualize data generated by Next Generation Sequencing machines. These are installed on each GenoMiner by default: * Reference assembly * De novo assembly * ChiP-Seq * BLAST * Hybrid de novo assembly * Hybrid reference assembly Add-on applications: * Quality assesment * RNA-Seq * Copy Number Variation (CNV) * Multiple Sequence Alignment * miRNA-Seq * Variant Calling

GenoViewer
type: Resource
type: NamedIndividual
has db xref: OMICS_02146
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Open source viewer / browser software for the SAM / BAM format commonly used in the assembly tasks of Next Generation Sequencing data.

sim4cc
type: Resource
type: NamedIndividual
has db xref: biotools:sim4cc
has db xref: OMICS_02145
IAO_0000115: Software tool as cross species spliced alignment program.Heuristic sequence alignment tool for comparing cDNA sequence with genomic sequence containing homolog of gene in another species.

GenomicTools
type: Resource
type: NamedIndividual
has db xref: biotools:genomictools
has db xref: OMICS_02144
synonym: GenomicTools: a computational platform for developing high-throughput analytics in genomics.
IAO_0000115: A flexible computational platform, comprising both a command-line set of tools and a C++ API, for the analysis and manipulation of high-throughput sequencing data such as DNA-seq, RNA-seq, ChIP-seq and MethylC-seq. It implements a variety of mathematical operations between sets of genomic regions thereby enabling the prototyping of computational pipelines that can address tasks from preprocessing and quality control to meta-analyses. The user can create average read profiles across transcriptional start sites or enhancer sites, quickly prototype customized peak discovery methods for ChIP-seq experiments, perform genome-wide statistical tests such as enrichment analyses, design controls via appropriate randomization schemes, among other applications. In addition to enabling rapid prototyping, the platform is designed to analyze large-datasets in a single-pass fashion in order to minimize memory and intermediate file requirements. The platform supports the widely used BED format to facilitate visualization as well as integration with existing platforms and pipelines such as Galaxy or BioConductor.

Omixon Target HLA Typing
type: Commercial Organization
type: NamedIndividual
has db xref: OMICS_02142
abbrev: Omixon Target HLA
IAO_0000115: An optional module in the Omixon Target application suite for HLA typing using NGS (next-generation sequencing) data that gives high resolution results with whole genome, exome or very targeted DNA data, or with RNA seq data.

Omixon Target Data Analysis
type: Commercial Organization
type: NamedIndividual
has db xref: OMICS_02141
abbrev: Omixon Target
IAO_0000115: Software application suite to help clinical labs adopt next generation sequencing for the analysis of diagnostic gene targets.

PARalyzer
type: Resource
type: NamedIndividual
has db xref: biotools:paralyzer
has db xref: OMICS_02137
synonym: PAR-CLIP data analyzer
synonym: PARalyzer (PAR-CLIP data analyzer)
IAO_0000115: Software tool to generate a high resolution map of interaction sites between RNA-binding proteins and their targets. The algorithm utilizes the deep sequencing reads generated by the newly developed PAR-CLIP (Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) protocol. The use of photoactivatable nucleotides in the PAR-CLIP protocol results in a more efficient crosslinking between the RNA-binding protein and its target relative to other CLIP methods; in addition a nucleotide substitution occurs at the site of crosslinking during Illumina library preparation. PARalyzer utilizes this nucleotide substition in a kernel density estimate classifier to generate the high resolution set of Protein-RNA interaction sites.

QualiMap
type: Resource
type: NamedIndividual
has db xref: biotools:qualimap
has db xref: OMICS_02133
synonym: QualiMap - Evaluating next generation sequencing alignment data
IAO_0000115: Software application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. It examines sequencing alignment data in SAM / BAM files according to the features of the mapped reads and provides an overall view of the data that helps to the detect biases in the sequencing and/or mapping of the data and eases decision-making for further analysis.

Lab7
type: Commercial Organization
type: NamedIndividual
has db xref: OMICS_02132
synonym: Lab7 Systems
IAO_0000115: Software to address all aspects of Next Generation Sequencing data workflow.

mlgt
type: Resource
type: NamedIndividual
has db xref: BioTools:mlgt
has db xref: biotools:mlgt
has db xref: OMICS_02131
synonym: mlgt: Multi-Locus Geno-Typing
synonym: Multi-Locus Geno-Typing
IAO_0000115: Software for processing and analysis of high throughput (Roche 454) sequences generated from multiple loci and multiple biological samples. Sequences are assigned to their locus and sample of origin, aligned and trimmed. Where possible, genotypes are called and variants mapped to known alleles.

BSSim
type: Resource
type: NamedIndividual
has db xref: OMICS_02130
synonym: BSSim: Bisulfite sequencing simulator for next-generation sequencing
IAO_0000115: Software to mimic various methylation level and bisulfite conversion rate in CpG, CHG and CHH context, respectively. It can also simulate genetic variations that are divergent from the reference sequence along with the sequencing error and quality distributions. In the output, both directional/non-directional, various read length, single/paired-end reads and alignment data in the SAM format can be generated. BSSim is a cross-platform BS-seq simulator offers output read datasets not only suitable for Illumina's Solexa, but also for Roche's 454 and Applied Biosystems' SOLiD.

Golden Helix GenomeBrowse
type: Resource
type: NamedIndividual
has db xref: OMICS_02129
abbrev: GenomeBrowse
IAO_0000115: Software tool that delivers visualizations of your genomic data that give you the power to see what is occurring at each base pair in your samples. A high performance backend is paired with an user interface to make sure that your discovery process is fluid and streamlined.

Weka
type: Resource
type: NamedIndividual
has db xref: SciRes_000174
synonym: Weka 3: Data Mining Software in Java
synonym: WEKA Data Mining Software
IAO_0000115: A collection of machine learning algorithms for data mining tasks. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. It is also well-suited for developing new machine learning schemes.

HiPipe
type: Resource
type: NamedIndividual
has db xref: biotools:hipipe
has db xref: OMICS_02128
synonym: HiPipe - High Performance Pipelines for NGS Data Analysis
IAO_0000115: Tool that provides high performance NGS (next-generation sequencing) data analysis pipelines so that researchers with minimum IT or bioinformatics knowledge can perform common analyses on NGS data. 3 TB of storage space is reserved for each task.

MADAM
type: Resource
type: NamedIndividual
has db xref: OMICS_02127
synonym: MADAM (TM4 Microarray Software Suite)
synonym: MADAM: MicroArray DAta Manager
synonym: MicroArray DAta Manager
synonym: TM4 MADAM
synonym: TM4 Microarray Software Suite: MADAM
synonym: TM4 Microarray Software Suite: MicroArray DAta Manager
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.Data management software implemented in Java that facilitates the entry of data into a relational database. It guides users through the microarray process from RNA procurement to data analysis, offering intelligent forms to simplify the tracking of experimental parameters and results that are essential for the interpretation of expression results in downstream analyses. Canned reports provide information on RNA samples, studies, slide maps and other pertinent data and a general SQL query window allows freeform access to the underlying database. MADAM also serves as a platform for launching other data entry and management tools. Through the use of these integrated modules, users can view and score PCR plates, design experiments and studies, and track laboratory materials.

WuXi AppTec Laboratory Services
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_30524
IAO_0000115: A commercial organization for pharmaceutical, biopharmaceutical, and medical device open-access capability and technology platform with global operations.

Microarray Data Analysis System
type: Resource
type: NamedIndividual
has db xref: OMICS_02126
synonym: MIDAS (TM4 Microarray Software Suite)
synonym: MIDAS: Microarray Data Analysis System
synonym: TM4 Microarray Software Suite: Microarray Data Analysis System
synonym: TM4 Microarray Software Suite: MIDAS
synonym: TM4 MIDAS
abbrev: MIDAS
IAO_0000115: Application that provides users an interface to design analysis protocols combining one or more normalization and filtering steps. In this way, data from many individual hybridizations can be treated in a uniform and reproducible manner.

Automated Microarray Pipeline
type: Resource
type: NamedIndividual
has db xref: OMICS_02125
synonym: AMP (TM4 Microarray Software Suite)
synonym: AMP: Automated Microarray Pipeline
synonym: TM4 AMP
synonym: TM4 Microarray Software Suite: AMP
synonym: TM4 Microarray Software Suite: Automated Microarray Pipeline
abbrev: AMP
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented November 4, 2015. Web application based on the TM4 Microarray Software Suite to provide a means of normalization and analysis of microarray data. Users can upload data in the form of Affymetrix CEL files, and define an analysis pipeline by selecting several intuitive options. It performs data normalization (eg RMA), basic statistical analysis (eg t-test, ANOVA), and analysis of annotation using gene classification (eg Gene Ontology term assignment). The analysis are performed without user intervention and the results are presented in a web-based summary that allows data to be downloaded in a variety of formats compatible with further directed analysis.

ChanTest
type: Organization
type: NamedIndividual
has db xref: nlx_152331
synonym: ChanTest.com
abbrev: CT
IAO_0000115: An ion channel focused Contract Research Organization (CRO) that does safety testing and screening for global pharma and biotech companies. ChanTest has developed a complete library of validated human ion channel-expressing cell lines to serve all the ion channel needs of its pharmaceutical and biotech customers. Services range from early functional screens for profiling drug candidates or ranking within profiles during the drug-discovery process to a complete set of in vitro GLP service products for cardiac risk assessment. ChanTest works in partnership with customers to speed the drug-development process, save time and money, and ultimately to help make better, safer drugs.

MergeMaid
type: Resource
type: NamedIndividual
has db xref: OMICS_02124
synonym: Merge Maid
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. R extension whose functions are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be "list", "matrix", or "ExpressionSet". The main function is "mergeExprs" which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function "intcor" calculate the correlation coefficients. Other functions use the output from "modelOutcome" to graphically display the results and cross-validate associations of gene expression data with survival.

OmicsOffice for NGS SeqSolve
type: Commercial Organization
type: NamedIndividual
has db xref: biotools:seqsolve
has db xref: OMICS_02111
synonym: OmicsOffice for NGS (SeqSolve)
synonym: SeqSolve
abbrev: OmicsOffice for NGS
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software for secondary and tertiary analysis of Next Generation Sequencing (NGS) data.

categoryCompare
type: Resource
type: NamedIndividual
has db xref: OMICS_02122
synonym: categoryCompare - Meta-analysis of high-throughput experiments using feature annotations
IAO_0000115: A software package for meta-analysis of high-throughput experiments using feature annotations. It calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).

Covance
type: Organization
type: NamedIndividual
has db xref: grid.469910.3
has db xref: nlx_152335
has db xref: Wikidata: Q29123945
synonym: Covance Inc.
synonym: Covance Research Products Inc
synonym: Covance Research Products Inc.
abbrev: CVD
IAO_0000115: A contract research organization providing drug development and animal testing services. Under the name Covance Research Products Inc., based in Denver, Pennsylvania, the company also deals in the import, breeding and sale of laboratory animals. It breeds dogs, rabbits, guinea pigs, non-human primates, and pigs, and runs the largest non-human primate laboratory in Germany. (Wikipedia)

metahdep
type: Resource
type: NamedIndividual
has db xref: biotools:metahdep
has db xref: OMICS_02121
synonym: metahdep - Hierarchical Dependence in Meta-Analysis
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies.

Brain Windows
type: Resource
type: NamedIndividual
has db xref: nlx_30989
synonym: Brain Windows Blog
IAO_0000115: Blog devoted to reporting, analyzing and interpreting the latest results in the field of brain imaging technologies, particularly at the levels of systems, circuits, single cells and below. The site content is produced by Andrew Hires.

Plantagora
type: Resource
type: NamedIndividual
has db xref: OMICS_02116
synonym: Plantagora - a resource for plant genome assembly
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. A web-based plant genome assembly simulation platform whose resources include out of the box scripts for analyzing assembly data, an on-demand web graphing tool to model your experiment, and a downloadable database with metrics and parameters from over 3,000 simulated genome assemblies.

QUAST
type: Resource
type: NamedIndividual
has db xref: biotools:quast
has db xref: OMICS_02115
synonym: QUAST: Quality Assessment Tool for Genome Assemblies
IAO_0000115: Quality assessment software tool for evaluating and comparing genome assemblies. It works both with and without a given reference genome. It produces many reports, summary tables and plots.

TileQC
type: Resource
type: NamedIndividual
has db xref: biotools:tileqc
has db xref: OMICS_02114
synonym: TileQC: A tile based approached to quality control
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May,10, 2021.Software providing a visually oriented tile based approach to error detection for Solexa next-gen sequencing data. It is written in R and has both qualitative and quantitative error detection features. This software was written with the idea that the researcher's visual pattern recognition is the best way to detect novel errors and contains variety of ways to visualize that data. Once a new type of error is identified the data extraction features of the program may then be used as a starting point for the programmatic detection and/or filtration of similar errors. A supplementary role of tileQC is to convert the Eland and Q-score data contained within the Solexa "*_prb.txt" and "*_eland_results.txt" text files to a more flexible database form. Once in database form, tileQC simplifies the mechanics of interacting with that data and supplements standard SQL with an expression subsitution mechanism that allows R to be easily comingled with SQL. This system requires access to a mySQL server and the R package RMySQL as well as a few standard UNIX tools (also available on Windows and Macintosh).

VectorFriends
type: Commercial Organization
type: NamedIndividual
has db xref: OMICS_02113
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Sequence analysis software for molecular biologists.

vcflib
type: Resource
type: NamedIndividual
has db xref: biotools:vcflib
has db xref: OMICS_02112
IAO_0000115: A C++ library for parsing and manipulating Variant Call Format (VCF) files, and many command-line utilities. The API provides a quick and extremely permissive method to read and write VCF files. Extensions and applications of the library provided in the included utilities (*.cpp) comprise the vast bulk of the library's utility for most users.

PHACCS
type: Resource
type: NamedIndividual
has db xref: OMICS_03529
IAO_0000115: Software that gives estimates of the structure and diversity of uncultured viral communities using metagenomic information.

Sequedex
type: Resource
type: NamedIndividual
has db xref: biotools:sequedex
has db xref: OMICS_02110
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025.Software to classify the function and phylogeny of reads as short as 30 bp. It is flexible, which can utilize multiple data modules and downstream analysis scripts. It is fast, reading in signature lists of 5-500 million peptide signatures in 1-15 minutes, and subsequently processes genomic fragments at the rate of 6 Gbp/hr. It parallelizes without significant increase in memory requirements until I/O bound on multiple input files; parallelization works well on 64 processors.

Genome Trax
type: Resource
type: NamedIndividual
has db xref: biotools:genome_trax
has db xref: OMICS_02109
synonym: Genome Trax for Next Generation Sequencing
IAO_0000115: Service that provides a comprehensive compilation of variant knowledge that allows you to identify pathogenic variants in human whole genome or exome sequences. It makes it easy to upload a complete genome?s worth of variations and identify the biologically relevant subset of known mutations, mutations that are novel and appear in a candidate disease genes, or mutations that are predicted to have a deleterious effect. The database includes a comprehensive collection of disease causing mutations from HGMD Professional, regulatory sites from TRANSFAC , and disease genes, drug targets and pathways from PROTEOME, as well as pharmacogenomic variants. It integrates the best public data-sets on somatic mutations, allele frequencies and clinical variants, in their most up-to-date version, for a total of more than 165 million annotations. It is possible to identify known pathogenic variants, remove harmless common variants, and obtain deleterious predictions for novel variants. With family data, it is possible to identify variants that are de novo, compound heterozygous only in the offspring. All of the results can be downloaded to Excel for further review. For core facilities and bioinformaticians, the complete underlying data is made available for download and easy integration into custom analysis pipelines. Genome Trax data is optimized to work with many other software packages, such as ANNOVARTM, CLC bio, Alamut, SimulConsult, and Cartagenia.

VCFtools
type: Resource
type: NamedIndividual
has db xref: biotools:vcftools
has db xref: OMICS_02105
has db xref: OMICS_05112
has db xref: SCR_012092
synonym: Variant Call Format Tools
IAO_0000115: Software package for working with VCF files. Used to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.Implements various utilities for processing Variant Call Format files, including validation, merging, comparing. Provides general Perl API.

NGSUtils
type: Resource
type: NamedIndividual
has db xref: biotools:ngsutils
has db xref: OMICS_02104
synonym: NGSUtils - Tools for next-generation sequencing analysis
IAO_0000115: A suite of software tools for analyzing and manipulating next-generation sequencing datasets, such as FASTQ, BED and BAM format files. These tools provide a stable and modular platform for data management and analysis.

ChIP-seq
type: Resource
type: NamedIndividual
has db xref: OMICS_02103
synonym: ChIP-seq - Tools for the analysis of ChIP-seq data
IAO_0000115: Set of software modules for performing common ChIP-seq data analysis tasks across the whole genome, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. The tools are designed to be simple, fast and highly modular. Each program carries out a well-defined data processing procedure that can potentially fit into a pipeline framework. ChIP-Seq is also freely available on a Web interface.

Knowledge Engineering from Experimental Design
type: Resource
type: NamedIndividual
has db xref: nif-0000-07745
abbrev: KEfED
IAO_0000115: Knowledge engineering software for reasoning with scientific observations and interpretations. The software has three parts: (a) the KEfED model editor - a design editor for creating KEfED models by drawing a flow diagram of an experimental protocol; (b) the KEfED data interface - a spreadsheet-like tool that permits users to enter experimental data pertaining to a specific model; (c) a "neural connection matrix" interface that presents neural connectivity as a table of ordinal connection strengths representing the interpretations of tract-tracing data. This tool also allows the user to view experimental evidence pertaining to a specific connection. The KEfED model is designed to provide a lightweight representation for scientific knowledge that is (a) generalizable, (b) a suitable target for text-mining approaches, (c) relatively semantically simple, and (d) is based on the way that scientist plan experiments and should therefore be intuitively understandable to non-computational bench scientists. The basic idea of the KEfED model is that scientific observations tend to have a common design: there is a significant difference between measurements of some dependent variable under conditions specified by two (or more) values of some independent variable.

Tally
type: Resource
type: NamedIndividual
has db xref: OMICS_02100
synonym: Tally - Deduplication of sequence fragments
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software program for deduplicating sequence fragments. It minimises memory usage by compressing sequences and using compact memory allocation techniques. A built-in parser allows a variety of input file formats and a simple specification language allows flexible output file formats. It can be made aware of paired-end reads, and it can handle degenerate sequence inserts intended to reveal amplification biases. Tally comes with reaper, a program for demultiplexing, trimming and filtering short read sequencing data.

mapDamage
type: Resource
type: NamedIndividual
has db xref: biotools:mapdamage
has db xref: OMICS_02099
synonym: mapDamage2.0
synonym: mapDamage 2.0
synonym: mapDamage: tracking and quantifying damage patterns in ancient DNA sequences
IAO_0000115: Software for tracking and quantifying DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.

freeIbis
type: Resource
type: NamedIndividual
has db xref: OMICS_02217
synonym: freeIbis - Improved Base Identification System
IAO_0000115: A software basecaller for Illumina sequencers with calibrated quality scores.

piCALL
type: Resource
type: NamedIndividual
has db xref: biotools:picall
has db xref: OMICS_02098
IAO_0000115: Software to detect short insertion / deletion variants (and SNPs) from population sequence data, i.e. sequence reads generated from a population of individuals. It uses a probabilistic model to utilize sequence reads from a population of individuals to automatically account for context-specific sequencing errors associated with indels. piCALL is implemented in C for use on Linux platforms and can be applied to sequence data from different sequencing platforms. However, the method requires each individual in a dataset to be sequenced using the same platform. The reads for each individual should be aligned to the same reference genome sequence. Note that the program will not be able to call indels from individual sequence datasets or data from a small number of individuals.

ERGO
type: Resource
type: NamedIndividual
has db xref: OMICS_02097
synonym: ERGO Genome Analysis & Discovery System
synonym: ERGO Genome Analysis and Discovery System
IAO_0000115: A web-based genome analysis platform that integrates proprietary functional genomic data, metabolic reconstructions, expression profiling, and biochemical and microbiological data with publicly available information. Focused on microbial genomics, it provides better and faster identification of gene function across all organisms. Building upon a comprehensive genomic database integrated with a collection of microbial metabolic and non-metabolic pathways and using proprietary algorithms, it assigns functions to genes, integrates genes into pathways, and identifies previously unknown or mischaracterized genes, cryptic pathways and gene products. . * Automated and manual annotation of genes and genomes * Analysis of metabolic and non-metabolic pathways to understand organism physiology * Comparison of multiple genomes to identify shared and unique features and SNPs * Functional analysis of gene expression microarray data * Data-mining for target gene discovery * In silico metabolic engineering and strain improvement

TALLYMER
type: Resource
type: NamedIndividual
has db xref: biotools:tallymer
has db xref: OMICS_02096
abbrev: Tallymer
IAO_0000115: A collection of flexible and memory-efficient software programs for k-mer counting and indexing of large sequence sets. It is based on enhanced suffix arrays which gives a much larger flexibility concerning the choice of the k-mer size. It can process large data sizes of several billion bases.

KMC
type: Resource
type: NamedIndividual
has db xref: OMICS_02095
synonym: K-mer Counter
synonym: KMC - K-mer Counter
IAO_0000115: Software utility for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects. It scans the raw reads and produces a compact representation of all non-unique reads accompanied with number of their occurrences. The algorithm implemented makes use mostly of disk space rather than RAM, which allows to use KMC even on rather typical personal computers.

DSK
type: Resource
type: NamedIndividual
has db xref: biotools:dsk
has db xref: OMICS_02094
synonym: disk streaming of k-mers
synonym: DSK: disk streaming of k-mers
IAO_0000115: A k-mer counting software that can count k-mers of large Illumina datasets on laptops and desktop computers.

Mutation Surveyor
type: Resource
type: NamedIndividual
has db xref: OMICS_01816
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for DNA sequencing analysis that integates with Sanger Sequencing files generated by Applied Biosystems Genetic Analyzers, MegaBACE, and Beckman CEQ electrophoresis systems. It can be used to find single nucleotide polymorphisms (SNPs), insertions and deletions (INDELS), and somatic mutations in direct sequencing, PCR sequencing, mitochondrial DNA sequencing, and resequencing projects.

BFCounter
type: Resource
type: NamedIndividual
has db xref: biotools:bfcounter
has db xref: OMICS_02093
synonym: BF Counter: Memory efficient K-mer counting Software
IAO_0000115: Software program for counting k-mers in DNA sequence data. It identifies all the k-mers that occur more than once in a DNA sequence data set using a Bloom filter, a probabilistic data structure that stores all the observed k-mers implicitly in memory with greatly reduced memory requirements.

snpStats: SnpMatrix and XSnpMatrix classes and methods
type: Resource
type: NamedIndividual
has db xref: OMICS_02091
abbrev: snpStats
IAO_0000115: Software for classes and statistical methods for large single nucleotide polymorphism (SNP) association studies.

CNVtools
type: Resource
type: NamedIndividual
has db xref: OMICS_02090
synonym: CNVtools - A package to test genetic association with CNV data
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package to facilitate the testing of Copy Number Variant data for genetic association, typically in case-control studies.

CGEN
type: Resource
type: NamedIndividual
has db xref: OMICS_02089
synonym: CGEN - An R package for analysis of case-control studies in genetic epidemiology
IAO_0000115: Software R package for analysis of case-control studies in genetic epidemiology.

Body System Terms from ICD11
type: Resource
type: NamedIndividual
has db xref: nlx_157339
abbrev: ICD11-BODYSYSTEM
IAO_0000115: Ontology of a set of body-system terms used in the ICD (International Classification of Diseases) 11 revision

RCASPAR
type: Resource
type: NamedIndividual
has db xref: OMICS_02087
IAO_0000115: Software package for survival time prediction based on a piecewise baseline hazard Cox regression model. It is meant to help predict survival times in the presence of high-dimensional explanatory covariates.

iterativeBMAsurv
type: Resource
type: NamedIndividual
has db xref: OMICS_02086
synonym: iterativeBMAsurv - The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis
synonym: The Iterative Bayesian Model Averaging (BMA) Algorithm For Survival Analysis
IAO_0000115: Software package providing a variable selection method for applying survival analysis to microarray data.

multtest
type: Resource
type: NamedIndividual
has db xref: biotools:multtest
has db xref: OMICS_02085
synonym: multtest - Resampling-based multiple hypothesis testing
IAO_0000115: Software package for non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.

globaltest
type: Resource
type: NamedIndividual
has db xref: biotools:globaltest
has db xref: OMICS_02084
IAO_0000115: A software package that tests groups of covariates (or features) for association with a response variable. The package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms.

SABER
type: Resource
type: NamedIndividual
has db xref: biotools:saber
has db xref: OMICS_02081
IAO_0000115: Software program suitable for genome-scale data which uses a Markov-hidden Markov model (MHMM) to estimate local ancestry. The MHMM makes it possible to identify genomic blocks of a particular ancestry by use of any high-density single-nucleotide-polymorphism panel. One application is to perform admixture mapping without genotyping special ancestry-informative-marker panels.

Local Ancestry in adMixed Populations
type: Resource
type: NamedIndividual
has db xref: OMICS_02080
abbrev: LAMP
IAO_0000115: A software package for the inference of locus-specific ancestry in recently admixed populations. LAMP-LD takes the genotypes of admixed individuals as well as reference haplotype panels approximating the mixing ancestral populations, and outputs the estimated number of alleles from each ancestry in each locus for each individual. The LAMP-LD package also includes the program LAMP-HAP, which processes haplotype data when high-quality phasing is available, and utilizes trio nuclear family designs to improve estimation accuracy. LAMP-LD is based on a window-based processing combined within a hierarchical Hidden Markov Model. It can process 2,3 or 5 mixing populations, and its short per-sample processing time makes it suitable for analyzing large datasets of dense SNP panels. The original program LAMP does not use the LD and therefore is not as accurate, but it is useful in cases where the SNP density is not high enough or when the ancestral haplotypes are unkown.

GemTools
type: Resource
type: NamedIndividual
has db xref: OMICS_02079
synonym: GemTools - A fast and efficient approach to estimating genetic ancestry
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software tools for modeling genetic ancestry based on the single nucleotide polymorphism (SNP) information. This package of functions helps the user account for genetic ancestry of a large number of individuals using spectral graph theory and projections to break a large problem into smaller pieces and calculate genetic ancestry information efficiently, i.e., a divide and conquer (dac) strategy. It is completely written in R and runs on any platform that supports R.

MinimumDistance
type: Resource
type: NamedIndividual
has db xref: OMICS_02066
synonym: MinimumDistance - A package for de novo CNV detection in case-parent trios
IAO_0000115: Software package for analysis of de novo copy number variants in trios from high-dimensional genotyping platforms.

Synthetic Biology Open Language Visual Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157601
abbrev: SBOL
IAO_0000115: Ontology to represent standardized graphical notation for synthetic biology.

ipPCA
type: Resource
type: NamedIndividual
has db xref: OMICS_02078
synonym: i2pPCA
synonym: Iterative pruning Principal Component Analysis
IAO_0000115: Software implementing a population structure analysis algorithm which assigns individuals to subpopulations and infers the total number of subpopulations present. Additional functions have been included that result in improved population assignment accuracy. # Universal genotype data encoding scheme which allows the population analysis of all types of genetic markers; Single Nucleotide Polymorphism (SNP), Short Tandem Repeat (STR) and RFLP. # New termination criterion called ?EigenDev? which is more robust to population sampling, thus provides the better estimation of number of assigned subpopulations (K) and higher accuracy for the analysis of large complex population datasets.

ADMIXTURE
type: Resource
type: NamedIndividual
has db xref: biotools:admixture
has db xref: OMICS_02077
synonym: ADMIXTURE: fast ancestry estimation
IAO_0000115: A software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. It uses a block relaxation approach to alternately update allele frequency and ancestry fraction parameters. Each block update is handled by solving a large number of independent convex optimization problems, which are tackled using a fast sequential quadratic programming algorithm. Convergence of the algorithm is accelerated using a novel quasi-Newton acceleration method., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

frappe
type: Resource
type: NamedIndividual
has db xref: OMICS_02076
IAO_0000115: Software using a f frequentist approach for estimating individual ancestry proportion.

Mutascope
type: Resource
type: NamedIndividual
has db xref: OMICS_02074
synonym: Mutascope - Analysis software designed for PCR-amplicon sequencing data
IAO_0000115: Software suite to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations.

metabnorm
type: Resource
type: NamedIndividual
has db xref: biotools:metabnorm
has db xref: OMICS_03548
IAO_0000115: Software tool as mixed model normalization method for metabolomics data.Uses normalization approach based on mixed model, with simultaneous estimation of correlation matrix.

VegaMC
type: Resource
type: NamedIndividual
has db xref: OMICS_02071
synonym: VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer
IAO_0000115: Software package that enables the detection of driver chromosomal imbalances including loss of heterozygosity (LOH) from array comparative genomic hybridization (aCGH) data. It performs a joint segmentation of a dataset and uses a statistical framework to distinguish between driver and passenger mutation. VegaMC has been implemented so that it can be immediately integrated with the output produced by PennCNV tool. In addition, it produces in output two web pages that allows a rapid navigation between both the detected regions and the altered genes. In the web page that summarizes the altered genes, the link to the respective Ensembl gene web page is reported.

VanillaICE
type: Resource
type: NamedIndividual
has db xref: OMICS_02070
synonym: vanilla-ice
IAO_0000115: Software package using Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays.

SNPchip
type: Resource
type: NamedIndividual
has db xref: biotools:snpchip
has db xref: OMICS_02069
IAO_0000115: Software package that contains classes and methods useful for storing, visualizing and analyzing high density SNP data. Originally developed from the SNPscan web-tool, SNPchip utilizes S4 classes and extends other open source R tools available at Bioconductor, including the R packages Biobase and oligo. This has numerous advantages, including the ability to build statistical models for SNP-level data that operate on instances of the class, and to communicate with other R packages that add additional functionality.

SMAP
type: Resource
type: NamedIndividual
has db xref: OMICS_02068
synonym: SMAP - A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling
IAO_0000115: Software package providing functions and classes for DNA copy number profiling of array-CGH data.

quantsmooth
type: Resource
type: NamedIndividual
has db xref: BioTools:quantsmooth
has db xref: biotools:quantsmooth
has db xref: OMICS_02067
IAO_0000115: Software package for quantile smoothing and genomic visualization of array data.

Benaroya Research Institute
type: Organization
type: NamedIndividual
has db xref: ISNI 0000 0004 0444 3749
has db xref: nlx_152837
has db xref: Wikidata Q4886865
synonym: Benaroya
synonym: Benaroya Research Institute at Virginia Mason
abbrev: BRI
IAO_0000115: Non-profit organization based out of Seattle, Washington that conducts medical research on autoimmune disease.

mBPCR
type: Resource
type: NamedIndividual
has db xref: OMICS_02065
synonym: mBPCR - Bayesian Piecewise Constant Regression for DNA copy number estimation
IAO_0000115: Software package that estimates the DNA copy number profile to detect regions with copy number changes.

ITALICS
type: Resource
type: NamedIndividual
has db xref: OMICS_02064
IAO_0000115: Software package to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set.

GenoSet
type: Resource
type: NamedIndividual
has db xref: OMICS_02063
synonym: genoset - Provides classes similar to ExpressionSet for copy number analysis
IAO_0000115: Software package to load, manipulate, and plot copynumber and BAF data by providing classes similar to ExpressionSet for copy number analysis. The class extends ExpressionSet by adding a locData slot for a RangedData or GRanegs object. This object contains feature genome location data and provides for efficient subsetting on genome location. CNSet and BAFSet extend GenoSet and require assayData matrices for Copy Number (cn) or Log-R Ratio (lrr) and B-Allele Frequency (baf) data. Implements and provides convenience functions for processing of copy number and B-Allele Frequency data.

exomeCopy
type: Resource
type: NamedIndividual
has db xref: OMICS_02062
synonym: exomeCopy - Copy number variant detection from exome sequencing read depth
IAO_0000115: Software package for detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.

Utopia Docs
type: Resource
type: NamedIndividual
has db xref: nif-0000-07746
synonym: Utopia Documents
IAO_0000115: A software application PDF reader which provides a modified method of reading scientific papers. Different programs are available with additional information concerning the PDF, including Altimetric, Mendeley, and SHERPA/RoMEO. Related, open access articles can be saved directly from Utopia Docs and terms within the PDF can be directly searched, with results appearing within the program.

CGHregions
type: Resource
type: NamedIndividual
has db xref: OMICS_02058
synonym: CGHregions - Dimension Reduction for Array CGH Data with Minimal Information Loss
IAO_0000115: Software package for dimension Reduction for Array CGH Data with Minimal Information Loss.

CGHbase
type: Resource
type: NamedIndividual
has db xref: OMICS_02057
synonym: CGHbase: Base functions and classes for arrayCGH data analysis
IAO_0000115: Software package that contains functions and classes that are needed by arrayCGH packages.

BlindCall
type: Resource
type: NamedIndividual
has db xref: OMICS_02216
IAO_0000115: Software for ultra-fast base-calling of second-generation sequencing data by blind deconvolution.

beadarraySNP
type: Resource
type: NamedIndividual
has db xref: OMICS_02056
synonym: beadarraySNP - Normalization and reporting of Illumina SNP bead arrays
IAO_0000115: Software package for importing data from Illumina SNP experiments and performing copy number calculations and reports.

SSCprofiler
type: Resource
type: NamedIndividual
has db xref: OMICS_02055
synonym: Sequence Structure and Conservation profiler
IAO_0000115: Tool which can be used to identify novel miRNA gene candidates in the human genome.

CGH-Explorer
type: Resource
type: NamedIndividual
has db xref: OMICS_02054
IAO_0000115: Software program for visualization and statistical analysis of microarray-based comparative genomic hybridization (array-CGH) data. The program has preprocessing facilities, tools for graphical exploration of individual arrays or groups of arrays, and tools for statistical identification of regions of amplification and deletion.

GLAD
type: Resource
type: NamedIndividual
has db xref: OMICS_02053
synonym: Gain and Loss Analysis of DNA
synonym: GLAD - Gain and Loss Analysis of DNA
IAO_0000115: Software for analysis of array CGH data: detection of breakpoints in genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified.

SNP and Variation Suite SNP Analysis
type: Resource
type: NamedIndividual
has db xref: OMICS_02052
synonym: SNP & Variation Suite (SVS) SNP Analysis
synonym: SNP & Variation Suite SNP Analysis
synonym: SNP & Variation Suite: SNP Analysis
synonym: SNP and Variation Suite: SNP Analysis
synonym: SNP Package of SVS 7
abbrev: SVS SNP Analysis
IAO_0000115: SNP Analysis software for basic to advanced analyses that incorporates a number of intuitive workflows to lead you beyond single marker associations. With support for case-control and quantitative traits, whole genome and candidate gene data, you can run a breadth of statistical tests under several genetic models. Advanced regression can further help elucidate even the most complex gene-gene and gene-environment interactions.

SNP and Variation Suite CNV Analysis
type: Commercial Organization
type: NamedIndividual
has db xref: OMICS_02051
synonym: CNV Package of SVS 7
synonym: SNP & Variation Suite (SVS) CNV Analysis
synonym: SNP & Variation Suite CNV Analysis
synonym: SNP & Variation Suite: CNV Analysis
abbrev: SVS CNV Analysis
IAO_0000115: A set of software tools for processing raw intensity data, identifying regions of copy number variation (CNV), visualizing copy number data, and performing association analyses on a variety of copy number covariates.

Merck
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100004334
has db xref: grid.417993.1
has db xref: ISNI: 0000 0001 2260 0793
has db xref: nlx_152409
has db xref: Wikidata: Q247489
synonym: Merck & Co.
synonym: Merck & Co. Inc.
synonym: Merck and Co.
synonym: Merck and Co. Inc.
IAO_0000115: An American pharmaceutical company aiming to make a difference in the lives of people globally through their medicines, vaccines, biologic therapies and animal health products.

ProbRNA
type: Resource
type: NamedIndividual
has db xref: biotools:probrna
has db xref: OMICS_02195
IAO_0000115: Software for computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data.

methylMnM
type: Resource
type: NamedIndividual
has db xref: OMICS_02047
synonym: methylMnM - detect different methylation level (DMR)
IAO_0000115: Software package to detect different methylation levels (DMR) that gives the exact p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparison.

methyAnalysis
type: Resource
type: NamedIndividual
has db xref: OMICS_02046
synonym: methyAnalysis - DNA methylation data analysis and visualization
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for DNA methylation data analysis and visualization. A new class is defined to keep the chromosome location information together with the data. The current version of the package mainly focuses on analyzing the Illumina Infinium methylation array data, but most methods can be generalized to other methylation array or sequencing data.

les
type: Resource
type: NamedIndividual
has db xref: biotools:les
has db xref: OMICS_02045
synonym: les package: Identifying Differential Effects in Tiling Microarray Data
synonym: Loci of Enhanced Significance
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package that estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes.

ARRmNormalization
type: Resource
type: NamedIndividual
has db xref: OMICS_02044
synonym: ARRmNormalization - Adaptive Robust Regression normalization for Illumina methylation data
IAO_0000115: Software package to perform the Adaptive Robust Regression method (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay.

ChIPsim
type: Resource
type: NamedIndividual
has db xref: OMICS_02042
synonym: ChIPsim - Simulation of ChIP-seq experiments
IAO_0000115: Software package providing a general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments.

Sherman
type: Resource
type: NamedIndividual
has db xref: biotools:sherman
has db xref: OMICS_02041
synonym: Sherman - bisulfite-treated Read FastQ Simulator
IAO_0000115: Software tool to simulate FastQ files for high-throughput sequencing experiments. It allows the user to introduce various "contaminants" into the sequences, such as basecall errors, SNPs, adapter fragments etc., in order to evaluate the influence of common problems observed in many Next-Gen Sequencing experiments.

yaqcaffy
type: Resource
type: NamedIndividual
has db xref: BioTools:yaqcaffy
has db xref: biotools:yaqcaffy
has db xref: OMICS_02040
synonym: yaqcaffy - Affymetrix expression data quality control and reproducibility analysis
IAO_0000115: Software package for quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.

wateRmelon
type: Resource
type: NamedIndividual
has db xref: biotools:watermelon
has db xref: OMICS_02039
IAO_0000115: Software package for Illumina 450 methylation array normalization and metrics including 15 flavors of betas and three performance metrics, with methods for objects produced by methylumi, minfi and IMA packages.

sRAP
type: Resource
type: NamedIndividual
has db xref: OMICS_02038
synonym: Simplified RNA-Seq Analysis
IAO_0000115: Software package that provides a pipeline for gene expression analysis (primarily for RNA-Seq data). The normalization function is specific for RNA-Seq analysis, but all other functions (Quality Control Figures, Differential Expression and Visualization, and Functional Enrichment via BD-Func) will work with any type of gene expression data.

spotSegmentation
type: Resource
type: NamedIndividual
has db xref: OMICS_02037
IAO_0000115: Model-based software package for processing microarray images so as to estimate foreground and background intensities. The method starts with a very simple but effective automatic gridding method, and then proceeds in two steps. The first step applies model-based clustering to the distribution of pixel intensities, using the Bayesian Information Criterion (BIC) to choose the number of groups up to a maximum of three. The second step is spatial, finding the large spatially connected components in each cluster of pixels. The method thus combines the strengths of the histogram-based and spatial approaches. It deals effectively with inner holes in spots and with artifacts. It also provides a formal inferential basis for deciding when the spot is blank, namely when the BIC favors one group over two or three.

SNM
type: Resource
type: NamedIndividual
has db xref: OMICS_02036
synonym: Supervised Normalization of Microarrays
IAO_0000115: Software package that uses a modeling strategy especially designed for normalizing high-throughput genomic data. The premise is that your data is a function of study-specific variables which are either biological variables that represent the target of the statistical analysis, or adjustment variables that represent factors arising from the experimental or biological setting the data is drawn from. The SNM approach aims to simultaneously model all study-specific variables in order to more accurately characterize the biological or clinical variables of interest.

Zebrafish - SCORE Imaging: Specimen in a Corrected Optical Rotational Enclosure
type: Resource
type: NamedIndividual
has db xref: nif-0000-07749
synonym: Specimen in a Corrected Optical Rotational Enclosure imaging
abbrev: SCORE imaging
IAO_0000115: Narrative resource describing a visual data analysis and collection approach that takes advantage of the cylindrical nature of the zebrafish allowing for an efficient and effective method for image capture called, Specimen in a Corrected Optical Rotational Enclosure (SCORE) Imaging. To achieve a non-distorted image, zebrafish were placed in a fluorinated ethylene propylene (FEP) tube with a surrounding, optically corrected imaging solution: water. By similarly matching the refractive index of the housing (FEP tubing) to that of the inner liquid and outer liquid (water), distortion was markedly reduced, producing a crisp imagable specimen that is able to be fully rotated 360 degrees. A similar procedure was established for fixed zebrafish embryos using convenient, readily available borosilicate capillaries surrounded by 75% glycerol. The method described could be applied to chemical genetic screening and other, related high-throughput methods within the fish community and among other scientific fields.

SNAGEE
type: Resource
type: NamedIndividual
has db xref: OMICS_02035
synonym: Signal-to-Noise applied to Gene Expression Experiments
IAO_0000115: Software package that uses signal-to-noise ratios (SNRs) as a proxy for quality of gene expression studies and samples. The SNRs can be calculated on any gene expression data set as long as gene IDs are available, no access to the raw data files is necessary. This allows to flag problematic studies and samples in any public data set.

Simpleaffy
type: Resource
type: NamedIndividual
has db xref: OMICS_02034
synonym: Simpleaffy - Very simple high level analysis of Affymetrix data
IAO_0000115: Software package that provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. It makes heavy use of the affy library. It also has some basic scatter plot functions and mechanisms for generating high resolution journal figures.

qcmetrics
type: Resource
type: NamedIndividual
has db xref: BioTools:qcmetrics
has db xref: biotools:qcmetrics
has db xref: OMICS_02032
synonym: qcmetrics - A Framework for Quality Control
IAO_0000115: Software package that provides a framework for generic quality control of data. It permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in various formats.

OLIN
type: Resource
type: NamedIndividual
has db xref: biotools:olin
has db xref: OMICS_02029
synonym: Optimised Local Intensity-dependent Normalisation
IAO_0000115: Software functions for normalization of two-color microarrays by optimised local regression and for detection of artifacts in microarray data.

MANOR
type: Resource
type: NamedIndividual
has db xref: OMICS_02028
synonym: CGH Micro-Array NORmalization
IAO_0000115: Software packqge for importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH (Comparative genomic hybridization) experiments.

limmaGUI
type: Resource
type: NamedIndividual
has db xref: biotools:limmagui
has db xref: OMICS_02027
synonym: limmaGUI - GUI for limma package
IAO_0000115: Software package for a Graphical User Interface for the limma Microarray package.

ffpe
type: Resource
type: NamedIndividual
has db xref: biotools:ffpe
has db xref: OMICS_02026
synonym: ffpe - Quality assessment and control for FFPE microarray expression data
IAO_0000115: Software to identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots).

dyebias
type: Resource
type: NamedIndividual
has db xref: biotools:dyebias
has db xref: OMICS_02025
synonym: dyebias - The GASSCO method for correcting for slide-dependent gene-specific dye bias
IAO_0000115: Software package using the GASSCO method for correcting for slide-dependent gene-specific dye bias.

DEXUS
type: Resource
type: NamedIndividual
has db xref: biotools:dexus
has db xref: OMICS_02024
synonym: DEXUS - Identifying Differential Expression in RNA-Seq Studies with Unknown Conditions or without Replicates
IAO_0000115: Software package that identifies differentially expressed genes in RNA-Seq data under all possible study designs such as studies without replicates, without sample groups, and with unknown conditions. It works also for known conditions, for example for RNA-Seq data with two or multiple conditions. RNA-Seq read count data can be provided both by the S4 class Count Data Set and by read count matrices. Differentially expressed transcripts can be visualized by heatmaps, in which unknown conditions, replicates, and samples groups are also indicated. This software is fast since the core algorithm is written in C. For very large data sets, a parallel version of DEXUS is provided in this package. DEXUS is a statistical model that is selected in a Bayesian framework by an EM algorithm. It does not need replicates to detect differentially expressed transcripts, since the replicates (or conditions) are estimated by the EM method for each transcript. The method provides an informative/non-informative value to extract differentially expressed transcripts at a desired significance level or power.

BeadDataPackR
type: Resource
type: NamedIndividual
has db xref: biotools:beaddatapackr
has db xref: OMICS_02023
synonym: BeadDataPackR - Compression of Illumina BeadArray data
IAO_0000115: Software that provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform.

Hypertexts for Biomedical Sciences
type: Resource
type: NamedIndividual
has db xref: nif-0000-07750
synonym: Biomedical Hypertexts
IAO_0000115: Portal for a variety of web-based, educational information sources. Subjects include biotechnology, medical genetics, digestive systems and endocrine systems. Animations require a Java-enabled browser.

aroma.light
type: Resource
type: NamedIndividual
has db xref: biotools:aroma.light
has db xref: OMICS_01998
IAO_0000115: Light-weight software package for normalization and visualization of microarray data using only basic R data types. Software can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.

ArrayTools
type: Resource
type: NamedIndividual
has db xref: OMICS_02022
synonym: ArrayTools - GeneChip Analysis Package
IAO_0000115: Software package for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. The package generates comprehensive analysis reports in HTML format. Hyperlinks on the report page will lead to a series of QC plots, processed data, and differentially expressed gene lists. Differentially expressed genes are reported in tabular format with annotations hyperlinked to online biological databases.

beadarray
type: Resource
type: NamedIndividual
has db xref: biotools:beadarray
has db xref: OMICS_02021
synonym: beadarray - Quality assessment and low-level analysis for Illumina BeadArray data
IAO_0000115: Software package to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.

arrayQuality
type: Resource
type: NamedIndividual
has db xref: OMICS_02020
synonym: arrayQuality - Assessing array quality on spotted arrays
IAO_0000115: Software functions for performing print-run and array level quality assessment.

Partners HealthCare Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_31066
IAO_0000115: Blood biobank for the Partners research program, which investigates the affects of genes, lifestyle and environment on human health.

arrayMvout
type: Resource
type: NamedIndividual
has db xref: OMICS_02019
synonym: arrayMvout - Multivariate outlier detection for expression array QA
IAO_0000115: Software package that supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate.

affyQCReport
type: Resource
type: NamedIndividual
has db xref: OMICS_02018
synonym: affyQCReport - QC Report Generation for affyBatch objects
IAO_0000115: Software package to create a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object.

affyPLM
type: Resource
type: NamedIndividual
has db xref: OMICS_02017
synonym: affyPLM - Methods for fitting probe-level models
IAO_0000115: Software for fitting probe-level models and tools using these models. Probe-level models (PLM) based quality assessment tools.

affylmGUI
type: Resource
type: NamedIndividual
has db xref: biotools:affylmgui
has db xref: OMICS_02016
synonym: Affymetrix linear modeling Graphical User Interface
IAO_0000115: R software package providing a Graphical User Interface for analysis of Affymetrix microarray data, using the limma package (Linear Models for MicroArray data). While not as powerful as limma to the expert user, it offers a simple point-and-click interface to many of the commonly-used limma and affy functions. You need to have R 1.9.0 or later, Tcl/Tk 8.3 or later (ActiveTcl for Windows, Tcl/Tk Source for Linux/Unix, or X11 Tcl/Tk for MacOSX) and the limma, affylmGUI, and tkrplot R packages. It has been succesfully tested on Windows 2000, Windows XP, RedHat/Fedora Linux, and on Mac OSX with X11.

AffyExpress
type: Resource
type: NamedIndividual
has db xref: OMICS_02015
synonym: AffyExpress - Affymetrix Quality Assessment and Analysis Tool
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data.

waveTiling
type: Resource
type: NamedIndividual
has db xref: OMICS_02014
synonym: waveTiling - Wavelet-Based Models for Tiling Array Transcriptome Analysis
IAO_0000115: Software package to conduct transcriptome analysis for tiling arrays based on fast wavelet-based functional models.

KAnalyze
type: Resource
type: NamedIndividual
has db xref: biotools:kanalyze
has db xref: OMICS_03565
IAO_0000115: A Java toolkit designed to convert DNA and RNA sequences into k-mers.

gprege
type: Resource
type: NamedIndividual
has db xref: biotools:gprege
has db xref: OMICS_02011
synonym: Gaussian Process Ranking and Estimation of Gene Expression time-series
IAO_0000115: Software R package for Gaussian Process Ranking and Estimation of Gene Expression time-series. The software fits two Gaussian processes (GPs) with an radial basis function (RBF) (+ noise diagonal) kernel on each profile. One GP kernel is initialized wih a short lengthscale hyperparameter, signal variance as the observed variance and a zero noise variance. It is optimized via scaled conjugate gradients (netlab). A second GP has fixed hyperparameters: zero inverse-width, zero signal variance and noise variance as the observed variance. The log-ratio of marginal likelihoods of the two hypotheses acts as a score of differential expression for the profile. Comparison via receiver operating characteristic curves (ROC curves) is performed against Bayesian hierarchical model for the analysis of time-series (BATS) (Angelini et.al, 2007).

oneChannelGUI
type: Resource
type: NamedIndividual
has db xref: biotools:onechannelgu
has db xref: OMICS_02004
IAO_0000115: Software library that provides a graphical interface for microarray gene and exon level analysis as well as miRNA/mRNA-seq data analysis. The package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code.

Roche
type: Organization
type: NamedIndividual
has db xref: grid.486917.5
has db xref: ISNI: 0000 0004 1759 0967
has db xref: nlx_152451
has db xref: Wikidata: Q41568432
synonym: F. Hoffmann-La Roche
synonym: F. Hoffmann-La Roche Ltd
synonym: Hoffmann-La Roche
synonym: Hoffmann-La Roche AG
synonym: Roche Holding AG
IAO_0000115: A Swiss global health-care company that operates under two divisions: Pharmaceuticals and Diagnostics.

Anthony Salvagno Protocols
type: Resource
type: NamedIndividual
has db xref: nif-0000-07751
IAO_0000115: Wiki of chemical and preparatory experimental protocols.

CYCLE
type: Resource
type: NamedIndividual
has db xref: biotools:cycle
has db xref: OMICS_02010
IAO_0000115: Software package for the identification of periodically expressed genes using Fourier analysis and the statistical assessment of significance using different background models.

LMGene
type: Resource
type: NamedIndividual
has db xref: OMICS_02009
IAO_0000115: Software package for Data Transformation and Identification of Differentially Expressed Genes in Gene Expression Arrays.

factDesign
type: Resource
type: NamedIndividual
has db xref: OMICS_02008
synonym: factDesign - Factorial designed microarray experiment analysis
IAO_0000115: Software package that provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection.

pickgene
type: Resource
type: NamedIndividual
has db xref: biotools:pickgene
has db xref: OMICS_02007
IAO_0000115: Software for adaptive Gene Picking for Microarray Expression Data Analysis.

betr
type: Resource
type: NamedIndividual
has db xref: OMICS_01997
synonym: Bayesian Estimation of Temporal Regulation
IAO_0000115: Software package that implements the Bayesian Estimation of Temporal Regulation algorithm to identify differentially expressed genes in microarray time-course data.

NGSrich
type: Resource
type: NamedIndividual
has db xref: biotools:ngsrich
has db xref: OMICS_03603
IAO_0000115: Software for target enrichment performance for next-generation sequencing.

SCAN.UPC
type: Resource
type: NamedIndividual
has db xref: OMICS_02006
synonym: Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
synonym: Single-channel array normalization and Universal exPression Codes
IAO_0000115: A microarray normalization software (SCAN) to facilitate personalized-medicine workflows with an extension (UPC) that estimates whether a given gene/transcript is active above background levels in a given sample. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The UPC method can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration. A

arrayQualityMetrics
type: Resource
type: NamedIndividual
has db xref: OMICS_02005
synonym: Quality metrics on microarray data sets
IAO_0000115: Software package that generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). Reports contain both general and platform-specific sections. Both one and two color array platforms are supported.

REviewer - sequence analysis tools
type: Resource
type: NamedIndividual
has db xref: nif-0000-07752
synonym: REviewer
synonym: REviewer-sequence analysis tools
IAO_0000115: Web-based resource that provides an integrated set of tools for DNA sequence anlaysis, plasmid map creation, sequence viewing, and various biochemical calculations.

Imagescience: Imaging Conferences Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-32987
synonym: Imagescience
IAO_0000115: Imagescience provides a database of scientific imaging conferences around the world. Sponsors: This database is supported by imagescience.org.

CALIB
type: Resource
type: NamedIndividual
has db xref: OMICS_02003
IAO_0000115: Software package that contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estimated from external control spikes.

DEDS
type: Resource
type: NamedIndividual
has db xref: OMICS_02002
synonym: Differential Expression via Distance Summary
synonym: Differential Expression via Distance Summary for Microarray Data
IAO_0000115: Software library that contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements methodology (Differential Expression via Distance Summary) which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach.

Harshlight
type: Resource
type: NamedIndividual
has db xref: OMICS_02001
synonym: Harshlight - A corrective make-up program for microarray chips
IAO_0000115: Software package used to detect extended, diffuse and compact blemishes on microarray chips. It automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection.

MiChip
type: Resource
type: NamedIndividual
has db xref: OMICS_02000
synonym: MiChip Parsing and Summarizing Functions
IAO_0000115: Software package that takes the MiChip miRNA microarray .grp scanner output files and parses these out, providing summary and plotting functions to analyse MiChip hybridizations. A set of hybridizations is packaged into an ExpressionSet allowing it to be used by other BioConductor packages.

OCplus
type: Resource
type: NamedIndividual
has db xref: OMICS_01999
synonym: Ocplus - Operating characteristics plus sample size and local fdr for microarray experiments
IAO_0000115: Software package that allows to characterize the operating characteristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes).

bridge
type: Resource
type: NamedIndividual
has db xref: biotools:bridge
has db xref: OMICS_01996
synonym: Bayesian Robust Inference for Differential Gene Expression
IAO_0000115: Software package to test for differentially expressed genes with microarray data. It can be used with both cDNA microarrays or Affymetrix chip. The packge fits a robust Bayesian hierarchical model for testing for differential expression. Outliers are modeled explicitly using a $t$-distribution. The model includes an exchangeable prior for the variances which allow different variances for the genes but still shrink extreme empirical variances. The model can be used for testing for differentially expressed genes among multiple samples, and can distinguish between the different possible patterns of differential expression when there are three or more samples. Parameter estimation is carried out using a novel version of Markov Chain Monte Carlo that is appropriate when the model puts mass on subspaces of the full parameter space.

FARMS
type: Resource
type: NamedIndividual
has db xref: biotools:farms
has db xref: OMICS_01995
synonym: Factor Analysis for Robust Microarray Summarization
IAO_0000115: Software using a model-based technique for summarizing high-density oligonucleotide array data at probe level for Affymetrix GeneChips. It is based on a factor analysis model for which a Bayesian maximum a posteriori method optimizes the model parameters under the assumption of Gaussian measurement noise.

fRMA
type: Resource
type: NamedIndividual
has db xref: biotools:frma
has db xref: OMICS_01994
synonym: fRMA - Frozen RMA and Barcode
IAO_0000115: Preprocessing and analysis software for single microarrays and microarray batches.

genArise
type: Resource
type: NamedIndividual
has db xref: OMICS_01993
synonym: genArise - Microarray Analysis tool
IAO_0000115: An easy to use software tool for dual color microarray data. Its GUI-Tk based environment lets any non-experienced user perform a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer.

lapmix
type: Resource
type: NamedIndividual
has db xref: biotools:lapmix
has db xref: OMICS_01992
synonym: Laplace Mixture Model in Microarray Experiments
IAO_0000115: Software to identify differentially expressed genes. A hierarchical Bayesian approach is used, and the hyperparameters are estimated using empirical Bayes.

maCorrPlot
type: Resource
type: NamedIndividual
has db xref: OMICS_01991
synonym: maCorrPlot - Visualize artificial correlation in microarray data
IAO_0000115: Software that graphically displays correlation in microarray data that is due to insufficient normalization.

maSigPro
type: Resource
type: NamedIndividual
has db xref: OMICS_01990
synonym: Significant Gene Expression Profile Differences in Time Course Microarray Data
IAO_0000115: A regression based software package to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray experiments.

MACAT
type: Resource
type: NamedIndividual
has db xref: biotools:macat
has db xref: OMICS_01989
synonym: MicroArray Chromosome Analysis Tool
IAO_0000115: Software library that contains functions to investigate links between differential gene expression and the chromosomal localization of the genes. It is motivated by the common observation of phenomena involving large chromosomal regions in tumor cells. MACAT is the implementation of a statistical approach for identifying significantly differentially expressed chromosome regions.

maigesPack
type: Resource
type: NamedIndividual
has db xref: OMICS_01988
IAO_0000115: Software package that uses functions to handle and analyze cDNA microarray data.

MDQC
type: Resource
type: NamedIndividual
has db xref: OMICS_01987
synonym: Mahalanobis Distance Quality Control for microarrays
IAO_0000115: A multivariate quality assessment software for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array's quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality.

metaArray
type: Resource
type: NamedIndividual
has db xref: OMICS_01986
synonym: metaArray - Integration of Microarray Data for Meta-analysis
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package for data transformation for meta-analysis of microarray Data: Transformation of gene expression data to signed probability scale (MCMC/EM methods) and combined differential expression on raw scale: Weighted Z-score after stabilizing mean-variance relation within platform.

nnNorm
type: Resource
type: NamedIndividual
has db xref: OMICS_01985
synonym: nnNorm - Spatial and intensity based normalization of cDNA microarray data based on robust neural nets
IAO_0000115: Software package that allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting.

plgem
type: Resource
type: NamedIndividual
has db xref: biotools:plgem
has db xref: OMICS_01984
synonym: Power Law Global Error Model
IAO_0000115: Software to detect differential expression in microarray and proteomics datasets. Its use has been shown to improve the detection of differentially expressed genes or proteins in these datasets.

PVCA
type: Resource
type: NamedIndividual
has db xref: OMICS_01983
synonym: Principal Variance Component Analysis
IAO_0000115: Software package that contains the function to assess the batch sourcs by fitting all sources as random effects including two-way interaction terms in the Mixed Model (depends on lme4 package) to selected principal components, which were obtained from the original data correlation matrix. This package accompanies the book Batch Effects and Noise in Microarray Experiements, chapter 12.

EIGENSOFT/EIGENSTRAT
type: Resource
type: NamedIndividual
has db xref: nlx_154296
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software)

RAMA
type: Resource
type: NamedIndividual
has db xref: OMICS_01982
synonym: Robust Analysis of MicroArrays
IAO_0000115: Software package for robust estimation of cDNA microarray intensities with replicates. It uses a Bayesian hierarchical model for the robust estimation. Outliers are modeled explicitly using a t-distribution, and the model also addresses classical issues such as design effects, normalization, transformation, and nonconstant variance.

stepNorm
type: Resource
type: NamedIndividual
has db xref: OMICS_01981
synonym: stepNorm - Stepwise normalization functions for cDNA microarrays
IAO_0000115: Software for stepwise normalization functions for cDNA microarray data.

UNAFold
type: Resource
type: NamedIndividual
has db xref: biotools:unafold
has db xref: nif-0000-07753
synonym: The UNAFold Web Server
synonym: UNAFold Web Server
IAO_0000115: Software package for nucleic acid folding and hybridization prediction. It has capabilities to predict folding for single-stranded RNA or DNA through a combination of free energy minimization, partition function calculations and stochastic sampling. The program runs on Unix and Linux platforms as well as Mac OS X and Windows.

virtualArray
type: Resource
type: NamedIndividual
has db xref: OMICS_01979
IAO_0000115: Software package that permits the user to combine raw data of different microarray platforms into one virtual array. It consists of several functions that act subsequently in a semi-automatic way. Doing as much of the data combination and letting the user concentrate on analyzing the resulting virtual array.

NiLearn
type: Resource
type: NamedIndividual
has db xref: nlx_155897
synonym: NiLearn: Machine learning for Neuro-Imaging in Python
IAO_0000115: A software package to facilitate the use of statistical learning on NeuroImaging data. Namely NiLearn leverages the scikit-learn Python toolbox for multivariate statistics with applications such as predictive modelling, classification, decoding, or connectivity analysis.

Integrated DNA Technologies OligoAnalyzer
type: Resource
type: NamedIndividual
has db xref: nif-0000-07754
synonym: IDT Oligo Analyzer
synonym: IDT OligoAnalyzer
synonym: OligoAnalyzer
synonym: OligoAnalyzer 3.1
IAO_0000115: Web-based application for analyzing oligonucleotides. Analysis proceeds after the sequence has been entered and the calculations modified based on target type, oligo concentration, sodium ion concentration, magnesium ion concentration, and dNTP concentration.

LPE
type: Resource
type: NamedIndividual
has db xref: OMICS_01978
synonym: Local Pooled Error
IAO_0000115: Software library used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional "BH" or "BY" procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions.

Australian Digital Futures Institute
type: Resource
type: NamedIndividual
has db xref: nif-0000-07755
abbrev: ADFI
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on December 14, 2016. The Australian Digital Futures Institute no longer exists. It has been replaced by the USQ Digital Life Lab. A portal for the Australian Digital Futures Institute, a cross-institutional, multidisciplinary Institute that focuses on software research for technology-enhanced innovation.

Jadavpur University; West Bengal; India
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100009589
has db xref: grid.216499.1
has db xref: ISNI:0000 0001 0722 3459
has db xref: nlx_149480
has db xref: Wikidata:Q2579702
synonym: Jadavpur University
abbrev: JU
IAO_0000115: Public state university in West Bengal, India. There is a focus on interdisciplinary learning and research; the university features a variety of centers such as school of education technology, cognitive sciences, and natural product studies.

Fascinator
type: Resource
type: NamedIndividual
has db xref: nif-0000-07756
synonym: The Fascinator
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. An extensible, open-source platform for managing your digital objects. Using a variety of plugins, you can transform your digital objects into new formats, search and browse through your collection, collaborate through tagging and annotations, and create packages of information for publishing to all manner of systems. Written in Python.

MitoMiner
type: Resource
type: NamedIndividual
has db xref: nlx_152504
synonym: MitoMiner - A database of the mitochondrial proteome
IAO_0000115: A database of mitochondrial proteomics data. It includes two sets of proteins: the MitoMiner Reference Set, which has 10477 proteins from 12 species; and MitoCarta, which has 2909 proteins from mouse and human mitochondrial proteins. MitoMiner provides annotation from the Gene Ontology (GO) and UniProt databases. This reference set contains all proteins that are annotated by either of these resources as mitochondrial in any of the species included in MitoMiner. MitoMiner data via is available via Application Programming Interface (API). The client libraries are provided in Perl, Python, Ruby and Java.

Integrated Content Environment
type: Resource
type: NamedIndividual
has db xref: nif-0000-07757
synonym: Integrated Content Environment (ICE)
abbrev: ICE
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The Integrated Content Environment (ICE) is a free Word-processor based system that allows authors to work individually or collaboratively on material for the Web, CD and print. This free web content management system, produced by the University of Southern Queensland, was initially developed by staff at the university to produce course content for online and print delivery. It has also been used for general web site development, and to manage documents in project intranets.

DDBJ Sequence Read Archive
type: Resource
type: NamedIndividual
has db xref: nlx_152515
has db xref: OMICS_01027
has db xref: r3d100013696
abbrev: DRA
IAO_0000115: Archive database for output data generated by next-generation sequencing machines including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, and others. DRA is a member of the International Nucleotide Sequence Database Collaboration (INSDC) and archiving the data in a close collaboration with NCBI Sequence Read Archive (SRA) and EBI Sequence Read Archive (ERA). Please submit the trace data from conventional capillary sequencers to DDBJ Trace Archive., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

PLoS Blogs
type: Resource
type: NamedIndividual
has db xref: nif-0000-07759
synonym: PLoS Blogs Network
synonym: Public Library of Science - Science Blog Network
synonym: Public Library of Science Blogs
IAO_0000115: PLoS Blogs has been set up to bring a select group of independent science and medicine bloggers together with the editors and staff who run our blogs. Our independent network is made up of writers who love science and medicine, and scientists and physicians that love to write. Here, you'll find an equal mix of blogs from journalists and researchers tackling diverse issues in science and medicine. There are three very distinct types of blogs on the PLoS Blogs network: the official PLoS blog, the PLoS journal blogs (collectively known as The PLoS Blogs), and blogs from the independent network (a.k.a. The PLoS Blogosphere) # The official PLoS blog: This content is produced, edited, and/or maintained by PLoS staff. # The journal blogs: This content is produced, edited, and/or maintained by PLoS journal staff: The current journal blogs are Speaking of Medicine (PLoS Medicine's blog) and everyONE (PLoS ONE's blog). # Our independent network of bloggers (The PLoS Blogosphere): This content is produced, edited, and/or maintained by the authors. * All of the content in The PLoS Blogosphere came from the minds of the authors. PLoS does not screen, edit, or otherwise meddle with content on the these blogs in any way. Our bloggers and our users are held to exactly the same standards, and the community guidelines apply to everyone that uses our site. If a blogger has posted content that you believe violates our site abuse policy, please contact PLoS. * Bloggers monitor their own comment threads: All comments will be reviewed by the author of the blog where you leave your thoughts. Just follow our simple community guidelines and we'll all get along just fine.

Neurospora crassa Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-20965
abbrev: NCD
IAO_0000115: It's strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated and reassembled. This method is standard for microbial genome sequencing, and has been successfully applied to Drosophila. Neurospora is an ideal candidate for this approach because of the low repeat content of the genome. Neurospora crassa Database has expanded the scope of its database by including a mitochondrial annotation, incorporating information from the Neurospora compendium, and assigning NCU numbers to tRNA and rRNAs. They have improved the annotation process to predict untranslated regions and to reduce the number of spurious predictions. As a result, version 3 contains 9,826 genes, 794 fewer than version 2. During the initial phase of a WGS project they sequence both ends of the 4 kb inserts from a plasmid library prepared using randomly sheared and sized-selected DNA. The shotgun reads are assembled by recognizing overlapping regions of sequence and making use of the knowledge of the orientation and distance of the paired reads from each plasmid. Obtaining deep sequence coverage though high levels of sequence redundancy assures that the majority of the genome is represented in the initial assembly and that the consensus sequence is of high quality. Their approach toward the initial assembly was conservative, meaning they would rather fail to join sequence contigs that might overlap each other than risk making false joins between two closely related but non-overlapping genomic regions. Hence, the initial assembly contains many sequence contigs and over time these contigs will increase in size and decrease in number as they are joined together. After shotgun sequencing and assembly there was a second phase of sequencing in which additional sequence was obtained from specific regions that were missing from the original assembly or are recognized to be of low quality in the consensus. The Neurospora crassa sequencing project reflects a close …

Resource for Biocomputing Visualization and Informatics
type: Resource
type: NamedIndividual
has db xref: nlx_152531
abbrev: RBVI
IAO_0000115: Biomedical technology resource center that develops software and web-based resources for the visualization and analysis of molecular structure, and related data, at scales ranging from the atomic to the supramolecular. They create tools for handling and integrating diverse types of biomolecular data, including atomic-resolution coordinates, density maps, sequences, annotations, and networks. Their primary efforts are in the visualization and analysis of structures of molecules and molecular assemblies, enzyme sequence-structure-function relationships, and network representations of protein similarity, binding interactions, and biological pathways. They provide technologies to enable identifying the molecular bases of disease and phenotypic variation, annotating proteins of unknown function, identifying targets for drug development, designing drugs, and engineering proteins with new functions. RBVI distributes software tools, including the popular UCSF Chimera visualization and analysis package, develops and hosts the Structure-Function Linkage Database, and provides access to state-of-the-art computational resources in support of research projects in these areas.

Structure-function linkage database
type: Resource
type: NamedIndividual
has db xref: nlx_152532
abbrev: SFLD
IAO_0000115: A database of hierarchical classification of enzymes that relates specific sequence-structure features to specific chemical capabilities. The SFLD classifies evolutionarily related enzymes according to shared chemical functions and maps these shared functions to conserved active site features. The classification is hierarchical, where broader levels encompass more distantly related proteins with fewer shared features. It thus serves as the analysis and archive site for superfamilies targeted by the Enzyme Function Initiative, and is developed by the Babbitt Laboratory in collaboration with the UCSF Resource for Biocomputing, Visualization, and Informatics. The resource also provides a collection of tools and data for investigating sequence-structure-function relationships and hypothesizing function.

Open metadata mark up language
type: Resource
type: NamedIndividual
has db xref: nlx_152533
synonym: open metadata Markup Language
abbrev: odML
IAO_0000115: Mark up language for collecting and exchanging metadata in an automated, computer-based fashion, developed for neuroscience, specifically, neurophysiology experiments. In odML arbitrary metadata information is stored as extended key-value pairs in a hierarchical structure. Central to odML is a clear separation of format and content, i.e., neither keys nor values are defined by the format. This makes odML flexible enough for storing all available metadata instantly without the necessity to submit new keys to an ontology or controlled terminology. Common standard keys can be defined in odML-terminologies for guaranteeing interoperability.

3DVC
type: Resource
type: NamedIndividual
has db xref: nlx_152536
synonym: 3D Virtual Cell
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, confirmed by curator 11/21/2018; Community of researchers attempting to build a comprehensive virtual cell model. The 3DVC will do for cell biology what the Large Hadron Collider (LHC) does for particle physics, but through a virtual rather than physical resource. It will bring together collaborators around a shared infrastructure to advance the field through efficient groundbreaking science and technology, the results of which will be broadly disseminated to an audience ranging from K12 to professionals. The 3DVC is committed to open science, yet strives for sustainability through new business models that leverages that open content.

Morpholino Database
type: Resource
type: NamedIndividual
has db xref: nlx_152566
synonym: MODB (MOprholino DataBase)
abbrev: MODB
IAO_0000115: Central database to house data on morpholino screens currently containing over 700 morpholinos including control and multiple morpholinos against the same target. A publicly accessible sequence-based search opens this database for morpholinos against a particular target for the zebrafish community. Morpholino Screens: They set out to identify all cotranslationally translocated genes in the zebrafish genome (Secretome/CTT-ome). Morpholinos were designed against putative secreted/CTT targets and injected into 1-4 cell stage zebrafish embryos. The embryos were observed over a 5 day period for defects in several different systems. The first screen examined 184 gene targets of which 26 demonstrated defects of interest (Pickart et al. 2006). A collaboration with the Verfaillie laboratory examined the knockdown of targets identified in a comparative microarray analysis of hematopoietic stem cells demonstrating how microarray and morpholino technologies can be used in conjunction to enrich for defects in specific developmental processes. Currently, many collaborations are underway to identify genes involved in morphological, kidney, skin, eye, pigment, vascular and hematopoietic development, lipid metabolism and more. The screen types referred to in the search functions are the specific areas of development that were examined during the various screens, which include behavior, general morphology, pigmentation, toxicity, Pax2 expression, and development of the craniofacial structures, eyes, kidneys, pituitary, and skin. Only data pertaining to specific tests performed are presented. Due to the complexity of this international collaboration and time constraints, not all morpholinos were subjected to all screen types. They are currently expanding public access to the database. In the future we will provide: * Mortality curves and dose range for each morpholino * Preliminary data regarding the effectiveness of each morpholino * Expanded annotation for each morpholino * External…

Cellular Scale
type: Resource
type: NamedIndividual
has db xref: nlx_153931
synonym: The Cellular Scale
synonym: TheCellularScale
IAO_0000115: Blog focusing on cellular-level neuroscience for everyone. While a higher level of neuroscience, such as behavioral studies and human fMRI scans level of neuroscience is interesting to everyone, some people might want to focus a little closer in. That is what The Cellular Scale is for.

Bioscholar
type: Resource
type: NamedIndividual
has db xref: nlx_152541
abbrev: BioScholar
IAO_0000115: Knowledge management and engineering system software for experimental biomedical scientists permitting a single scientific worker (at the level of a graduate student or postdoctoral worker) to design, construct and manage a shared knowledge repository for a research group derived on a local store of PDF files. Usability is especially emphasized within a laboratory so that this software could provide support to experimental scientists attempting to construct a personalized representation of their own knowledge on a medium scale. The BioScholar system uses a graphical interface to create experimental designs based on the experimental variables in the system. The design is then analyzed to construct a tabular input form based on the data flow. They call this methodology "Knowledge Engineering from Experimental Design" or "KEfED". The approach is domain-independent but domain-specific modules reasoning can be constructed to generate interpretations from the observational data represented in the KEfED model. The application is available for download as platform-specific installers including Linux, Unix, Mac OS, and Windows. The installer will install an application that will run the BioScholar server. This server uses Jetty as its integrated web server.

Sumatra
type: Resource
type: NamedIndividual
has db xref: nlx_152549
synonym: Sumatra: automated tracking of scientific computations
IAO_0000115: A software tool for managing and tracking projects based on numerical simulation or analysis to support reproducible research. It can be thought of as an automated electronic lab notebook for simulation/analysis projects. Sumatra consists of: a command-line interface, smt, for launching simulations/analyses with automatic recording of information about the context, annotating these records, linking to data files, etc.; a web interface with a built-in web-server, smtweb, for browsing and annotating simulation/analysis results; a LaTeX package and Sphinx extension for including Sumatra-tracked figures and links to provenance information in papers and other documents; and a Python API, on which smt and smtweb are based, that can be used in personalized scripts in place of using smt.

NeuralEnsemble
type: Resource
type: NamedIndividual
has db xref: nlx_152550
synonym: neuralensemble.org
abbrev: Resource:NeuralEnsemble
IAO_0000115: Community-based initiative to promote and co-ordinate open-source software development in neuroscience hosting a number of software projects for computational and systems neuroscience, including PyNN, NeuroTools, Brian, Neo, OpenElectrophy, libNeuroML and Sumatra. Some of the projects use their Trac installation, others are on GitHub. By grouping these projects together under the NeuralEnsemble umbrella, the aim is to maximize interoperability and build components that can easily be combined into powerful systems for brain simulations and advanced data analysis. An annual CodeJam workshop is organized, bringing together scientists, graduate students, and scientific programmers to share ideas, present their work, and write code together. These workshops have been hugely effective in catalyzing open-source neuroscience software development. There is a NeuralEnsemble Google group for discussion of collaborative neuroscience software development (mainly in Python, but users of other languages are welcome!) and to provide software support.

Semantic Measures Library
type: Resource
type: NamedIndividual
has db xref: nlx_152555
synonym: Semantic Measures Library & ToolKit
synonym: Semantic Measures Library and ToolKit
synonym: SML-Toolkit
abbrev: SML
IAO_0000115: Open source Java library dedicated to semantic measures computation and analysis. Tools based on the SML are also provided through the SML-Toolkit, a command line software giving access to some of the functionalities of the library. The SML and the toolkit can be used to compute semantic similarity and semantic relatedness between semantic elements (e.g. concepts, terms) or entities semantically characterized (e.g. entities defined in a semantic graph, documents annotated by concepts defined in an ontology).

Center for Gamma Ray Imaging
type: Resource
type: NamedIndividual
has db xref: nlx_152567
abbrev: Center for Gamma-Ray Imaging
IAO_0000115: Biomedical technology resource center that develops new gamma-ray imaging instruments and techniques that yield substantially improved spatial and temporal resolutions. The Center makes its imagers and expertise available to a wide community of biomedical and clinical researchers through collaborative and service-oriented interactions. The collaborative research applies these new imaging tools to basic research in functional genomics, proteomics, cancer, cardiovascular disease and cognitive neuroscience, and to clinical research in tumor detection and other selected topics. There are five core research projects: * Detector technology research and development * Reconstruction algorithms and system modeling * Data acquisition, signal processing, and system development * Image-quality assessment and system optimization * Techniques for molecular imaging

LYSIS
type: Resource
type: NamedIndividual
has db xref: nlx_152571
IAO_0000115: Interactive software of a set of modular programs (each performing a specific task) that provide an integrated computing environment for data analysis and system modeling. Unique capabilities of LYSIS include input-output nonlinear system modeling and the novel methodology of Principal Dynamic Modes (PDMs). LYSIS is currently available in two versions: one for LYSIS 7.1 Windows and one for LYSIS 7.2 Matlab. Early versions are also available for UNIX environments, distributed as source code that can be compiled for each UNIX implementation (e.g., Solaris, HPUX, Linux). Specific features of LYSIS that cannot be found in commercially available packages include the efficient kernel estimation using Laguerre expansions and the use of Principal Dynamic Modes (PDMs). These enable input-output modeling of dynamic nonlinear systems with relatively short data-records (even in the presence of considerable noise). System Requirements * Operating System ** Windows XP/Vista/7 ** Sun/Unix: Solaris 2.x

ODIN
type: Resource
type: NamedIndividual
has db xref: nlx_152557
synonym: ORCID and DataCite Interoperability Network
IAO_0000115: Service (Beta) that allows users to search the DataCite Metadata Store, and add their research outputs including datasets, software, and others to their ORCID profile. This should increase the visibility of these research data, and will make it easier to use these data citations in applications that connect to the ORCID Registry. In addition, the service is also providing formatted citations in several popular citation styles, supports COinS, links to related resources, and displays the attached Creative Commons license where this information is available. The DataCite Metadata Store of course also contains many text documents from academic publishers and services such as figshare or PeerJ Preprints, and these works can also be claimed. This tool is a collaborative effort by ORCID, CrossRef and DataCite.

Clarity resources
type: Resource
type: NamedIndividual
has db xref: nlx_152559
synonym: Clarity resource
abbrev: CLARITY Resources
IAO_0000115: Protocols and other training materials related to the CLARITY protocol, a technique for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable.

CODR: C PATH On Line Data Repository
type: Resource
type: NamedIndividual
has db xref: nlx_152562
synonym: C PATH On Line Data Repository
synonym: C-PATH Online Data Repository
synonym: C-Path Online Data Repository (CODR)
synonym: CPATH online data repository
abbrev: CODR
IAO_0000115: A repository of de-identified control arm data of patients from clinical studies of Alzheimer's disease and Mild Cognitive Impairment. It provides the ability to analyze the data online with the R statistical analysis program, create and download standard reports, run complex queries, or download data to a desktop for further analysis. Additional data will be added to the database over time. Critical Path Institute consortia members and qualified researchers may upload and work on scientific data relevant to biomarkers of drug toxicity, neurodegenerative diseases, and patient-reported outcomes.

CAMD
type: Resource
type: NamedIndividual
has db xref: nlx_152563
synonym: Coalition Against Major Diseases
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 8, 2022. Consortium developing new technologies and methods to accelerate the development and review of medical products for neurodegenerative diseases. It is focused on accelerating drug development for patients with chronic neurodegenerative disease, namely, Alzheimer's disease (AD) and Parkinson's disease (PD), by advancing drug development tools for evaluating drug efficacy, conducting clinical trials, and streamlining the process of regulatory review. The consortium focuses on sharing precompetitive patient-level data from the control arms of legacy clinical trials, developing new tools to be submitted to the regulatory agencies, and developing consensus data standards. CAMD has the following areas of focus: (1) qualification of biomarkers, (2) development of common data standards, (3) creation of integrated databases for clinical trials data, and (4) development of quantitative model-based tools for drug development. Regulatory milestones include a qualification opinion with EMA for the use of low baseline hippocampal volume for patient enrichment in pre-dementia trials, and most recently, positive regulatory decisions from the FDA and EMA for the use of a clinical trial simulation tool to aid in trials for mild to moderate stages of AD., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

NIH Common Data Element Repository
type: Resource
type: NamedIndividual
has db xref: nlx_152564
synonym: Common Data Element (CDE) Resource Portal
synonym: NIH Common Data Element (CDE) Resource Portal
abbrev: CDE Resource Portal
abbrev: NIH CDE Resource Portal
IAO_0000115: A repository of Common Data Elements (CDE). The CDE is a standardized, precisely defined question, paired with a set of allowable responses, used systematically across different sites, studies, or clinical trials to ensure consistent data collection. Multiple CDEs (from one or more Collections) can be curated into Forms. Forms in the Repository might be original, or might recreate the format of real-world data collection instruments or case report forms. NIH has endorsed collections of CDEs that meet established criteria. NIH-endorsed CDEs are designated with a gold ribbon. Users can Browse NIH-Endorsed CDEs, Browse All CDEs, or Browse Forms.

PNEUMA
type: Resource
type: NamedIndividual
has db xref: nlx_152572
IAO_0000115: A set of modules that are used to simulate the autoregulation of the cardiovascular and respiratory systems under conditions of changing sleep-wake state and a variety of physiological and pharmacological interventions. It models the dynamic interactions that take place among the various component mechanisms, including those involved in the chemical control of breathing, heart rate, and blood pressure, as well as the effects of changes in the sleep-wake state and arousal from sleep. PNEUMA includes the autonomic control of the cardiovascular system, chemoreflex and state-related control of breath-to-breath ventilation, state-related and chemoreflex control of upper airway potency, as well as respiratory and circulatory mechanics. The model is capable of simulating the cardiorespiratory responses to sleep onset, arousal, continuous positive airway pressure, the administration of inhaled carbon dioxide and oxygen, Valsalva and Mueller maneuvers, and Cheyne-Stokes respiration during sleep. In PNEUMA 3.0, we have extended the existing integrative model of respiratory, cardiovascular, and sleepwake state control, to incorporate a sub-model of glucoseinsulinfatty acid regulation. The extended model is capable of simulating the metabolic control of glucoseinsulin dynamics and its interactions with the autonomic nervous system. The interactions between autonomic and metabolic control include the circadian regulation of epinephrine secretion, epinephrine regulation on dynamic fluctuations in glucose and free fatty acids in plasma, metabolic coupling among tissues and organs mediated by insulin and epinephrine, as well as the effect of insulin on peripheral vascular sympathetic activity. This extended model represents a starting point from which further in silico investigations into the interaction between the autonomic nervous system and the metabolic control system can proceed. Features in PNEUMA 3.0 * Incorporates metabolic component based on prior models of glucose-insuli…

TARGETgene
type: Resource
type: NamedIndividual
has db xref: nlx_152573
IAO_0000115: MATLAB tool to effectively identify potential therapeutic targets and drugs in cancer using genetic network-based approaches. It can rapidly extract genetic interactions from a precompiled database stored as a MATLAB MAT-file without the need to interrogate remote SQL databases. Millions of interactions involving thousands of candidate genes can be mapped to the genetic network within minutes. While TARGETgene is currently based on the gene network reported in (Wu et al.,Bioinformatics 26:807-813, 2010), it can be easily extended to allow the optional use of other developed gene networks. The simple graphical user interface also enables rapid, intuitive mapping and analysis of therapeutic targets at the systems level. By mapping predictions to drug-target information, TARGETgene may be used as an initial drug screening tool that identifies compounds for further evaluation. In addition, TARGETgene is expected to be applicable to identify potential therapeutic targets for any type or subtype of cancers, even those rare cancers that are not genetically recognized. Identification of Potential Therapeutic Targets * Prioritize potential therapeutic targets from thousands of candidate genes generated from high-throughput experiments using network-based metrics * Validate predictions (prioritization) using user-defined benchmark genes and curated cancer genes * Explore biologic information of selected targets through external databases (e.g., NCBI Entrez Gene) and gene function enrichment analysis Initial Drug Screening * Identify for further evaluation existing drugs and compounds that may act on the potential therapeutic targets identified by TARGETgene * Explore general information on identified drugs of interest through several external links Operating System: Windows XP / Vista / 7

Open Source Brain
type: Resource
type: NamedIndividual
has db xref: nlx_152590
synonym: OpenSourceBrain
abbrev: OSB
IAO_0000115: A resource for sharing and collaboratively developing computational models of neural systems. While models can be submitted and developed in any format, the use of open standards such as NeuroML and PyNN is encouraged, to ensure transparency, modularity, accessibility and cross simulator portability. OSB will provide advanced facilities to analyze, visualize and transform models in these formats, and to connect researchers interested in models of specific neurons, brain regions and disease states. Research themes include: Basal ganglia modelling, Cerebellar Granule cell modelling, Cerebellar modelling, Hippocampal modelling, Neocortical modelling, Whole brain models. Additional themes are welcome.

NeuroMorpho.Org light species ontology
type: Resource
type: NamedIndividual
has db xref: nif-0000-07761
synonym: NeuroMorpho.Org Species Ontology
synonym: NMO Species Ontology
IAO_0000115: NeuroMorpho.Org light species ontology is a customized taxonomy for species available in NeuroMorpho.Org. This file is created from the existing resources like NCBI Taxonomy, NIF organism, Rat strain ontology, and Jax mice catalogue. The OBO file can be explored and downloaded from the NCBO bioportal service. The current NCBI_NMOsp_v1.2.2.obo file consists of 887 concepts of which 24 unique classes are mapped onto species & strains data in NeuroMorpho.Org database.

Happy
type: Resource
type: NamedIndividual
has db xref: nlx_152594
synonym: reconstructing HAPlotYpes
abbrev: HAPPY
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals (entry from Genetic Analysis Software) The method is implemented in a C-program and there is now an R version of HAPPY. You can run HAPPY remotely from their web server using your own data (or try it out on the data provided for download).

Ochsner Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_31470
synonym: Ochsner Biobank Unit
synonym: Ochsner Tumor Tissue Bank
IAO_0000115: Biospecimen and clinical data repository for researchers that includes tumor and normal tissue, blood samples, and other bio fluids. Samples are refrigerated, frozen, deep frozen, or frozen in liquid nitrogen. Four service lines are provided: ExpressBank offers access to biospecimens, which are collected under IRB-approved core protocol for future unknown research projects; Service Bank offers services such as biospecimen procurement, processing, and temporary banking; PathBank offers access to high-quality, annotated formalin-fixed paraffin-embedded (FFPE) tissues and H&E slides from Pathology department on fee-for-sample basis; and On-DemandBank allows targeted development of a temporary Biobank that strictly meets the specifications of an IRB-approved collection protocol of a sponsor on fee-for-service basis.

Online Neuroscience Lectures - Maintained by the Kilgard Lab
type: Resource
type: NamedIndividual
has db xref: nif-0000-08126
synonym: Online Neuroscience Lectures
IAO_0000115: List of lectures, slides and videos concerning neuroscience and neurophysiology.

MRI Studio
type: Resource
type: NamedIndividual
has db xref: nif-0000-00291
synonym: DTI Studio
synonym: dtiStudio
IAO_0000115: An image processing program running under Windows suitable for such tasks as tensor calculation, color mapping, fiber tracking, and 3D visualization. Most of operations can be done with only a few clicks. This tool evolved from DTI Studio. Tools in the program can be grouped in the following way: * Image Viewer * Diffusion Tensor Calculations * Fiber Tracking and Editing * 3D Visualization * Image File Management * Region of Interesting (ROI) Drawing and Statistics * Image Registration

Retinal Topography Maps Database
type: Resource
type: NamedIndividual
has db xref: nlx_152606
synonym: Retinal topography maps
synonym: retinalmaps.org
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A database of over 700 retinal topography maps of a wide variety of species published in a diversity of journals. It has been assembled to assist vision and neuroscience researchers to locate and compare the distribution of retinal neurons within and across species. The maps can be searched by taxonomic or common name classification, cell type sampled, type of retinal specialization and staining/visualization method. Maps can be compared by selecting multiple maps and clicking the Compare Selected button. An interactive spreadsheet can be also downloaded.

THOR Center for Neuroinformatics
type: Resource
type: NamedIndividual
has db xref: nif-0000-08128
synonym: Technology by Highly Oriented Research Center for Neuroinformatics
abbrev: THOR Center
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.Center hosting a number of related projects concerning neural networks, functional neuroimaging, multimedia signal processing, and biomedical signal processing. Neuroinformatics is a research field rooted in classical disciplines like signal processing, biology, physics, computer science and engineering. Neuroinformatics combines learning from the brain and learning about the brain. By studying information processing in the brain neuroinformatics invents new computing paradigms (e.g., artificial neural networks) with the objective of understanding the dynamics of the conscious mind. Artificial neural networks is an active neuroinformatics research field, which combines many approaches to adaptive signal processing in solving real world problems. They began using neural networks for general nonlinear adaptive signal processing. Since 1991 the CONNECT groups have participated in the development of neural computing as an advanced, non-linear statistical tool, which has been applied to forecasting within dynamical systems, pattern recognition, and medical image analysis, particularly functional neuroimages. While neural computing has largely been viewed as a black box approach, they have initiated research aimed at opening this black box, using hypertext, multimedia, and interactivity. Their key objective is to convert abstract models into intuitive knowledge through interactive visualization.

UCSD Center for NMR Spectroscopy and Imaging of Proteins
type: Resource
type: NamedIndividual
has db xref: nlx_152626
synonym: Center for NMR Spectroscopy and Imaging of Proteins
synonym: Resource for NMR Molecular Imaging of Proteins
abbrev: NMR Resource at UCSD
IAO_0000115: Biomedical technology research center that develops new technology for NMR spectroscopy and makes it available to the biomedical research community for structure determination of proteins in biological supramolecular assemblies, such as membrane proteins or virus particles. The principal applications are to membrane-associated proteins; however, the approach is generally applicable to polypeptides that cannot be prepared in forms suitable for X-ray crystallography or multidimensional solution NMR spectroscopy. As a result, there are also applications to viruses and other biological systems. The principal instrumentation consists of high-field NMR spectrometers dedicated to high-resolution solid-state NMR spectroscopy. The spectrometers are capable of the full-range of multiple-resonance experiments on stationary and spinning samples; however, the major emphasis is on methods that utilize mechanically or magnetically oriented samples. Development encompasses preparation of samples, including: * Expression and purification of membrane proteins * Design and construction of instrumentation, especially probes * Implementation of new pulse sequences and other experimental protocols for solid-state NMR spectroscopy * Calculations for the processing of experimental data and protein structure determination from the orientational constraints derived from these data

WegoLoc
type: Resource
type: NamedIndividual
has db xref: OMICS_01636
synonym: weighted gene ontology term based subcellular locallization prediction
IAO_0000115: Data analysis service that predicts protein subcellular localizations of animal, fungal, plant, and human proteins based on sequence similarity and gene ontology information.

Israel Plant Gene Bank
type: Resource
type: NamedIndividual
has db xref: nlx_61310
IAO_0000115: Biobank which collects, preserves, and assesses gene information related to species of plants indigenous to Israel. The Bank's goal is to conserve representative gene pools of species whose economic potential has yet to be developed.

Resource Center for Medical Ultrasonic Transducer Technology
type: Resource
type: NamedIndividual
has db xref: nlx_152627
synonym: Resource on Medical Ultrasonic Transducer Technology
synonym: Ultrasonic Transducer Resource Center
synonym: USC Resource Center for Medical Ultrasonic Transducer Technology
abbrev: UTRC
IAO_0000115: Biomedical technology research center focusing on the development of very high frequency (above 20 MHz) ultrasonic transducers/arrays for applications in medicine and biology that include ophthalmology, dermatology, vascular surgery, and small animal imaging. The research is pursued simultaneously in three directions: novel piezoelectric materials, very high frequency single element transducers and linear arrays, and finite element modeling and material property measurements. The Center also serves the community through collaborative efforts with investigators having a research interest in high-frequency ultrasound imaging. In addition, it performs the function of training and information dissemination by offering conferences, seminars and specialized courses at the University of Southern California. The Center has set forth a number of goals which define its mission: * Conduct novel research and development of very high frequency (>20MHz) ultrasonic transducers, arrays and imaging applications * Collaborate with other academic institutions, non-profit organizations, and small businesses supported by the NIH to further the development of these high-frequency applications and provide the expertise in transducers necessary for project success * Serve as an educational center for training scientists and engineers interested in ultrasonic transducer technology One of the primary goals of the Center is to provide service to outside investigators and small business. Often an investigator or company has a specific application in mind but is without the expertise to develop the necessary ultrasonic device. Investigators at academic institutions, research institutes, or small businesses supported by NIH grants who have a need for medical ultrasound transducers and are interested in a collaborative effort should contact Dr. Hyung Ham Kim or Dr. K. Kirk Shung. Ultrasound transducers and components can be fabricated either completely by center personnel or in a joint effort wit…

Hyperpolarized MRI Technology Resource Center
type: Resource
type: NamedIndividual
has db xref: nlx_152628
synonym: UCSF Hyperpolarized MRI Technology Resource Center
IAO_0000115: Biomedical technology research center developing, investigating, and disseminating new hyperpolarized MR techniques, new 13C agents and specialized analysis open-source software for data reconstruction and interpretation. The Technology Research & Development projects will leverage the extensive DNP facilities and experience of the project leaders to develop improved, robust hyperpolarized MRI methods. These technology developments will be driven by Collaborative Projects led by outstanding clinical and basic scientists who aim to use hyperpolarized 13C MRI to accomplish the scientific goals of their funded research. These technical developments will also be disseminated to the Service Project investigators for extramural feedback and then widely to the scientific community via a dedicated website and onsite training. This center will provide state-of-the-art training in this new metabolic imaging field and sponsor a yearly symposium focused on hyperpolarized MR technology development.

Richard M. Lucas Center for Imaging
type: Resource
type: NamedIndividual
has db xref: nlx_152629
synonym: Center for Advanced Magnetic Resonance Technology
synonym: Lucas Center for Imaging
abbrev: CAMRT
abbrev: Lucas Center
IAO_0000115: Biomedical technology research center that develops innovative technologies in five core research areas of magnetic resonance imaging and spectroscopy (MRI/MRS): # image reconstruction, fast imaging and radiofrequency (RF) pulse design methods, # R hardware development, # body imaging methods, # neuroimaging methods. # MR spectroscopy methods. In each of these areas, they capitalize on the long-standing, successful partnership and extensive experience in Stanford's Radiology and Electrical Engineering departments to improve and expand imaging technology for use in basic research and clinical care, and to provide cutting edge opportunities to the extramural community for biomedical research with MRI. Over its more than 18 years of existence, CAMRT has been motivated by and has served a wide base of extramurally sponsored collaborators and service users from leading medical and research institutions. Examples of collaborative projects are the development of real-time functional MRI biofeedback methods for neuroscience and clinical applications such as pain remediation, development of methods to mitigate metal artifacts in musculoskeletal imaging, development of novel RF pulses for many applications, and studies of breast cancer with efficient MRS methods.

BraVa
type: Resource
type: NamedIndividual
has db xref: nlx_152630
IAO_0000115: A database of digital reconstructions of the human brain arterial arborizations from 61 healthy adult subjects along with extracted morphological measurements. The arterial arborizations include the six major trees stemming from the circle of Willis, namely: the left and right Anterior Cerebral Arteries (ACAs), Middle Cerebral Arteries (MCAs), and Posterior Cerebral Arteries (PCAs).

Pittsburgh NMR Center for Biomedical Research
type: Resource
type: NamedIndividual
has db xref: nlx_152651
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 19,2024. Biomedical Technology Research Center that develops methodologies for the acquisition of morphological, biochemical, cellular, and functional information in living animals using nuclear magnetic resonance imaging (MRI) and spectroscopy (MRS). Novel techniques utilizing multidimensional MR imaging, magnetic resonance microscopy (MRM), and multinuclear in vivo spectroscopy are being applied to a wide range of problems in the biomedical sciences.

Laser Microbeam and Medical Program
type: Resource
type: NamedIndividual
has db xref: nlx_152631
abbrev: LAMMP
IAO_0000115: Biomedical technology research center dedicated to the use of lasers and optics in biology and medicine with activities in technological research and development, collaborative research, service, training, and dissemination. One of the primary goals of LAMMP is to facilitate translational research by rapidly moving basic science and technology discoveries from blackboard to benchtop to bedside. This is accomplished by combining state of the art optical technologies with specialized resource facilities for cell and tissue engineering, histopathology, pre-clinical animal models, and clinical care. The resource center has been organized into 3 cores: * Microscopy and Microbeam Technologies (MMT) for high-resolution functional imaging and manipulation of living cells and tissues * Medical Translational Technologies (MTT) for non- and minimally-invasive monitoring, treating, and imaging pre-clinical animal models and human subjects, and * Virtual Photonics Technologies (VPT) for developing computational models and methods that advance the performance of biophotonic technologies, and enhance the information content derived from optical measurements. LAMMP cores contain complementary technologies that are capable of quantitatively characterizing, imaging, and perturbing structure and biochemical function in cells and tissues with scalable resolution and depth sensitivity ranging from micrometers to centimeters.

Center for EPR Imaging in Vivo Physiology
type: Resource
type: NamedIndividual
has db xref: nlx_152632
synonym: Center for Electron Paramagnetic Resonance (EPR) Imaging in Vivo Physiology
synonym: Center for Electron Paramagnetic Resonance Imaging in Vivo Physiology
synonym: Very Low Frequency ERP Imaging In Vivo Physiology
IAO_0000115: Biomedical technology research center that develops instrumentation, analysis techniques, spin probes and spin traps, and methodologies for imaging physiologically relevant aspects of tissue fluids, including high-resolution oxygen maps, with very low frequency electron paramagnetic resonance imaging (EPRI). Novel bridges and high-access, low-field magnet/gradient systems have produced physiologically relevant measurements and accommodate a number of resonant structures. The Center is a consortium between the University of Chicago, the University of Denver, the University of Maryland and Novosibirsk Institute of Organic Chemistry (NIOC), Russia.

Brede Wiki
type: Resource
type: NamedIndividual
has db xref: nif-0000-08130
synonym: Brede Wiki - a neuroinformatics wiki
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 10, 2025. Semantic wiki with structured information, primarily from functional and molecular neuroimaging papers, but there are also other types of papers, e.g., from personality genetics. It lists results from neuroimaging studies, such as Talairach coordinates and brain volume measurements, as well as software packages and brain regions. SQL dumps of the structured information in the wiki is available so complex queries can be formed. The Brede Wiki templates store the structured information from neuroscience papers and editors may add free format text. Template definitions format the data so it is presented as tables on the formatted wiki-page. From a given PMID a web-service can format information from PubMed for inclusion in the Brede Wiki. A Matlab script can extract coordinates from SPM5 and format them in the Talairach coordinate template format.

MIT/ Harvard Center for Magnetic Resonance
type: Resource
type: NamedIndividual
has db xref: nlx_152635
synonym: MIT/ Harvard Center for Magnetic Resonance 900 MHz NMR Facility
synonym: MIT/ Harvard Center for Magnetic Resonance (CMR) 900 MHz NMR Facility
synonym: MIT/Harvard Center for Magnetic Resonance
abbrev: CMR
IAO_0000115: Biomedical technology research center designated as a biotechnology nuclear magnetic resonance (NMR) resource that hosts research efforts into cancer, neurological diseases, and many other areas. The heart of the 900 MHz magnetic resonance instrument is a superconducting magnet with a field strength of 21 Tesla, the highest field currently available for magnetic resonance spectroscopy, roughly 400,000 times stronger than the earth's magnetic field. Magnetic resonance is a powerful tool for determining the structure of molecules, and has proven especially useful for elucidating the role of proteins in biological processes and diseases. The state of the art facility includes two 17.6 T magnets with a third to be delivered in 2000. With multiple 17.6 T NMR magnets, the CMR is a valuable resource in New England and will continue to serve this research community for years to come. The advent of high magnetic fields has placed demands on the hardware needed to run experiments in these very high fields. The CMR has recently produced new advances in NMR probe technology, in electron magnetic resonance, and in using microwaves to enhance NMR experiments. The results are powerful new methods for performing biological research and they are looking forward to the continued growth of these exciting new areas!

Computer Integrated Systems for Microscopy and Manipulation
type: Resource
type: NamedIndividual
has db xref: nlx_152648
synonym: UNC Chapel Hill Computer Integrated Systems for Microscopy and Manipulation
abbrev: CISMM
IAO_0000115: Biomedical technology research center that develops force technologies applicable over a wide range of biological settings, from the single molecule to the tissue, with integrated systems that orchestrate facile instrument control, multimodal imaging, and analysis through visualization and modeling. The Force Microscope Technologies Core designs instruments in an area of science where there are unusual opportunities: the measurement of forces and the integration with optical microscopy. Force technologies play the obvious role of both measuring events in the sample and modifying the sample during the experiment. It is through the microscope that the force data is correlated with simultaneous 3D optical images. The force technology development includes the magnetic bead technology in the 3D Force Microscope project, Atomic Force Microscopy in the nanoManipulator project, and Control Software to drive the instrumentation. This core is focused on providing the physical capability to perform the experiments and probe structure/property correlations. The Ideal User Interfaces core makes the connection between the user and the instrument, the model building, and the data. This includes control systems that allow the user to move the bead inside the cell culture with a handheld pen and the visualization techniques to view the optical microscope data as a rendered 3D image collocated with the force data. Using data to create, change, and understand a model is the focus of the Advanced Model Fitting and Analysis core. The quantitative reduction of images to structural, shape, and velocity parameters is the goal of Image Analysis. The immediate understanding of correlations across image fields and between data sets in the challenge of Visualization. The power of combining the strength of a computer science graphics group with a microscopy technology group is most evident in the Graphics Hardware Acceleration project, which seeks to harness the speed of graphics processors for…

Mugsy
type: Resource
type: NamedIndividual
has db xref: OMICS_03606
IAO_0000115: Software resource for multiple whole genome alignment. It uses Nucmer, a custom graph-based segmentation procedure, for pairwise alignment, and the Seqan:TCoffee's multiple alignment strategy.

Diabetic Complications Consortium
type: Resource
type: NamedIndividual
has db xref: nlx_152636
synonym: AMDCC
synonym: Animal Models of Diabetic Complications Consortium
abbrev: DiaComp
IAO_0000115: Consortium serving the diabetic complications community that sponsors annual meetings in complications-relevant scientific areas, solicits and funds pilot projects in high impact areas of complications research, and provides resources and data including animal models, protocols and methods, validation criteria, reagents and resources, histology, publications and bioinformatics for researchers conducting diabetic complications research.

National Resource for Imaging Mass Spectrometry
type: Resource
type: NamedIndividual
has db xref: nlx_152638
abbrev: NRIMS
IAO_0000115: Biomedical technology research center with the focus on the application to biomedical research of a new generation of secondary ion mass spectrometer (SIMS), the Multi-Isotope Imaging Mass Spectrometer (MIMS). MIMS is an ion microscope and an ion counter. MIMS provides high mass separation at high transmission (M/lambdaM > 10,000), high spatial resolution (< 40 nm) and has the unique capability of simultaneously recording several atomic mass images. Of the utmost importance, MIMS makes it possible for the first time (and at the intracellular level) to simultaneously image the distribution and measure the accumulation of molecules labeled with any isotopes, in particular with stable isotopes, for example with 15N. Thus, MIMS allows one to study localization, accumulation and turnover of proteins, fats, sugars and foreign molecules in cellular microdomains, donor-receiver cellular trafficking, stem cell nesting and localization of drugs. Their aim is to be a technological, methodological, and intellectual resource for researchers from a variety of disciplines. They seek to explore and develop the unique capabilities of MIMS and to bring cutting-edge information to biology and medicine that is currently unobtainable using existing technologies.

BioMEMS Resource Center
type: Resource
type: NamedIndividual
has db xref: nlx_152639
synonym: Bio MicroElectroMechanical Systems (BioMEMS) Resource Center
synonym: Bio MicroElectroMechanical Systems Resource Center
synonym: BioMEMS
synonym: Biomicroelectromechanical Systems (BioMEMS) Resource Center
abbrev: BMRC
IAO_0000115: Biomedical technology research center that provides biomedical investigators with novel microsystems engineering tools for biological discovery, diagnostic, prognostic, and therapeutic applications. Thrust areas of interest are the development of novel living cell-based, lab-on-a-chip type devices for sorting blood cells, for high-throughput biochemistry in small volumes, and for studying cellular behavior in controlled microenvironments.

Center for Biomedical OCT Research
type: Resource
type: NamedIndividual
has db xref: nlx_152640
synonym: Center for Biomedical OCT Research and Translation
abbrev: CBORT
IAO_0000115: Biomedical technology research center that pioneers and provides access to microscopic imaging instruments for biologic and clinical research. Optical coherence tomography (OCT) has evolved over the last two decades to become a standard of care for diagnostic ophthalmic imaging and is poised to make significant impact in the fields of cardiology and gastrointestinal endoscopy. Access to state-of-the-art instrumentation, however, has been limited to a relatively few research laboratories and the optimization of instruments for new biomedical applications has hindered the investigation of new opportunities. A major focus of CBORT will be to cultivate strategic research collaborations and respond to a pressing need for application-specific OCT instrumentation and hardware.

National Center for Image-Guided Therapy
type: Resource
type: NamedIndividual
has db xref: nlx_152641
synonym: National Center for Image Guided Therapy
abbrev: NCIGT
IAO_0000115: Biomedical Technology Resource Center that serves as a national resource for all aspects of research into medical procedures that are enhanced by imaging. Its common goal is to provide more effective patient care. The center is focused on the multidisciplinary development of innovative image-guided intervention technologies to enable effective, less invasive clinical treatments that are not only more economical, but also produce better results for patients. The NCIGT is helping to implement this vision by serving as a proving ground for some of the next generation of medical therapies.

James Cook University; Townsville; Australia
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100008451
has db xref: grid.1011.1
has db xref: ISNI:0000 0004 0474 1797
has db xref: nlx_62328
has db xref: Wikidata:Q536512
synonym: James Cook University
abbrev: JCU
IAO_0000115: Public university in Townsville, Australia that functions as a research and teaching institution. Some well-known divisions of the university include the division of Tropical Environments and Societies, Tropical Health and Medicine, and Research and Innovation.

Integrated Animals
type: Resource
type: NamedIndividual
has db xref: nif-0000-08137
synonym: Integrated Animal
synonym: NIF Animals
synonym: NIF Integrated Animals
IAO_0000115: Integrated Animals is a virtual database currently indexing available animal strains and mutants from: AGSC (Ambystoma), BCBC (mice), BDSC (flies), CWRU Cystic Fibrosis Mouse Models (mice), DGGR (flies), FlyBase (flies), IMSR (mice), MGI (mice), MMRRC (mice), NSRRC (pig), NXR (Xenopus), RGD (rats), Sperm Stem Cell Libraries for Biological Research (rats), Tetrahymena Stock Center (Tetrahymena), WormBase (worms), XGSC (Xiphophorus), ZFIN (zebrafish), and ZIRC (zebrafish).

Vital Signs Ontology
type: Resource
type: NamedIndividual
has db xref: nif-0000-02605
synonym: vital-signs-ontology
abbrev: VSO
IAO_0000115: Ontology for the four consensus human vital signs: blood pressure, body temperature, respiration rate, pulse rate. It provides a controlled structured vocabulary for describing vital signs measurement data, the various processes of measuring vital signs, and the various devices and anatomical entities participating in such measurements.

Center for Functional Neuroimaging Technologies
type: Resource
type: NamedIndividual
has db xref: nlx_152644
abbrev: CFNT
IAO_0000115: Biomedical technology research center that develops and applies innovative neuroimaging technologies and techniques to enable closer examination of the human brain, and thereby contribute to better understanding of the brain in health and disease. They develop new techniques and advance existing technologies for acquisition and analysis of functionally specific images of the working brain, with unprecedented physiological precision and spatiotemporal resolution. The research and development aims to improve and extend existing methods for non-invasive magnetic resonance image analysis and acquisition, electromagnetic source imaging, optical neuroimaging, and most recently, combined MR-PET neuroimaging. The Resource provides an essential interactive environment, within which an interdisciplinary team of highly skilled scientists, engineers, and clinicians with diverse expertise in multiple modalities and disciplines. The resource supports service use of the Center's facilities by neuroscientists throughout the country, provide extensive training opportunities for students, fellows, and staff scientists, and seek to advance the field of brain mapping through active dissemination of new knowledge and technology.

RESBIO
type: Resource
type: NamedIndividual
has db xref: nlx_152646
synonym: Integrated Technologies for Polymeric Biomaterials
synonym: Polymeric Biomaterials Resource
IAO_0000115: Biomedical technology research center that works to develop integrated tools and technologies that advance the discovery of polymeric biomaterials for regenerative medicine, the delivery of biological agents, and the next generation of medical implants. To achieve its mission, RESBIO's research is focused on the development of combinatorial and computational approaches to biomaterials design and optimization. Within this framework, RESBIO employs and uses: * Advanced multi-photon confocal laser microscopy to explore, understand, and control the response of cells in contact with artificial surfaces * Electron microscopy techniques to study the effect of nano-scale surface morphological features on cell behavior RESBIO research emphasizes the integration of a strong synthetic effort to create new biomaterial candidates with the development of rapid screening techniques for key material and biological properties relevant to the performance of a biomaterial in a given medical application.

Radiological Research Accelerator Facility
type: Resource
type: NamedIndividual
has db xref: nlx_152647
synonym: Columbia University Radiological Research Accelerator Facility
abbrev: RARAF
IAO_0000115: Biomedical technology research center dedicated for radiobiological research with available ionizing radiations such as protons, alpha particles, and neutrons. RARAF is well-established and highly user-friendly. The focus of RARAF is the development of high-throughput single-cell/single-particle microbeams, which can deliver defined amounts of ionizing radiation into individual cells with a spatial resolution of a few microns or better. The ability of a microbeam to put double strand break damage at any specific known location in a given cell has allowed new approaches to the study of damage signaling.

Center for In Vivo Microscopy
type: Resource
type: NamedIndividual
has db xref: nlx_152650
synonym: Duke Center for In Vivo Microscopy
abbrev: CIVM
IAO_0000115: Biomedical technology research center dedicated to the development of novel imaging methods for the basic scientist and the application of the methods to important biomedical questions. The CIVM has played a major role in the development of magnetic resonance microscopy with specialized MR imaging systems capable of imaging at more than 500,000x higher resolution than is common in the clinical domain. The CIVM was the first to demonstrate MR images using hyperpolarized 3He which has been moved from mouse to man with recent clinical trials performed at Duke in collaboration with GE. More recently the CIVM has developed the molecular imaging workbench---a system dedicated to multimodality cardiopulmonary imaging in the rodent. Their collaborators are employing these unique imaging systems in an extraordinary range of mouse and rat models of neurologic disease, cardiopulmonary disease and cancer to illuminate the underlying biology and explore new therapies.

Open Colleges Interactive Brain
type: Resource
type: NamedIndividual
has db xref: nlx_155867
IAO_0000115: Interactive infographic of a brain exploring more than 100,000 chemical reactions, highlighted by areas and explanations of what that area is known to do.

Center for Magnetic Resonance and Optical Imaging
type: Resource
type: NamedIndividual
has db xref: nlx_152652
abbrev: CMROI
IAO_0000115: Biomedical technology research center dedicated to the development and application of innovative, novel magnetic resonance and optical imaging techniques. The facility's core sections provide research and computing resources for numerous user, collaborative, and training projects. The focus of this resource is on developing instrumentation, methodologies, and data analysis techniques for the quantitative assessment of functional, structural, and metabolic parameters in humans with the use of multinuclear magnetic resonance, novel spectral, perfusion, functional, and optical imaging techniques. These technological developments are driven by collaboration with scientists from within and outside University of Pennsylvania, the primary institution. Specifically, the Resource is focused on the development of quantitative, noninvasive MR and optical imaging based biomarkers for studying tissue metabolism and function, with an eye towards clinical translation through early diagnosis. The Center also provides support in the development and evaluation of new therapies in a variety of diseases.

Southwestern NMR Center for In Vivo Metabolism
type: Resource
type: NamedIndividual
has db xref: nlx_152653
synonym: Southwestern NMR Center for in vivo Metabolism - NIBIB
abbrev: Southwestern NMR Center
IAO_0000115: Biomedical technology research center that develops and applies new methods for analysis of metabolic networks in intact tissues, animals and human patients. The importance of understanding abnormal metabolism in common diseases such as cancer, diabetes and heart disease has long been appreciated. Because of constraints in technology, however, much of this research has been conducted in isolated systems where clinical relevance may be uncertain. Progress in magnetic resonance technology provides a foundation for major advances towards new ways of imaging metabolism in patients. These new techniques offer the advantage of imaging biochemical pathways without radiation. The focus of this Resource is to bring these technologies to a level where clinical research is feasible through the development of new MR contrast agents, NMR spectroscopy at high fields, and imaging of hyperpolarized 13C.

National ESCA and Surface Analysis Center for Biomedical Problems
type: Resource
type: NamedIndividual
has db xref: nlx_152654
synonym: NESAC/BIO - National ESCA and Surface Analysis Center for Biomedical Problems
abbrev: NESAC/BIO
IAO_0000115: Biomedical technology research center that provides state-of-the-art surface analysis expertise, instrumentation, experimental protocols, and data analysis methods to address surface-related biomedical problems. NESAC/BIO develops and applies surface science methodologies that produce a full understanding of the surface composition, structure, spatial distribution, and orientation of biomaterials and adsorbed biomolecules. The NESAC/BIO program identifies areas where surface science must evolve to keep pace with the growth in biochemical knowledge and biomaterial fabrication technology, and develops instrumentation, experimental protocols, and data analysis methods to achieve this evolution. NESAC/BIO provides state-of-the-art surface analysis tools to researchers in the biomedical community. You can gain access to the NESAC/BIO facilities in one of the following ways: * Collaborative: Propose a project to collaborate on with NESAC/BIO. The project should be rewarding for both groups, and the results should reflect the utility of surface analysis for biomedical research * Service: Ask NESAC/BIO to analyze your biomaterial specimens. The spectra obtained from the analyses will be interpreted for you. * Training: Visit the University of Washington to receive training in surface analysis and personally run experiments for your individual research projects. These experiments should have a high probability for yielding useful information and should not involve the development of new ESCA techniques or methodologies.

Mspire-Simulator
type: Resource
type: NamedIndividual
has db xref: biotools:mspire-simulator
has db xref: OMICS_03359
IAO_0000115: A free, open-source shotgun proteomic simulator that goes beyond previous simulation attempts by generating LC-MS features with realistic m/z and intensity variance along with other noise components.

Colorado University at Boulder EM Services Core Facility
type: Resource
type: NamedIndividual
has db xref: nlx_152656
has db xref: SCR_018991
synonym: Boulder Electron Microscopy Laboratory Core
synonym: Boulder EM Services Core Facility
synonym: Boulder Lab for 3D Electron Microscopy
synonym: Colorado University Boulder Electron Microscopy Core Facility
IAO_0000115: Core provides access to instruments including:FEI Tecnai 12 Spirit TEM, FEI Tecnai F20 (200kV) FEG-TEM 200kV FEG-TEM,Gatan US4000 4k x 4k CCD, bottom-mount,CryoTEM and electron tomography,High-resolution TEM;FEI Tecnai F20 (200kV) FEG-TEM,300kV FEG-TEM,Gatan US4000 4k x 4k CCD, bottom-mount,CryoTEM and electron tomography,High-resolution TEM,FEI/Phillips CM100 (100kV) TEM,100kV, tungsten TEM,2k x 2k AMT CCD, bottom-mount.

National Center for X-ray Tomography
type: Resource
type: NamedIndividual
has db xref: nlx_152657
synonym: National Center for X-ray Tomography: Cellular imaging at the mesoscale
abbrev: NCXT
IAO_0000115: Biomedical technology research center that develops novel cellular imaging technologies, specifically soft X-ray tomography, for visualizing and quantifying the internal structure of whole, hydrated cells, and high-numerical aperture fluorescence microscopy for locating the position of specific cellular molecules. Data from these two imaging modalities can be combined to form a single, correlated imaging view of a cell.

Anxiety Treatment Australia: Anxiety Disorder Help, Information and Psychologist List
type: Resource
type: NamedIndividual
has db xref: nif-0000-10151
synonym: Anxiety Treatment Australia
IAO_0000115: Anxiety Treatment Australia provides information about anxiety disorders, the treatment options, psychologists around Australia who treat anxiety disorders, group therapy & workshops, support groups, articles, resources and links to other sites. Sponsors: his website is brought to you by Catherine Madigan, a Melbourne Clinical Psychologist who specializes in the treatment of Anxiety Disorders (ABN 51 109 368 630).

NIH Center for Macromolecular Modeling and Bioinformatics
type: Resource
type: NamedIndividual
has db xref: nlx_152659
synonym: NIH Center for Macromolecular Modeling & Bioinformatics
synonym: Resource for Macromolecular Modeling and Bioinformatics
synonym: Theoretical and Computational Biophysics Group
abbrev: Center for Macromolecular Modeling and Bioinformatics
abbrev: TCBG
IAO_0000115: Biomedical technology research center focusing on the structure and function of supramolecular systems in the living cell as well as on the development of new algorithms and efficient computing tools for physical biology. They bring the most advanced molecular modeling, bioinformatics, and computational technologies to bear on questions of biomedical relevance. They extend, refine and deliver these technologies in response to experimental progress and emerging needs of the wide biomedical research community. They magnify the impact of their work through direct collaboration with experimental researchers, the distribution of cutting-edge and user-friendly software, and via extensive training, service, and dissemination efforts. The multidisciplinary team is engaged in the modeling of large macromolecular systems in realistic environments, and has produced ground-breaking insights into biomolecular processes coupled with mechanical force, bioelectronic processes in metabolism and vision, and with the function and mechanism of membrane proteins. They are committed and work towards further advancement of * Molecular modeling tools which can integrate structural information with bioinformatics databases and molecular dynamics simulations, and which can be used by a wide audience; * High performance molecular visualization and simulation software, capable of modeling biomolecules in realistic environments of 100,000,000 atoms or more; * Conceptual and methodological foundations of molecular modeling in the fields of quantum biology, mechanobiology, and interactive modeling; * Biomedical science through collaborations between theoretical and experimental researchers; * Support of the entire research process and training through a web-enabled collaborative environment; and * Service, training, and dissemination by leveraging web-based molecular graphics and integrated modeling technologies.

YPED
type: Resource
type: NamedIndividual
has db xref: nlx_152660
synonym: Yale Protein Expression Database
IAO_0000115: Open source system for storage, retrieval, and integrated analysis of large amounts of data from high throughput proteomic technologies. YPED currently handles LCMS, MudPIT, ICAT, iTRAQ, SILAC, 2D Gel and DIGE. The repository contains data sets which have been released for public viewing and downloading by the responsible Primary Investigators. It includes proteomic data generated by the Yale NIDA Neuroproteomics Center (http://medicine.yale.edu/keck/nida/index.aspx). Sample descriptions are compatible with the evolving MIAPE standards.

Laboratory for Fluorescence Dynamics
type: Resource
type: NamedIndividual
has db xref: nlx_152663
synonym: Laboratory for Fluorescence Dynamics (LFD)
abbrev: LFD
IAO_0000115: Biomedical technology research center and training resource that develops novel fluorescence technologies, including instrumentation, methods and software applicable to cellular imaging and the elucidation of dynamic processes in cells. The LFD's main activities are: * Services and Resources: the LFD provides a state-of-the-art laboratory for fluorescence measurements, microscopy and spectroscopy, with technical assistance to visiting scientists. * Research and Development: the LFD designs, tests, and implements advances in the technology of hardware, software, and biomedical applications. * Training and Dissemination: the LFD disseminates knowledge of fluorescence spectroscopic principles, instrumentation, and applications to the scientific community.

Philips Users Community
type: Resource
type: NamedIndividual
has db xref: nlx_155922
IAO_0000115: Communnity project to help support the efforts of investigators using Philips Healthcare systems. This clearingsite helps users find forums, mailinglists, etc. that support this community. If you have suggestions for inclusion, let the project admin know!

BioCARS
type: Resource
type: NamedIndividual
has db xref: nlx_152665
synonym: BioCARS: A Synchrotron Structural Biology Resource
IAO_0000115: Biomedical technology research center and training resource that is a state-of-the art, national user facility for synchrotron-based studies of dynamic and static properties of macromolecules by X-ray scattering techniques such as crystallography (specializing in time-resolved), small- and wide-angle X-ray scattering and fiber diffraction. BioCARS operates two X-ray beamlines, embedded in a Biosafety Level 3 (BSL-3) facility unique in the U.S. that permits safe studies of biohazardous materials such as human pathogens., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

BioCAT
type: Resource
type: NamedIndividual
has db xref: nlx_152666
synonym: Biophysics Collaborative Access Team
IAO_0000115: Biomedical technology research center and training resource for the study of the structure of partially ordered biological molecules, complexes of biomolecules and cellular structures under conditions similar to those present in living cells and tissues. The goal of research at BioCAT is to determine the detailed structure and mechanism of action of biological systems at the molecular level. The techniques used are X-ray fiber diffraction, X-ray solution scattering and X-ray micro-emission and micro-absorption spectroscopy, with an emphasis on time-resolved studies and the development of novel techniques.

Current Research Information System
type: Resource
type: NamedIndividual
has db xref: nlx_152704
synonym: Current Research Information System (CRIS)
synonym: U.S. Department of Agriculture Current Research Information System
abbrev: CRIS
IAO_0000115: A database of documentation and reporting for ongoing agricultural, food science, human nutrition, and forestry research, education and extension activities for the United States Department of Agriculture; with a focus on the National Institute of Food and Agriculture (NIFA) grant programs. Projects are conducted or sponsored by USDA research agencies, state agricultural experiment stations, land-grant universities, other cooperating state institutions, and participants in NIFA-administered grant programs, including Small Business Innovation Research and Agriculture and Food Research Initiative.

Macromolecular Crystallography Research Resource
type: Resource
type: NamedIndividual
has db xref: nlx_152667
synonym: Macromolecular Crystallography Research Resource at the National Synchrotron Light Source
synonym: Macromolecular Crystallography Research Resource at the NSLS
synonym: Research Resource for Macromolecular Crystallography at the National Synchrotron Light Source
abbrev: PXRR
abbrev: PXRR at the NSLS
IAO_0000115: Biomedical technology research center that creates optimal facilities and environments and support for macromolecular structure determination by synchrotron X-ray diffraction at the National Synchrotron Light Source for the benefit of outside and in-house investigators. The PXRR innovates new access modes such as Mail-in crystallography, builds new facilities, currently on the X25 undulator, advances automation, develops remote participation software, collaborates with outside groups, teaches novice users, and supports vising investigators with 7-day, 20-hours staff coverage.

MacCHESS
type: Resource
type: NamedIndividual
has db xref: nlx_152668
synonym: MacCHESS Synchrotron Source for Structural Biology
IAO_0000115: MacCHESS Synchrotron Source for Structural Biology advances structural characterization of proteins and biomolecules critical for understanding key biological processes and properties through leveraging both established and emerging X-ray synchrotron technologies. Used to collect data that comprises all or part of research programs.

National Biomedical Center for Advanced ESR Technology
type: Resource
type: NamedIndividual
has db xref: nlx_152669
synonym: ACERT National ESR Center
synonym: National Biomedical Center for Advanced Electron Spin Resonance Technology
abbrev: ACERT
IAO_0000115: Biomedical technology research center that develops methods, both experimental and theoretical, of modern electron spin resonance (ESR) for biomedical applications. Center technologies are applicable to the determination of the structure and complex dynamics of proteins. Principal areas of expertise: * Pulsed Fourier Transform and Two Dimensional ESR * High Frequency-High Field (HFHF) ESR * High Resolution ESR Microscopy * Theory and Computational Methods for Modern ESR Activities include: * making resources available to the biomedical community, * publishing results, * running workshops on the new methodologies, * addressing the need to bring these new technologies to other laboratories.

National Center for Macromolecular Imaging
type: Resource
type: NamedIndividual
has db xref: nlx_152670
abbrev: NCMI
IAO_0000115: Biomedical technology research center establishing the infrastructure for fast, routine, atomic structure determination of subcellular complexes by electron cryo-microscopy, computer reconstruction and modeling. Their emphasis is on specimens that cannot currently be studied by conventional structural techniques such as x-ray crystallography or NMR. The ultimate outcome of their research is a three-dimensional image of the complex that can be used for design of drugs and vaccines for a variety of diseases. The center is focused on extending the resolution, speed and flexibility of cryo-electron microscopy for the three-dimensional structure determination of biological macromolecular assemblies. Cryo-electron microscopy can visualize molecules under near-native conditions at resolutions ranging from 0.3 to 5 nm and can yield images of individual molecules in a range of different conformations as they exist in solution. Other cryo-electron mycroscopy techniques, such as cryo-electron tomography, are being developed to capture molecular structures in situ. The equipment, techniques and expertise developed are available to the research community through collaborative projects. The NCMI also provides training through workshops and other forms of dissemination via both traditional and modern Internet-based methods.

Healthy People
type: Resource
type: NamedIndividual
has db xref: nlx_152705
synonym: Healthy People 2020
synonym: HealthyPeople.gov
IAO_0000115: Database portal for science-based, 10-year national objectives resulting from a multiyear process that reflects input from a diverse group of individuals and organizations for improving the health of all Americans. 2020 Topics & Objectives are available in an A-Z format. DATA2020, the Healthy People 2020 interactive data tool, allows users to explore the data and technical information related to the Healthy People 2020 objectives. For 3 decades, Healthy People has established benchmarks and monitored progress over time in order to: * Encourage collaborations across communities and sectors. * Empower individuals toward making informed health decisions. * Measure the impact of prevention activities. Healthy People 2020 strives to: * Identify nationwide health improvement priorities. * Increase public awareness and understanding of the determinants of health, disease, and disability and the opportunities for progress. * Provide measurable objectives and goals that are applicable at the national, State, and local levels. * Engage multiple sectors to take actions to strengthen policies and improve practices that are driven by the best available evidence and knowledge. * Identify critical research, evaluation, and data collection needs.

Besluit Subsidies Investeringen Kennisinfrastructuur
type: Organization
type: NamedIndividual
has db xref: nlx_67583
synonym: Netherlands Enterprise Agency
synonym: NL Enterprise Agency
abbrev: BSIK
IAO_0000115: Agency that is part of the Netherlands Ministry of Economic Affairs. The agency encourages entrepreneurs in sustainable, agrarian, innovative and international business. It helps with grants, finding business partners, know-how and compliance with laws and regulations.

National Resource for Automated Molecular Microscopy
type: Resource
type: NamedIndividual
has db xref: nlx_152671
abbrev: NRAMM
IAO_0000115: Biomedical technology research center that develops, tests and applies technology aimed toward completely automating the processes involved in solving macromolecular structures using cryo-electron microscopy. The goal is to establish a resource that will serve both as a center for high-throughput molecular microscopy as well as for transferring this technique to the research community. Current Core Technology Research and Development is focused on 4 areas: improving grid substrates and specimen preparation; further automation and optimization of image acquisition; development of an integrated single particle analysis and processing pipeline; and the development of automated high throughput EM screening. NRAMM welcomes applications of both collaborative and service projects.

National Magnetic Resonance Facility at Madison
type: Resource
type: NamedIndividual
has db xref: nlx_152672
abbrev: NMRFAM
IAO_0000115: Provides access and developes NMR technology to advance range of applications and improves the efficiency, rigor and reproducibility of NMR data acquisition and analysis. Houses NMR spectrometers equipped with state-of-the-art probe technology and protocols to support acquisition of high-quality data. Spectrometers range from 500 MHz to 1100 MHz. Service is tailored to the needs of individual users and projects. Provides training and advice on experimental design, best practices for data acquisition, and data analysis. Experienced staff support users with training opportunities including workshops, video tutorials and protocols.

Vanderbilt University Medical Center Pharmacology
type: Organization
type: NamedIndividual
has db xref: nif-0000-02295
synonym: Vanderbilt Department of Pharmacology
abbrev: Vanderbilt Pharmacology
IAO_0000115: At the Department of Pharmacology at Vanderbilt University Medical Center we engage in scientific discovery to elucidate biological mechanisms and develop novel therapeutics. We provide training focused on critical thinking to promote innovation, scholarship and integrity. To this end, we foster creativity, collegiality, and leadership. The Department is one of the most distinguished Pharmacology departments in the country and have placed in the top two NIH ranking positions for sixteen of the last twenty years. Research interests in the Department include five major areas: signal transduction, neuroscience, bioactive lipid metabolism, genetic basis of cardiovascular dysfunction, and drug metabolism. Molecules under investigation include G-protein coupled receptors (rhodopsin, adrenergic, serotonin and receptors), heterotrimeric G-proteins, ion channels, transporters and regulatory proteins such as arrestins, protein kinases and protein phosphatases. A strength in our research and training environment is that Vanderbilt University has a world-acclaimed Division of Clinical Pharmacology, which links the Department of Medicine with the Department of Pharmacology. Faculty members in the Division of Clinical Pharmacology focus on human disease and clinical enigmas as the origin of their questions for research. Basic scientists who pursue their inquiries in this environment are continually informed by their colleagues of the pathophysiological and potential therapeutic relevance that can be achieved by appropriate focus of their efforts. We have created one of the first programs in the country to answer the call from the National Institutes of Health (NIH) for more scientists trained in the area of drug discovery and development. A unique feature of the department is our outstanding Ph.D. training program. Almost 60 scientists in training are addressing important issues in fields such neuroscience, cardiovascular development, receptor signaling, and drug metabolism. Scie…

Kawasaki Disease Dataset
type: Resource
type: NamedIndividual
has db xref: nif-0000-08189
synonym: Kawasaki Disease Data Set1
synonym: Kawasaki Disease Data Set 1
synonym: Kawasaki Disease Dataset 1
synonym: KD Data
synonym: KD Data1
IAO_0000115: Collection of data sets on Kawasaki disease, a rare childhood illness that affects the blood vessels. The data includes biochemical measurements of myocardial strain, oxidative stress, and cardiomyocyte injury as well as protein level analysis.

EEGbase
type: Resource
type: NamedIndividual
has db xref: nif-0000-08190
IAO_0000115: EEG base is a system for storage and management of EEG/ERP resources - data, metadata, tools and materials related to EEG/ERP experiments. EEG base advances electrophysiology research by enabling access to public data, tools and results of research groups. The system essentially offers the following set of features (the set of accessible features depends on a specific user role): * User authentication * Storage, update, and download of EEG/ERP data and metadata * Storage, update and download of EEG/ERP experimental design (experimental scenarios) * Storage, update and download of data related to testing subjects * Fulltext search * Sharing of knowledge and working in groups The system is based on tree layer architecture (MVC pattern) consisting of persistent layer (relational database), application layer (object oriented code, object relational mapping from persistence layer) and presentation layer (JSP). The persistence layer uses Hibernate framework; Oracle 11g database server is used to ensure the processing of large data files. Application and presentation layers are designed and implemented using Spring technology. This framework supports MVC architecture, Dependency injection and Aspect Oriented Programming. There were no significant difficulties with integration of both frameworks, Hibernate and Spring MVC. Spring Security framework is used to ensure management of authentication and user roles. Since the system is thought to be finally open to the whole EEG/ERP community it is necessary to protect EEG/ERP data and metadata, and especially personal data of testing subjects stored in the database from an unauthorized access. Then a restricted user policy is applied and user roles are introduced. The complete overview of the system features and user roles (use case diagram) is available in (Pergler 2009). Concerning the architectural layers there is a question which layer is more feasible for mapping of its structure into ontology. Currently we have studied two …

Wake Forest University School of Medicine: Department of Neurology
type: Organization
type: NamedIndividual
has db xref: nif-0000-10549
synonym: WFUBMC Neurology
IAO_0000115: Department at the Wake Forest University's School of Medicine that hosts physicians who specialize in neurological topics such as neuromuscular disease, epilepsy, pediatric neurology, strokes, neuropsychology, neurosonology, and neurorehabilitaiton.

GeneWiz browser
type: Resource
type: NamedIndividual
has db xref: nif-0000-08429
IAO_0000115: An interactive web application for visualizing genomic data of sequenced prokaryotic chromosomes. It allows users to carry out various analyses such as mapping alignments of homologous genes to other genomes, mapping of short sequencing reads to a reference chromosome, and calculating DNA properties such as curvature or stacking energy along the chromosome. The GeneWiz browser produces an interactive graphic that enables zooming from a global scale down to single nucleotides, without changing the size of the plot. Its ability to disproportionally zoom provides optimal readability and increased functionality compared to other browsers. The tool allows the user to select the display of various genomic features, color setting and data ranges. Custom numerical data can be added to the plot allowing, for example, visualization of gene expression and regulation data. Further, standard atlases are pre-generated for all prokaryotic genomes available in GenBank, providing a fast overview of all available genomes, including recently deposited genome sequences.

GQuery
type: Resource
type: NamedIndividual
has db xref: nif-0000-08510
synonym: Entrez - The Life Sciences Search Engine
synonym: NCBI Entrez
abbrev: Entrez
IAO_0000115: Search engine for the National Library of Medicine and the National Institutes of Health. It contains databases such as PubMed, EST, and BioSystems.

BD FACSDiva Software
type: Commercial Organization
type: NamedIndividual
has db xref: SciRes_000115
IAO_0000115: A collection of tools for flow cytometer and application setup, data acquisition, and data analysis that help streamline flow cytometry workflows. It provides features to help users integrate flow systems into new application areas, including index sorting for stem cell and single-cell applications, as well as automation protocols for high-throughput and robotic laboratories.

CytoSPADE
type: Resource
type: NamedIndividual
has db xref: OMICS_05644
synonym: Cytoscape-driven Spanning tree Progression of Density normalized Events
synonym: CytoSPADE Cytoscape Plugin for SPADE
synonym: CytoSPADE: Cytoscape-driven Spanning tree Progression of Density normalized Events
IAO_0000115: Cytoscape plugin that provides a high-performance implementation of an interface for the Spanning-tree Progression Analysis of Density-normalized Events (SPADE) algorithm for tree-based analysis and visualization of high-dimensional cytometry data.

Eddy Lab Software
type: Resource
type: NamedIndividual
has db xref: biotools:pknots
has db xref: nif-0000-08778
synonym: Eddy Lab - Software
synonym: Eddy Lab: Software
IAO_0000115: Software library containing tools for statistical manipulations of data. Tools include profile hidden Markov models for biological sequence analysis, RNA structure analysis, and a prototype noncoding RNA genefinder.

vsn
type: Resource
type: NamedIndividual
has db xref: biotools:vsn
has db xref: OMICS_01977
synonym: vsn - Variance stabilization and calibration for microarray data
IAO_0000115: Software package that implements a method for normalizing microarray intensities, both between colours within array, and between arrays. The method uses a robust variant of the maximum-likelihood estimator for the stochastic model of microarray data described in the references. The model incorporates data calibration (a.k.a. normalization), a model for the dependence of the variance on the mean intensity, and a variance stabilizing data transformation. Differences between transformed intensities are analogous to normalized log-ratios. However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.

Ridom SpaServer
type: Resource
type: NamedIndividual
has db xref: nif-0000-08852
synonym: SpaServer
IAO_0000115: Database of information of spa-typing of MRSA, or Staphylococcus aureus, that can be used to collate and harmonize data from various geographic regions.

NIDDK Inflammatory Bowel Disease Genetics Consortium
type: Resource
type: NamedIndividual
has db xref: nlx_152706
synonym: IBD Genetics Consortium
synonym: Inflammatory Bowel Disease Genetic Consortium
synonym: NIDDKIBD Genetics Consortium
abbrev: IBDGC
abbrev: NIDDKIBDGC
IAO_0000115: Repository of biospecimen and phenotype data collected from Crohn's disease and ulcerative colitis cases and controls recruited at six sites throughout North America that are available to the scientific community. Phenotyping is performed using a standardized protocol, and lymphoblastoid cell lines are established for each subject. Phenotype data for each subject are collected by the Consortium's Data Coordinating Center (DCC), and phenotype data for all subjects with DNA samples are available. The resulting DNA samples have already been utilized by the Consortium to complete various association studies, including genome-wide association studies using dense genotyping arrays. Researchers can obtain DNA samples and phenotype, genotype, and pedigree data through the Data Repository. GWAS data must be requested through dbGAP. The IBDGC is involved with independent genetic research studies and actively works with members of the IBD and genetic communities on collaborative projects. They are also members of the International IBD Genetics Consortium. Phenotype Tools: The Consortium Phenotype Committee, led by Dr. Hillary Steinhart designed and validated paper forms to collect extensive phenotype data on Crohn's Disease and ulcerative colitis. Consortium phenotype tools are available for use by non-Consortium members.

medInria
type: Resource
type: NamedIndividual
has db xref: nif-0000-00292
IAO_0000115: Software tool as multi platform medical image processing and visualization software. Functionalities include 2D/3D/4D image visualization, image registration, diffusion MR processing and tractography, filtering.

Acute Liver Failure Study Group
type: Resource
type: NamedIndividual
has db xref: nlx_152690
synonym: Acute Liver Failure Study Group (ALFSG)
synonym: Adult Acute Liver Failure Study Group
synonym: UT Southwestern Acute Liver Failure Study Group
abbrev: ALFSG
IAO_0000115: Clinical research network for gathering prospective data and bio-samples on acute liver failure in adults since 1998. Clinical histories and laboratory and outcome data are available. Sample types include serum, plasma, urine, DNA, and liver tissue.

ACME
type: Resource
type: NamedIndividual
has db xref: OMICS_01976
synonym: Algorithms for Calculating Microarray Enrichment
IAO_0000115: A set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing enrichment. It does not rely on a specific array technology (although the array should be a tiling array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory.

GenGIS
type: Resource
type: NamedIndividual
has db xref: OMICS_04013
IAO_0000115: A bioinformatics application that allows users to combine digital map data with information about biological sequences collected from the environment. It provides a 3D graphical interface in which the user can navigate and explore the data, as well as a Python interface that allows easy scripting of statistical analyses using the Rpy libraries.

Collaborative Islet Transplant Registry
type: Resource
type: NamedIndividual
has db xref: nlx_152693
abbrev: CITR
IAO_0000115: Collect, analyze, and communicate on comprehensive and current data on all islet/beta cell transplants in human recipients performed in North America, as well as some European and Australian centers to expedite progress and promote safety in islet/beta cell transplantation. This site serves as a repository for general information concerning protocols, clinical transplantation sites, publications, and other information of interest to the general community. Annual Reports are available. Islet/beta cell transplantation is a complex procedure with many factors contributing to the outcome. Compiling and analyzing data from all transplant centers in the US, Canada, as well as some European and Australian centers will accelerate the identification of both critical risk factors and key determinants of success and thereby guide transplant centers in developing and refining islet/beta cell transplant protocols. The inclusion of the term collaborative in the name of the Registry emphasizes the importance of collaboration in fulfilling the CITR mission and goals. Close collaboration with the transplant centers will ensure that relevant questions are addressed, that data submitted are accurate and complete, and that the needs of the transplant community are served. Information on how to participate as a CITR Transplant Center and to receive a transplant center application is available through the website. Progress in islet transplantation depends entirely on complete, high-quality medical data, including the information patients consented to report to the Collaborative Islet Transplant Registry. To make it as easy as possible to provide updated information about patient's health, an on-line questionnaire is available or patients can mail it to their transplant center. This information is very important in the continuing search for a cure for Type 1 diabetes.

Diabetes Prevention Type 1
type: Resource
type: NamedIndividual
has db xref: nlx_152696
synonym: Diabetes Prevention Trial--Type 1 (DPT-1) dataset
synonym: DPT-1 (The Diabetes Prevention Type 1)
abbrev: DPT-1
IAO_0000115: Data set and biosepecimens of a multi-center clinical trial to determine if treatment with beta-cell antigens can delay the onset of Type 1 Diabetes Mellitus (Type 1 DM) in non-diabetic relatives of persons with Type 1 DM. Insulin is a well characterized antigen specifically produced by beta-cells, and it was used for this purpose in the initial DPT-1 studies. The protocol for high risk subjects uses daily subcutaneous insulin injections and an annual course of intravenous insulin treatment, while the protocol for intermediate risk subjects uses daily doses of insulin administered orally. Neither injected nor oral insulin at the doses used were observed to delay or prevent diabetes, although further studies are needed to test whether oral insulin can delay diabetes in people in the intermediate risk group with high titers of insulin autoantibodies.

Epidemiology of Diabetes Interventions and Complications
type: Resource
type: NamedIndividual
has db xref: nlx_152698
abbrev: EDIC
IAO_0000115: Publications from a multi-center, longitudinal, observational study examining the risk factors associated with the long-term complications of type 1 diabetes. The study began in 1994 and follows the 1441 participants previously enrolled in the Diabetes Control and Complications Trial (DCCT), http://diabetes.niddk.nih.gov/dm/pubs/control/index.aspx. The primary aim of EDIC is to examine the long-term effects of conventional vs. intensive diabetes treatment received during the DCCT on the subsequent development and progression of microvascular, neuropathic and cardiovascular complications. This involves studying the influence of genetic factors and other factors such as HbA1c, blood pressure, lipid levels, and treatment modalities on the development and progression of these complications. Annual or biennial measurements (using DCCT methods, standardized protocols and central laboratories) of vascular events, albumin excretion, GFR, ECG, ankle-brachial BP index, serum lipids and HbA1c allows the following analyses: 1) continuation of intention-to-treat analyses to determine long-term effects of prior separation of glycemic levels; 2) risk factors for macrovascular outcomes; 3) correlation of progression of micro- and macrovascular outcomes. The current updated version of the EDIC Protocol is available for download. EDIC is made up of 28 clinical centers, one data coordinating center and one clinical coordinating center.

NIH Division of Nutrition Research Coordination
type: Resource
type: NamedIndividual
has db xref: nlx_152699
synonym: Division of Nutrition Research Coordination
abbrev: DNRC
IAO_0000115: Coordinates nutritional sciences-related research and research training across the National Institutes of Health (NIH) and among Federal Agencies by providing mechanisms to communicate research, research training, policy, and education initiatives. The DNRC facilitates the exchange of information, coordinates workshops and seminars on critical issues, encourages national and international research collaborations, and serves as the NIH primary point of contact for the Department of Health and Human Services (DHHS) and other agencies, departments, and organizations in matters pertaining to nutritional sciences and physical activity. Through its dedicated efforts to promote scientific policy reviews, innovative research, interagency collaboration, and technical advancements, the DNRC strives to define the increasing roles of nutritional sciences and physical activity in health promotion and disease prevention and treatment.

anage
type: Resource
type: NamedIndividual
has db xref: nlx_152700
synonym: AnAge Database of Animal Ageing and Longevity
synonym: AnAge: The Animal Ageing and Longevity Database
synonym: Animal Ageing and Longevity Database
abbrev: AnAge
IAO_0000115: Curated database of aging and life history in animals, including extensive longevity records and complementary traits for > 4000 vertebrate species. AnAge was primarily developed for comparative biology studies, in particular studies of longevity and aging, but can also be useful for ecological and conservation studies and as a reference for zoos and field biologists.

Human Nutrition Research Information Management
type: Resource
type: NamedIndividual
has db xref: nlx_152702
synonym: Federal Human Nutrition Research and Information Management (HNRIM) System Database
synonym: Federal Human Nutrition Research and Information Management System Database
synonym: HNRIM System Database
abbrev: HNRIM
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of human nutrition research and research training activities supported by the federal government. Information regarding trends in nutrition research, specific institutions and investigators involved in this research, or areas of agency emphases can be obtained from database searches or from published summary reports. Data for the system is prepared and submitted by participating agencies, and is updated annually. The database contains several thousand projects for each of fiscal years 1985present. Participating agencies include the Department of Health and Human Services, the U.S. Department of Agriculture, the Department of Veteran Affairs, the Agency for International Development, the Department of Defense, Department of Commerce, National Science Foundation, and the National Aeronautics and Space Administration.

NIA Mouse cDNA Project Home Page
type: Resource
type: NamedIndividual
has db xref: nif-0000-09471
synonym: Mouse cDNA Project
synonym: NIA Mouse cDNA Project
abbrev: niaEST
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Project portal housing NIA Mouse EST Project, NIA Mouse cDNA Clone Sets, a NIA Mouse Gene Index, NIA Mouse cDNA Database, and NIA Mouse Microarrays. Characteristics of NIA 15K Mouse cDNA Clone Set * ~15,000 unique cDNA clones were rearrayed among 52,374 ESTs from pre- and periimplantation embryos, E12.5 female gonad/mesonephros, and newborn ovary. * Up to 50% are derived from novel genes. * ~1.5 kb average insert size. * Clones were sequenced from 5' and 3' termini to obtain longer reads and verify sequence. Sequence information is available at this Web Site. Clone names are from H3001A01 to H3159G07. * Handling of NIA 15k cDNA Clone Set(June3, 2000) Characteristics of NIA mouse 7.4K cDNA Clone Set * ~7407 cDNA clones with no redundancy within the set or with NIA Mouse 15K. * ~1.5 kb average insert size for short insert clones and ~2.5-3.0 kb average insert size for long-insert enriched clones.. * Clones were sequenced from 5' and 3' termini to obtain longer reads and verify sequence. Sequence information is available at this Web Site. Clone names are from H4001A01 to H4079G07. * Handling of NIA mouse 7.4k cDNA Clone Set (similar to handling of NIA mouse 15K, to be updated) Individual Clones are available from ATCC and MRC geneservice, UK. To obtain Clone, search the database using either the rearrayed clone name or GenBank accession number at the Key Word Search page. Follow the link to the sequence information page for the rearrayed clone to obtain source clone ATCC number. Clicking the ATCC number will bring up the ATCC ordering page for the source clone. There is essentially no overlap between the two clone sets (7.4K and 15K) said Minoru S.H. Ko, M.D., Ph.D., head of the Developmental Genomics and Aging Section in the NIA's Laboratory of Genetics. In addition, all cDNA clones in the NIA 7.4K set were purified by single colony isolation and sequence-verified, and more than half were prepared…

NRF Contacts
type: Resource
type: NamedIndividual
has db xref: nif-0000-09488
synonym: Neuroscience Research Funding Contacts
synonym: Neuroscience Research Funding Contacts in the Federal Government
IAO_0000115: This resource provides a list of federal program officials in the neurosciences. An informal compendium of names and contact information for nearly 300 research grant and scientific review administrators in 21 organizational units.

Bilkent University; Ankara; Turkey
type: Organization
type: NamedIndividual
has db xref: nlx_95218
synonym: Bilkent University
IAO_0000115: Private university located in Ankara, Turkey that offers undergraduate and graduate programs in fields that include economics, art and architecture, languages, and neuroscience.

Type 1 Diabetes Resource
type: Resource
type: NamedIndividual
has db xref: nlx_152730
abbrev: T1DR
IAO_0000115: International repository for importation, curation, genotypic and phenotypic validation, cryopreservation, and distribution of mouse stocks of value to the type 1 diabetes scientific community holding over 250 genetically modified or congenic mouse stocks that are being used to dissect genetic and biologic features of T1D. They provide extensive genotypic and phenotypic quality control and genetic stabilization for these strains, as well as incidence studies when available. An added value of T1DR stocks is their ability to propel advances in related areas of science, including research in non-T1D autoimmunity and infectious diseases. The staff provides information and technical assistance regarding selection and use of existing T1DR models, and will provide limited support for development of new models considered to be of high-value for the T1D community. The resource includes strains generated at the Jackson Laboratory as well as strains donated by external scientists. Investigators are highly encouraged to donate a strain to ensure its preservation and availability to other researchers.

Harvard - Oxford Cortical Structural Atlas
type: Resource
type: NamedIndividual
has db xref: nlx_152707
synonym: Harvard Oxford Atlas
synonym: Harvard Oxford Cortical Structural Atlas
synonym: Harvard-Oxford cortical and subcortical structural atlases
abbrev: Atlases
IAO_0000115: Probabilistic atlases covering 48 cortical and 21 subcortical structural areas, derived from structural data and segmentations kindly provided by the Harvard Center for Morphometric Analysis. T1-weighted images of 21 healthy male and 16 healthy female subjects (ages 18-50) were individually segmented by the CMA using semi-automated tools developed in-house. The T1-weighted images were affine-registered to MNI152 space using FLIRT (FSL), and the transforms then applied to the individual labels. Finally, these were combined across subjects to form population probability maps for each label. Segmentations used to create these atlases were provided by: David Kennedy and Christian Haselgrove, Centre for Morphometric Analysis, Harvard; Bruce Fischl, the Martinos Center for Biomedical Imaging, MGH; Janis Breeze and Jean Frazier from the Child and Adolescent Neuropsychiatric Research Program, Cambridge Health Alliance; Larry Seidman and Jill Goldstein from the Department of Psychiatry of Harvard Medical School.

National Diabetes Education Program
type: Resource
type: NamedIndividual
has db xref: nlx_152708
abbrev: NDEP
IAO_0000115: Federal government public education program that promotes diabetes prevention and control. They aim to reduce the morbidity and mortality associated with diabetes and its complications. The NDEP is jointly sponsored by the National Institutes of Health and the Centers for Disease Control and Prevention and over 200 partner organizations. Target audiences include people with diabetes and those at risk, including the racial and ethnic populations disproportionately affected by the disease, health care providers and payers and purchasers of health care.

Pediatric Acute Liver Failure Study
type: Resource
type: NamedIndividual
has db xref: nlx_152715
synonym: Pediatric Acute Liver Failure (PALF) Study
synonym: Pediatric Acute Liver Failure (PALF) Study Group
abbrev: PALF
IAO_0000115: Study group and network for a 2008 longitudinal study for the etiology, diagnosis, treatment, and outcome of acute liver failure in infants, children, and adolescents. Data from patients include urine, bile, serum, liver tissue, cell lines derived from fibroblast culture, and DNA.

CoGAPS
type: Resource
type: NamedIndividual
has db xref: OMICS_01973
synonym: Coordinated Gene Activity in Pattern Sets
IAO_0000115: Software that infers biological processes which are active in individual gene sets from corresponding microarray measurements. It achieves this inference by combining a MCMC matrix decomposition algorithm (GAPS) with a novel statistic inferring activity on gene sets.

Globin Gene Server
type: Resource
type: NamedIndividual
has db xref: nlx_152723
abbrev: Globin Gene Server
IAO_0000115: Data and tools for studying the function of DNA sequences, with an emphasis on those involved in the production of hemoglobin. It includes information about naturally-occurring human hemoglobin mutations and their effects, experimental data related to the regulation of the beta-like globin gene cluster, and software tools for comparing sequences with one another to discover regions that are likely to play significant roles.

Integrated Models
type: Resource
type: NamedIndividual
has db xref: nlx_152726
synonym: Integrated Model
synonym: Integrated Model View
synonym: NIF Integrated Model
synonym: NIF Integrated Models
synonym: NIF Integrated Models View
synonym: NIF Models
IAO_0000115: A virtual database of several model resources including: CellML Model Repository, ModelDB, Open Source Brain, SimTK, and ModelRun.

NIH Chronic Prostatitis Symptom Index
type: Resource
type: NamedIndividual
has db xref: nlx_152732
synonym: Chronic Prostatitis Symptom Index
synonym: National Institutes of Health Chronic Prostatitis Symptoms Index
abbrev: CPSI
abbrev: NIH-CPSI
IAO_0000115: Questionnaire developed by physicians in NIDDK's Chronic Prostatitis Collaborative Research Network that can help physicians to accurately measure the severity of prostatitis symptoms and their impact on a patient's lifestyle. The CPSI questionnaire assesses pain, urination, and the effect of chronic prostatitis on daily activities. With this information, researchers and physicians can reliably evaluate whether potential treatments are working. The questionnaire was originally published in the Journal of Urology in August 1999 (Vol. 162, pages 369-375). It is available as a PDF document in English, Spanish, German and Korean.

Sequencing of Idd regions in the NOD mouse genome
type: Resource
type: NamedIndividual
has db xref: nlx_152738
synonym: Sequencing of Insulin-dependent diabetes regions in the NOD mouse genome
abbrev: Sequencing of Idd regions in the NOD mouse genome
IAO_0000115: Genetic variations associated with type 1 diabetes identified by sequencing regions of the non-obese diabetic (NOD) mouse genome and comparing them with the same areas of a diabetes-resistant C57BL/6J reference mouse allowing identification of single nucleotide polymorphisms (SNPs) or other genomic variations putatively associated with diabetes in mice. Finished clones from the targeted insulin-dependent diabetes (Idd) candidate regions are displayed in the NOD clone sequence section of the website, where they can be downloaded either as individual clone sequences or larger contigs that make up the accession golden path (AGP). All sequences are publicly available via the International Nucleotide Sequence Database Collaboration. Two NOD mouse BAC libraries were constructed and the BAC ends sequenced. Clones from the DIL NOD BAC library constructed by RIKEN Genomic Sciences Centre (Japan) in conjunction with the Diabetes and Inflammation Laboratory (DIL) (University of Cambridge) from the NOD/MrkTac mouse strain are designated DIL. Clones from the CHORI-29 NOD BAC library constructed by Pieter de Jong (Children's Hospital, Oakland, California, USA) from the NOD/ShiLtJ mouse strain are designated CHORI-29. All NOD mouse BAC end-sequences have been submitted to the International Nucleotide Sequence Database Consortium (INSDC), deposited in the NCBI trace archive. They have generated a clone map from these two libraries by mapping the BAC end-sequences to the latest assembly of the C57BL/6J mouse reference genome sequence. These BAC end-sequence alignments can then be visualized in the Ensembl mouse genome browser where the alignments of both NOD BAC libraries can be accessed through the Distributed Annotation System (DAS). The Mouse Genomes Project has used the Illumina platform to sequence the entire NOD/ShiLtJ genome and this should help to position unaligned BAC end-sequences to novel non-reference regions of the NOD genome. Further information about the BAC end-sequ…

Bioinformatics Jobs Board
type: Resource
type: NamedIndividual
has db xref: nlx_152739
abbrev: bioinformatics.ca Job Postings
IAO_0000115: Job postings available to Bioinformatics.ca members. To become a member please sign up for an account. DISCLAMER: OICR and the Canadian Bioinformatics Workshops are not affiliated with and have not investigated the companies listing jobs on this site. OICR is not making any representations with respect to the positions and is not acting as an agent for the companies listed.

Bioinformatics Experts
type: Resource
type: NamedIndividual
has db xref: nlx_152740
synonym: Bioinformatics Experts in Canada
synonym: bioinformatics.ca Bioinformatics Experts
IAO_0000115: Investigators interested in Bioinformatics in Canada including practitioners as well as developers of algorithms, databases or resources. Principal investigators and group leaders from academia, government labs and industry are welcome on this page. All present have an interest in the development of bioinformatics resources in Canada.

Multiple-Path Particle Dosimetry Model
type: Resource
type: NamedIndividual
has db xref: nlx_152744
synonym: Multiple Path Particle Dosimetry Model
abbrev: MPPD
IAO_0000115: Computational model that can be used for estimating human and rat airway particle dosimetry. The model is applicable to risk assessment, research, and education. The MPPD model calculates the deposition and clearance of monodisperse and polydisperse aerosols in the respiratory tracts of rats and human adults and children (deposition only) for particles ranging in size from ultrafine (0.01 micrometers) to coarse (20 micrometers). The models are based on single-path and multiple-path methods for tracking air flow and calculating aerosol deposition in the lung. The single-path method calculates deposition in a typical path per airway generation, while the multiple-path method calculates particle deposition in all airways of the lung and provides lobar-specific and airway-specific information. Within each airway, deposition is calculated using theoretically derived efficiencies for deposition by diffusion, sedimentation, and impaction within the airway or airway bifurcation. Filtration of aerosols by the nose and mouth is determined using empirical efficiency functions. The MPPD model includes calculations of particle clearance in the lung following deposition.

National Science Foundation Graduate Research Fellowship Program
type: Resource
type: NamedIndividual
has db xref: nif-0000-10366
synonym: NSF GRFP
IAO_0000115: The National Science Foundation's Graduate Research Fellowship Program (GRFP) helps ensure the vitality of the human resource base of science and engineering in the United States and reinforces its diversity. The program recognizes and supports outstanding graduate students in NSF-supported science, technology, engineering, and mathematics disciplines who are pursuing research-based master's and doctoral degrees in the U.S. and abroad. The NSF welcomes applications from all qualified students and strongly encourages under-represented populations, including women, under-represented racial and ethnic minorities, and persons with disabilities, to apply for this fellowship. Fellows share in the prestige and opportunities that become available when they are selected. Fellows benefit from a three-year annual stipend of $30,000 along with a $10,500 cost of education allowance for tuition and fees, a one-time $1,000 international travel allowance and the freedom to conduct their own research at any accredited U.S., or foreign institution of graduate education they choose. NSF Fellows are anticipated to become knowledge experts who can contribute significantly to research, teaching, and innovations in science and engineering. So that the nation can build fully upon the strength and creativity of a diverse society, the Foundation welcomes applications from all qualified individuals. Women, under-represented minorites and people with disabilities are encouraged to apply. Those with disabilities are additionally accommodated by the Foundation to provide for the most successful graduate experience possible. Sponsors: This program is supported by the National Science Foundation (NSF).

NTAP
type: Resource
type: NamedIndividual
has db xref: OMICS_00808
synonym: NimbleGen Tiling array Analysis Package
synonym: NimbleGen Tilingarray Analysis Package
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for tiling array data analysis to survey the genome-wide binding sites of transcription factor HY5 in Arabidopsis and the genome-wide histone modifications/DNA methylation level in rice. It was developed in the process of generating NimbleGen analysis. Written in R and Perl.

PDB2MultiGif
type: Resource
type: NamedIndividual
has db xref: nlx_152874
synonym: PDB to MultiGIF
IAO_0000115: A web tool that takes a 3D structure (a PDB input file) and generates an animated image which can be displayed using any browser without the need for any additional molecular visualization software.

Look AHEAD
type: Resource
type: NamedIndividual
has db xref: nlx_152745
synonym: Action for Health in Diabetes
synonym: Look AHEAD - Action for Health in Diabetes
abbrev: Look AHEAD
IAO_0000115: 16-center, randomized clinical trial investigating the long-term health consequences of an intensive lifestyle intervention program designed to achieve and maintain weight loss by decreased caloric intake and increased physical activity in overweight volunteers with type 2 diabetes. The Look AHEAD cohort comprises approximately 5,000 overweight or obese participants with type 2 diabetes, aged 45-76. Participants were randomized to one of two interventions: an intensive lifestyle intervention designed to produce and sustain weight loss over the long term or a diabetes support and education arm. Participants will be followed for a total of 11 to 13.5 years from randomization. The primary hypothesis is that the incidence rate of the first post-randomization occurrence of a composite outcome, which includes * cardiovascular death (including fatal myocardial infarction and stroke), * non-fatal myocardial infarction, * hospitalized angina, and * non-fatal stroke, over a planned follow-up period of up to 13.5 years will be reduced among participants assigned to the Lifestyle Intervention compared to those assigned to the control condition, Diabetes Support and Education. Look AHEAD will also test for reductions in the incidence of three secondary composite outcomes and examine the effect of the intervention on cardiovascular disease risk factors, diabetes control and complications, general health, and quality of life, and psychological outcomes. The cost and cost-effectiveness of the Lifestyle Intervention relative to Diabetes Support and Education will be assessed. The Look AHEAD intensive lifestyle intervention ended September, 2012. Participants continue to be followed to determine the long-term effects of the intervention on health outcomes.

Human Immunology Project Consortium
type: Resource
type: NamedIndividual
has db xref: SciRes_000173
synonym: immune profiling
synonym: immuneprofiling.org
abbrev: HIPC
IAO_0000115: Consortium established to capitalize on recent advances in immune profiling methods in order to create a novel public resource that characterizes diverse states of the human immune system following infection; prior to and following vaccination against an infectious disease; or prior to and following treatment with an immune adjuvant that targets a known innate immune receptor(s). Through this program, well-characterized human cohorts are studied using a variety of modern analytic tools, including multiplex transcriptional, cytokine, and proteomic assays; multiparameter phenotyping of leukocyte subsets; assessment of leukocyte functional status; and multiple computational methods. Centralized research resources and a comprehensive, centralized database will be constructed for use by the greater scientific community. The information gained from the program will provide a comprehensive understanding of the human immune system and its regulation, and will reveal novel associations between components of the immune system and other biological systems, identify novel immune mediators and pathways, establish predictors of vaccine safety in different populations, and enable the rapid evaluation of different vaccine formulations and administration regimens in human populations.

Teen-Longitudinal Assessment of Bariatric Surgery
type: Resource
type: NamedIndividual
has db xref: nlx_152747
synonym: Adolescent Bariatrics: Assessing Health Benefits and Risks
synonym: Adolescent Bariatrics: Assessing Health Benefits and Risks (Teen-LABS)
synonym: Teen-LABS
synonym: Teen-Longitudinal Assessment of Bariatric Surgery
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Consortium made up of five clinical centers and a data coordinating center. The goal of Teen-LABS is to conduct clinical, epidemiological, and behavioral research in adolescent bariatric surgery, through an observational prospective study protocol. Teen-LABS is an ancillary study to LABS, an observational study of adult bariatric surgery. Research staff, certified in standardized uniform data collection according to the protocol, collect data at pre-operative research visits, at surgery, 30 days and six months post-operative, and annual post-operative research visits at the five participating centers.

Parkinson's Disease Online Research
type: Resource
type: NamedIndividual
has db xref: nif-0000-09529
synonym: PD Online Research
synonym: The Michael J Fox Foundation for Parkinson's Research
IAO_0000115: Portal for the Michael J. Fox Foundation dedicated to research on Parkinson's Disease.

Adult to Adult Living Donor Liver Transplantation Cohort Study
type: Resource
type: NamedIndividual
has db xref: nlx_152749
synonym: A2ALL: The Adult to Adult Living Donor Liver Transplantation Cohort Study
abbrev: A2ALL
IAO_0000115: Study consisting of nine liver transplant centers with expertise in adult living-donor liver transplantation (LDLT) and a central data coordinating center to provide valuable information on the outcomes of adult to adult living donor liver transplantation (AALDLT) to aid decisions made by physicians, patients, and potential donors. The study will establish and maintain the infrastructure required to accrue and follow sufficient numbers of patients being considered for and undergoing AALDLT to provide generalizable data from adequately powered studies. The major aims of A2ALL are as follows: * Quantify the impact of choosing LDLT on the candidate for transplantation * Characterize the difference between LDLT and deceased donor liver transplant (DDLT) in terms of post-transplant outcomes, including patient and graft survival, surgical morbidity, and resource utilization on the recipient of a transplant * Determine the short- and long-term health and quality of life (QOL) impact of donation, including (a) morbidity after liver donation and (b) long-term health-related QOL of donors. * Standardize and assess the role of informed consent in affecting the decision to donate and satisfaction after living liver donation * Other aims include comparison of the severity of recurrence of hepatocellular carcinoma for DDLT versus LDLT, the systematic characterization of liver regeneration and function in donors and recipients, the evaluation of the differences in the immune response to LDLT versus DDLT, and the establishment of a robust data and sample repository on liver transplantation that may be used to study clinical and biological questions as new technologies and resources become available. Patients enrolled in the study will be followed and managed in a standardized fashion.

Behavior Enhances Drug Reduction of Incontinence
type: Resource
type: NamedIndividual
has db xref: nlx_152752
abbrev: BE-DRI
IAO_0000115: Multi-center randomized clinical trial to determine if the addition of behavioral treatment to drug therapy for the treatment of urge incontinence will make it possible to discontinue the drug and still maintain a reduced number of accidents. The most popular treatments for urge incontinence are drug therapy and behavior therapy, each with its own limitations. In this clinical study, the Urinary Incontinence Treatment Network (UITN) aims to determine differences with the addition of behavioral treatment to drug therapy alone.

BARI 2D
type: Resource
type: NamedIndividual
has db xref: nlx_152754
synonym: Bypass Angioplasty Revascularization Investigation 2 Diabetes
synonym: Bypass Angioplasty Revascularization Investigation (BARI) 2 Diabetes
abbrev: BARI-2D
IAO_0000115: A multicenter randomized clinical trial that aims to determine the best therapies for people with type 2 diabetes and moderately severe cardiovascular disease. 2368 participants were randomized at 49 sites in 6 countries. All subjects were given intensive medical therapy to control cholesterol and blood pressure and given counseling, if needed, to quit smoking and to lose weight. Beyond that, they compared whether prompt revascularization, either bypass surgery or angioplasty, e.g. stents, was more effective than medical therapy alone. At the same time, they also looked at which of two diabetes treatment strategies resulted in better outcomes����??insulin-providing versus insulin-sensitizing - that is, increasing the amount of insulin or making the insulin work better. Only patients with known type 2 diabetes and heart disease that could be treated appropriately with a revascularization OR medical therapy alone were eligible for the trial. Patients entered the study between January 2001 ����?? March 2005 and were followed for an average of five years. When a patient entered the study, physicians first decided whether that patient should receive stenting or bypass surgery. The patient then received their randomization assignment. All patients were treated in BARI 2D for both their diabetes and heart disease, as well as other risk factors that might effect those diseases, regardless of which group they were in. Diabetes-specific complications including retinopathy, nephropathy, neuropathy, and peripheral vascular disease were monitored regularly. Tests, blood samples, urine samples, and treatment cost data were obtained periodically through the trial and examined by experts at 7 central laboratories and other research partners. Experts on risk factors routinely oversaw treatments of all patients at 4 central management centers. A panel of independent experts reviewed data every six months to make sure that all patients were receiving safe care.

Childhood Liver Disease Research and Education Network
type: Resource
type: NamedIndividual
has db xref: nlx_152755
synonym: Childhood Liver Disease Research and Education Network (ChiLDREN)
abbrev: ChiLDREN
IAO_0000115: Database of clinical information and serum and tissue samples from children across the United States and Canada with Biliary Atresia, Idiopathic Neonatal Hepatitis, Cystic Fibrosis Liver Disease, Alagille Syndrome, Alpha-1 Antitrypsin Deficiency, Bile Acid Synthesis Defects, Mitochondrial Hepatopathies, and Progressive Familial Intrahepatic Cholestasis in order to facilitate research and to perform clinical, epidemiological, and therapeutic trials in these important pediatric liver diseases. Three NIDDK-funded consortia, Biliary Atresia Research Consortium (BARC), Cholestatic Liver Disease Consortium (CLiC), and the Cystic Fibrosis Liver Disease (CFLD) Network were consolidated to form ChiLDREN. Most of the ChiLDREN studies are natural history studies aimed at acquiring information and data that will provide a better understanding of these rare conditions. Participants will be asked to allow study personnel to obtain information from medical records and an interview, and to collect blood, urine, and tissue samples when clinically indicated, in order to understand the causes of these diseases and to improve the diagnosis and treatment of children with these diseases. All of the information obtained in these studies is confidential and no names or identifying information are used in the study.

Alpha-1 Foundation
type: Resource
type: NamedIndividual
has db xref: nlx_152756
IAO_0000115: A not-for-profit organization to increase awareness of and find a cure for Alpha-1 Antitrypsin Deficiency that has invested nearly $39 million to support Alpha-1 research at more than 70 institutions in North America, Europe and Australia. They are dedicated to providing the leadership and resources that will result in increased research, improved health, worldwide detection, and a cure for Alpha-1 Antitrypsin Deficiency. The Foundation has developed a solid infrastructure to promote research and the development of new therapies for improving the quality of life for those diagnosed with Alpha-1. It has fostered collaborations with investigators throughout the United States and Europe, working closely with the National Institutes of Health (NIH), the Food and Drug Administration (FDA), individuals affected by Alpha-1, and the pharmaceutical industry to expedite the development of improved therapies. The Foundation participates in industry and government liaison groups and develops strategic alliances with government, industry and other national and international health and research organizations. They're the source for all Alpha-1 and COPD-related info.

Standardization of C-peptide measurements
type: Resource
type: NamedIndividual
has db xref: nlx_152766
synonym: C-peptide Standardization
abbrev: Standardization of c-peptide
IAO_0000115: Standardization of c-peptide by calibrating C-peptide measurement to a reference method can increase comparability between laboratories. The C-peptide standardization program is supported to establish reliability in results and facilitate the conduct of international clinical trials. For c-peptide, purified or processed material shows significant matrix effects and cannot be used for calibration. The C-peptide program has evaluated the use of single donor and pooled specimens for use by manufacturers in the calibration of these assays and determined that this strategy will reduce C-peptide variability among different assay methods. The standardization process through manufacturer re-calibration is ongoing.

CKID A Prospective Cohort Study of Kidney Disease in Children
type: Resource
type: NamedIndividual
has db xref: nlx_152790
synonym: Chronic Kidney Disease in Children
synonym: CKID: A Prospective Cohort Study of Kidney Disease in Children
abbrev: CKID
IAO_0000115: Prospective, observational cohort study of children with mild to moderate chronic kidney disease (CKD) to: (1) determine risk factors for progression of pediatric chronic kidney disease (CKD); (2) examine the impact of CKD on neurocognitive development; (3) examine the impact of CKD on risk factors for cardiovascular disease, and; (4) examine the impact of CKD on growth. The CKiD study population will include a cohort of 540 children, age 1 16 years, expected to be enrolled over a 24-month period.

Diabetes Prevention Program
type: Resource
type: NamedIndividual
has db xref: nlx_152799
abbrev: DPP
IAO_0000115: Multicenter clinical research study aimed at discovering whether modest weight loss through dietary changes and increased physical activity or treatment with the oral diabetes drug metformin (Glucophage) could prevent or delay the onset of type 2 diabetes in study participants. At the beginning of the DPP, all 3,234 study participants were overweight and had blood glucose levels higher than normal but not high enough for a diagnosis of diabetesa condition called prediabetes. In addition, 45 percent of the participants were from minority groups-African American, Alaska Native, American Indian, Asian American, Hispanic/Latino, or Pacific Islander-at increased risk of developing diabetes. The DPP found that participants who lost a modest amount of weight through dietary changes and increased physical activity sharply reduced their chances of developing diabetes. Taking metformin also reduced risk, although less dramatically. In the DPP, participants from 27 clinical centers around the United States were randomly divided into different treatment groups. The first group, called the lifestyle intervention group, received intensive training in diet, physical activity, and behavior modification. By eating less fat and fewer calories and exercising for a total of 150 minutes a week, they aimed to lose 7 percent of their body weight and maintain that loss. The second group took 850 mg of metformin twice a day. The third group received placebo pills instead of metformin. The metformin and placebo groups also received information about diet and exercise but no intensive motivational counseling. A fourth group was treated with the drug troglitazone (Rezulin), but this part of the study was discontinued after researchers discovered that troglitazone can cause serious liver damage. The participants in this group were followed but not included as one of the intervention groups. In the years since the DPP was completed, further analyses of DPP data continue to yield important insigh…

Diabetes Prevention Program Outcomes Study
type: Resource
type: NamedIndividual
has db xref: nlx_152800
abbrev: DPPOS
IAO_0000115: Observational clinical trial studying the long term effect of diet and exercise and the diabetes medication, metformin, on the delay of type 2 diabetes in participants of the Diabetes Prevention Program (DPP). The Diabetes Prevention Program (DPP) was a multi-center trial examining the ability of an intensive lifestyle or metformin to prevent or delay the development of diabetes in a high risk population due to the presence of impaired glucose tolerance (IGT). The DPP has ended early demonstrating that lifestyle reduced diabetes onset by 58% and metformin reduced diabetes onset by 31%. The DPPOS is designed to take advantage of the scientifically and clinically valuable DPP participants. This group of participants is nearly 50% minority and represents the largest IGT population ever studied. Clinically important research questions remain that focus on 1)durability of the prior DPP intervention, 2) determination of the clinical course of precisely known new onset diabetes, in particular regarding CVD, CVD risk factors and atherosclerosis and microvascular disease, 3)close examination of these topics in men vs women and in minority populations. More than 87% of the original surviving DPP cohort has joined DPPOS as of December, 2007 and, to date, after 5 years of DPPOS and 10 years of combined DPP/DPPOS, 93% of the DPPOS cohort continue to attend annual follow-up visits. Interim analyses performed after 5 years of DPPOS have demonstrated a durable effect of diabetes prevention associated with the lifestyle and metformin interventions with 34 and 19% reductions in diabetes incidence, respectively, compared with the placebo group. Interim analyses also reveal significant reductions from baseline in CVD risk factors in the lifestyle intervention group, but with decreased utilization of glucose-lowering and lipid-lowering medications. Analyses of the participants in the placebo group who have developed diabetes during DPP/DPPOS, compared with those who have remained non-di…

ToppCluster
type: Resource
type: NamedIndividual
has db xref: biotools:toppcluster
has db xref: nlx_152801
has db xref: OMICS_02225
synonym: ToppCluster: A multiple gene list feature analyzer for the dissection of biological systems
abbrev: ToppCluster
IAO_0000115: A tool for performing multi-cluster gene functional enrichment analyses on large scale data (microarray experiments with many time-points, cell-types, tissue-types, etc.). It facilitates co-analysis of multiple gene lists and yields as output a rich functional map showing the shared and list-specific functional features. The output can be visualized in tabular, heatmap or network formats using built-in options as well as third-party software. It uses the hypergeometric test to obtain functional enrichment achieved via the gene list enrichment analysis option available in ToppGene.

Irritable Bowel Syndrome Outcome Study
type: Resource
type: NamedIndividual
has db xref: nlx_152839
abbrev: IBSOS
IAO_0000115: Multi-center placebo-controlled randomized clinical trial to assess the short-term and long-term efficacy of cognitive behavior therapy (CBT) for irritable bowel syndrome (IBS) using two treatment delivery systems: self administered CBT and therapist administered CBT. Long term project goals are to develop an effective self-administered behavioral treatment program that can enhance the quality of patient care, improve clinical outcomes, and decrease the economic and personal costs of one of the most prevalent and intractable gastrointestinal disorders.

Folic Acid for Vascular Outcome Reduction in Transplantation
type: Resource
type: NamedIndividual
has db xref: nlx_152827
synonym: Folic Acid for Vascular Outcome Reduction in Transplantation (FAVORIT)
abbrev: FAVORIT
IAO_0000115: Multi-center, randomized, double blind controlled clinical trial to determine whether treatment with a standard multivitamin augmented with high doses of folic acid, vitamin B6 and vitamin B12 reduces the rate of cardiovascular disease outcomes in renal transplant recipients relative to participants receiving a similar multivitamin that contains no folic acid. This study hopes to show that by reducing the level of homocysteine in the body, the risk of heart disease is also reduced among kidney transplant patients.

EuMMCR
type: Resource
type: NamedIndividual
has db xref: nlx_152805
synonym: EuMMCR - European Mouse Mutant Cell Repository
synonym: European Mouse Mutant Cell Repository
IAO_0000115: Embryonic stem cell distribution unit that distributes material arising within European Conditional Mouse Mutagenesis Program consortium, currently targeting vectors and ES cells. Upon user request EUCOMM grow targeting vectors from glycerol stocks and prepare vector DNA. Identity of vector is verified by restriction mapping. Upon user request EUCOMM thaw, expand and re-freeze several aliquots of desired ES cell clone. Standard controls include PCR based assay. Upon additional request EuMMCR unit develops genotyping PCR, which can be used to genotype chimeric mice that may be generated using those ES cell clones.

Beijing: Eyes Open Eyes Closed Study
type: Resource
type: NamedIndividual
has db xref: nlx_152810
synonym: Beijing Eyes Open Eyes Closed Study
synonym: Beijing Normal University State Key Laboratory of Cognitive Neuroscience and Learning Eyes Open Eyes Closed Sample
synonym: BNU Eyes Open Eyes Closed Sample
synonym: Eyes Open Eyes Closed Sample
abbrev: Beijing EOEC
IAO_0000115: Data set of 48 healthy controls from a community (student) sample from Beijing Normal University in China with 3 resting state fMRI scans each. During the first scan participants were instructed to rest with their eyes closed. The second and third resting state scan were randomized between resting with eyes open versus eyes closed. In addition this dataset contains a 64-direction DTI scan for every participant. The following data are released for every participant: * 6-minute resting state fMRI scan (R-fMRI) * MPRAGE anatomical scan, defaced to protect patient confidentiality * 64-direction diffusion tensor imaging scan (2mm isotropic) * Demographic information and information on the counterbalancing of eyes open versus eyes closed.

Type 1 Diabetes TrialNet
type: Resource
type: NamedIndividual
has db xref: nlx_152812
abbrev: TrialNet
IAO_0000115: International network of researchers who are exploring ways to prevent, delay and reverse the progression of type 1 diabetes. It is conducting clinical trials with researchers from 18 Clinical Centers in the United States, Canada, Finland, United Kingdom, Italy, Germany, Australia and New Zealand. In addition, more than 150 medical centers and physician offices are participating in the TrialNet network. Studies are available for people newly diagnosed with type 1 diabetes, as well as for relatives of people with type 1 diabetes who are at greater risk of developing the disease. This NIH-sponsored clinical trials network conducts studies designed to evaluate new approaches to prevent or ameliorate type 1 diabetes specifically by interdicting the type 1 diabetes disease process. These include interventions designed to decrease beta-cell destruction and/or enhance beta-cell survival. Studies are conducted in non-diabetic persons at risk of type 1 diabetes in an effort to delay the development of type 1 diabetes as a clinical disease; or (if initiated prior to appearance of autoimmunity) in an effort to delay the appearance of autoimmunity; or in individuals with type 1 diabetes who are either newly diagnosed or have evidence of sustained beta cell function. Studies include long-term follow-up of subjects developing type 1 diabetes. The TrialNet network also supports natural history and genetics studies in populations screened for or enrolled in studies conducted by the TrialNet study group. In addition, TrialNet will evaluate methodologies that enhance the conduct of clinical trials interdicting the type 1 diabetes disease process.

Anatomy of the Laboratory Mouse
type: Resource
type: NamedIndividual
has db xref: nlx_153862
synonym: The Anatomy of the Laboratory Mouse
IAO_0000115: A book adapted for the Web on the anatomy of the laboratory mouse by Margaret J. Cook, 143 pages, M.R.C. Laboratory Animals Centre, Carshalton, Surrey, England. Academic Press 1965. Mouse Externals, Skeleton, Viscera and Circulatory System are covered.

Living Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_152813
synonym: TrialNet Living Biobank
IAO_0000115: Provides investigators with the opportunity to obtain on-demand biological samples from selected individuals that TrialNet has developed through the longitudinal monitoring of individuals at risk for the development of type 1 diabetes within the Natural History study. Exploratory research is encouraged under this initiative. Studies must use TrialNet screened subjects, and cannot interfere with ongoing clinical trials or studies. Investigators can select the clinical characteristics needed for their study as well as the sample type and collection frequency. Although many Living Biobank studies may be implemented through cost-sharing with the TrialNet network, special sample collections and visits outside of the normal visit schedules will incur additional costs which should be covered by the approved applicant. In addition, some studies may require effort from the TrialNet coordinating center, with costs covered by the approved ancillary study. Living biobank studies will be evaluated with careful consideration for their potential impact on the objectives and performance of the TrialNet Natural History study. To protect the interests of TrialNet, each living biobank study must be reviewed and approved by the Ancillary Studies Committee before its initiation. All approved living biobank studies will be reviewed yearly to evaluate their progress, and impact on TrialNet as a whole. TrialNet welcomes the submission of living biobank studies as an adjunct to ongoing protocols.

PyLOH
type: Resource
type: NamedIndividual
has db xref: biotools:pyloh
has db xref: OMICS_03559
IAO_0000115: Software for deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity. The model resolves the identifiability problem by integrating two types of sequencing information - somatic copy number alterations and loss of heterozygosity - within an unified probabilistic framework.

Diabetes Research in Children Network
type: Resource
type: NamedIndividual
has db xref: nlx_152814
synonym: Diabetes Research in Children Network (DirecNet)
abbrev: DirecNet
IAO_0000115: Network of clinical centers and a coordinating center that investigate the potential use of glucose monitoring technology and its impact on the management of type 1 diabetes in children. Specific goals for the network include the following: * Assess the accuracy of continuous monitoring devices in order to determine if these devices are useful in improving glycemic control and preventing hypoglycemia in children with T1DM. * Determine the optimal utilization of continuous glucose monitors in the management of T1DM in children. * Assess the impact of continuous glucose monitoring on quality of life for the child and family. * Develop tools for the child and parents to use for incorporating continuous glucose monitors into diabetes self-management. * To assess possible changes in neurocognitive function and how it relates to frequency of hypoglycemia in young children with type 1 diabetes. * Evaluate and develop distinct, age-appropriate treatment approaches to T1DM in children. * Use continuous glucose monitoring to characterize the glycemic profile of nondiabetic children. * Develop statistical methods for the analysis of continuous glucose monitoring data. Closed and active studies are listed along with the associated protocols, public datasets, and publications.

Jaeb Center for Health Research
type: Organization
type: NamedIndividual
has db xref: grid.414912.b
has db xref: ISNI: 0000 0004 0586 473X
has db xref: nlx_152815
abbrev: JCHR
IAO_0000115: Freestanding, nonprofit coordinating center for multi-center clinical trials and epidemiologic research that focus on projects involving eye disorders or type 1 diabetes.

Diabetic Retinopathy Clinical Research Network
type: Resource
type: NamedIndividual
has db xref: nlx_152816
synonym: Diabetic Retinopathy Clinical Research Network (DRCR.net)
synonym: DRCR Network
abbrev: DRCR.net
abbrev: DRCRnet
IAO_0000115: A collaborative network to facilitate multicenter clinical research of diabetic retinopathy, diabetic macular edema and associated conditions. It supports the identification, design, and implementation of multicenter clinical research initiatives focused on diabetes-induced retinal disorders. Principal emphasis is placed on clinical trials, but epidemiologic outcomes and other research may be supported as well. It currently includes over 109 participating sites (offices) with over 320 physicians throughout the United States. Closed and active studies are listed along with the associated protocols, public datasets, and publications.

Clinical Islet Transplantation Study
type: Resource
type: NamedIndividual
has db xref: nlx_152840
synonym: Clinical Islet Transplantation Trial
synonym: Islet Transplantation Trials for Type 1 Diabetes
abbrev: CIT Study
IAO_0000115: Network of centers to conduct studies of islet transplantation in patients with type 1 diabetes to improve the safety and long-term success of methods for transplanting islets. It is the aim of this trial to improve methods of isolating islets, to improve techniques for the administering those transplanted islets; and to develop approaches to minimize the toxic effects of immunosuppressive drugs required for transplantation.

Nebula
type: Resource
type: NamedIndividual
has db xref: OMICS_00424
synonym: Nebula - A web-server for advanced ChIP-seq data analysis
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Web portal that allows users to analyze ChIP-seq data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Brain Gene Expression Map
type: Resource
type: NamedIndividual
has db xref: nif-0000-09579
synonym: BGEM - Brain Gene Expression Map
synonym: Mousebrain Gene Expression Map
abbrev: BGEM
IAO_0000115: This database contains gene expression patterns assembled from mouse nervous tissues at 4 time points throughout brain development including embryonic (e) day 11.5, e15.5, postnatal (p) day 7 and adult p42. Using a high throughput in situ hybridization approach we are assembling expression patterns from selected genes and presenting them in a searchable database. The database includes darkfield images obtained using radioactive probes, reference cresyl violet stained sections, the complete nucleotide sequence of the probes used to generate the data and all the information required to allow users to repeat and extend the analyses. The database is directly linked to Pubmed, LocusLink, Unigene and Gene Ontology Consortium housed at the National Center for Biotechnology Information (NCBI) in the National Library of Medicine. These data are provided freely to promote communication and cooperation among research groups throughout the world.

WordPress
type: Resource
type: NamedIndividual
has db xref: nlx_152818
synonym: WordPress.org
IAO_0000115: Web software which helps users create a website or blog. WordPress software can be downloaded and installed with an appropriate web host and minimum requirements. There is also a service called WordPress.com which allows users to get started with a new and free WordPress-based blog in seconds, though it varies in several ways and is less flexible than the self-installed WordPress. An array of plugins and themes are available to further customize a site.

Nonalcoholic Steatohepatitis Clinical Research Network
type: Resource
type: NamedIndividual
has db xref: nlx_152845
synonym: Clinical Research Network in Nonalcoholic Steatohepatitis
synonym: Nonalcoholic Steatohepatitis Clinical Research Network (NASH CRN)
abbrev: NASH CRN
IAO_0000115: Clinical research network to focus on the etiology, contributing factors, natural history, complications, and therapy of nonalcoholic steatohepatitis. They research the nature and underlying cause of Nonalcoholic Steatohepatitis (NASH) and conduct clinical studies on prevention and treatment. Approximately 1,500 pediatric and adult participants throughout the United States and Canada with nonalcoholic fatty liver disease (NAFLD) have enrolled into a database. The NASH CRN has recently reopened the database to enroll additional pediatric and adult participants with NAFLD. Serum, liver tissue, and genomic DNA samples are being collected and stored in the NIDDKrepository for ongoing as well as future studies. A three-arm randomized, placebo-controlled clinical trial of pioglitazone versus vitamin E completed enrollment in 2009. In addition to this adult trial, a similar trial in pediatric NASH patients randomized 180 children to receive treatment with vitamin E, metformin, or placebo.

BacPac Resources Center
type: Resource
type: NamedIndividual
has db xref: nif-0000-09578
has db xref: nlx_152819
has db xref: SCR_007215
synonym: BAC Clones Distribution Center
synonym: BACPAC Resources Center
synonym: BacPac Resources Center: BAC Clones Distribution Center
abbrev: BPRC
IAO_0000115: It is the distribution arm of their academic laboratory. They operate on a cost-recovery mechanism in order to make the resources generated in their laboratory available to the academic scientific community. While clones and screening services are widely available, library arrays are primarily available to researchers with a scientific need to analyze most clones in the library. This site contains information on currently available BAC and PAC genomic DNA libraries, BAC Clones, PAC Clones, Fosmid Clones, cDNA collections, high-density colony hybridization filters, and BAC and PAC cloning vectors. Protocols used in our laboratory for the hybridization-based screening of colony filters, purification of BAC and PAC DNA, and end-sequencing methodologies, are also provided. BPRC does not list clones, for two reasons: 1)most clones have not been characterized and lack specific data. 2)all clones are part of libraries and all clones from a particular library share common characteristics. Hence, to find out if BPRC has a particular clone, one needs either use Automatic Clone Validation or else find out if the clone is compatible with the range of clone names for a corresponding clone library. Typically (although not always), clone names are derived from the library name. BPRC uses the NCBI-recommended clone nomenclature & library nomenclature. Most arrayed libraries are available in frozen microtiter dish format to academic and non-academic users provided that there is a scientific need for complete-library access. (for instance to annotate, modify or analyze all BAC clones as part of a genome project).

Chemistry Add-in for Word
type: Resource
type: NamedIndividual
has db xref: nlx_152820
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for the insertion and modification of chemical information within Microsoft Word. Capabilities include inserting labels, formulas, and 2D depictions of chemical structures, as well as creating in-line chemical zones, rendering visual depictions of chemical structures, and the ability to store chemical information in a semantically rich manner.

Juvenile Diabetes Research Foundation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100008871
has db xref: grid.429307.b
has db xref: ISNI: 0000 0004 0575 6413
has db xref: nlx_152841
has db xref: Wikidata: Q6107958
synonym: JDRF International
synonym: Juvenile Diabetes Research Foundation International
abbrev: JDRF
IAO_0000115: Global funder of type 1 diabetes (T1D) research that aims to progressively remove the impact of T1D from people's lives until a world without T1D is achieved. JDRF collaborates with a wide spectrum of partners and is the only organization with the scientific resources, regulatory influence, and a working plan to better treat, prevent, and eventually cure T1D. More than 80 percent of JDRF's expenditures directly support research and research-related education. In 2012 Forbes magazine named JDRF one of its five All-Star charities, citing the organization's efficiency and effectiveness. The organization awards research grants for laboratory and clinical investigations and sponsors a variety of career development and research training programs for new and established investigators. JDRF also sponsors international workshops and conferences for biomedical researchers. Individual chapters offer support groups and other activities for families affected by diabetes.

MINT
type: Resource
type: NamedIndividual
has db xref: nlx_152821
has db xref: r3d100010414
synonym: MINT - the Molecular INTeraction database
synonym: Molecular INTeraction database
synonym: Molecular Interactions Database
synonym: the Molecular INTeraction database
IAO_0000115: A database that focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The curated data can be analyzed in the context of the high throughput data and viewed graphically with the MINT Viewer. This collection of molecular interaction databases can be used to search for, analyze and graphically display molecular interaction networks and pathways from a wide variety of species. MINT is comprised of separate database components. HomoMINT, is an inferred human protein interatction database. Domino, is database of domain peptide interactions. VirusMINT explores the interactions of viral proteins with human proteins. The MINT connect viewer allows you to enter a list of proteins (e.g. proteins in a pathway) to retrieve, display and download a network with all the interactions connecting them.

Drug-Induced Liver Injury Network
type: Resource
type: NamedIndividual
has db xref: nlx_152822
abbrev: DILIN
IAO_0000115: Prospective and retrospective registry of well-characterized cases of drug-induced liver disease. The goals of Network include the development of standardized procedures to identify and fully characterize bona fide cases of drug- and complementary and alternative medicines (CAM)-induced liver injury, and to conduct controlled, clinical studies that will include extensive collection of data, serum, DNA, and tissue specimens. Cases of liver injury due to herbal medications are also included. The network will also develop terminology and standardized definitions for DILI, and to develop causality assessment instruments that are sensitive, specific, and reproducible. DILIN is funded by a cooperative agreement and includes five clinical centers and a central data coordinating center. The research goals of DILIN are to: * Create a registry of carefully documented DILI cases * Identify clinical, immunological, and environmental risk factors for drug- and CAM-mediated hepatotoxicity * Create a bank of biological specimens consisting of DNA, plasma, and immortalized lymphocytes to facilitate detailed genetic analyses * Characterize the natural history of drug- and CAM-induced DILI for at least six months following enrollment * Develop the capability to recontact these individuals over an extended period of time so that additional studies exploring DILI mechanisms can be performed Two studies are being initiated by the network. In the Retrospective Study, the implicated drugs are restricted to isoniazid, phenytoin, combination clavulanic acid/amoxicillin, and valproic acid (Depakote), Nitrofurantoin, Trimethoprim-sulfamethoxazole, Minocycline, and Quinolone antibiotics. These drugs were chosen because they are frequently administered to patients not receiving other hepatotoxic drugs, making it easier to establish causality. Patients must be alive, and the date of onset of the DILI episode must be on or after January 1, 1994. In the Prospective Study, all incident cases of dru…

Family Investigation of Nephropathy of Diabetes
type: NamedIndividual
has db xref: nlx_152825
synonym: Family Investigation of Nephropathy & Diabetes
synonym: Family Investigation of Nephropathy and Diabetes (F.I.N.D.)
abbrev: F.I.N.D.
abbrev: FIND
IAO_0000115: Multicenter observational study designed to identify genetic determinants of diabetic nephropathy. It is conducted in eleven U.S. clinical centers and a coordinating center, and with four ethnic groups (European Americans, African Americans, Mexican Americans, and American Indians). Two strategies are used to localize susceptibility genes: a family-based linkage study and a case-control study using mapping by admixture linkage disequilibrium (MALD). In the family-based study, probands with diabetic nephropathy are recruited with their parents and selected siblings. Linkage analyses will be conducted to identify chromosomal regions containing genes that influence the development of diabetic nephropathy or related quantitative traits such as serum creatinine concentration, urinary albumin excretion, and plasma glucose concentrations. Regions showing evidence of linkage will be examined further with both genetic linkage and association studies to identify genes that influence diabetic nephropathy or related traits. Two types of MALD studies are being done. One is a case-control study of unrelated individuals of Mexican American heritage in which both cases and controls have diabetes, but only the case has nephropathy. The other is a case-control study of African American patients with nephropathy (cases) and their spouses (controls) unaffected by diabetes and nephropathy; offspring are genotyped when available to provide haplotype data. The specific goals of this program: * Delineate genomic regions associated with the development and progression of renal disease(s) * Evaluate whether there is a genetic link between diabetic nephropathy and diabetic retinopathy * Improve outcomes * Provide protection for people at risk and slow the progression of renal disease * Help establish a resource for genetic studies of kidney disease and diabetic complications by creating a repository of genetic samples and a database * Encourage studies of the genetics of progressive renal dis…

International Mouse Strain Resource
type: Resource
type: NamedIndividual
has db xref: nif-0000-09876
synonym: IMSR
IAO_0000115: Database of mouse strains and stocks available worldwide, that will assist international research community in finding mouse resources they need, including inbred, mutant, and genetically engineered mice. IMSR is multi institutional international collaboration supporting use of mouse as model system for studying human biology and disease. IMSR began with initial collaboration between Mouse Genome Informatics (MGI) group at Jackson Laboratory and Medical Research Council Mammalian Genetics Unit at Harwell. Additional institutions and collaborators are now contributing mouse resource information to IMSR. Data content found in IMSR is as it was supplied by data provider sites. You are encouraged to participate in making this database as complete as possible for all worldwide mouse strain resources. If you or your institution hold mice, cryopreserved gametes or embryos, or ES cell lines that you distribute to other researchers, contributing information about them to IMSR catalog will make them more widely known.

Frequent Hemodialysis Network Daily Trial
type: Resource
type: NamedIndividual
has db xref: nlx_152828
synonym: Frequent Hemodialysis Network (FHN) Daily Trial
abbrev: FHN Daily Trial
IAO_0000115: Randomized controlled clinical trial to understand how increasing hemodialysis to six times a week from the standard of three times a week may result in improved heart health. Subjects were recruited from dialysis units associated with designated Clinical Centers in the U.S. and Canada and followed for 1 year. Subjects will be randomized to either conventional hemodialyis Daily HD delivered for at least 2.5 hours (typically 3 to 4 hours), 3 days per week, or to more frequent hemodialysis delivered for 1.5 - 2.75 hours, 6 days per week. The study has two co-primary outcomes: 1) a composite of mortality with the change over 12 months in left ventricular mass by magnetic resonance imaging, and 2) a composite of mortality with the change over 12 months in the SF-36 RAND physical health composite (PHC) quality of life scale. In addition, main secondary outcomes have been designated for each of seven outcome domains: 1) cardiovascular structure and function (change in LV mass), 2) health-related quality of life/physical function (change in the PHC), 3) depression/burden of illness (change in Beck Depression Inventory), 4) nutrition (change in serum albumin), 5) cognitive function (change in the Trail Making Test B), 6) mineral metabolism (change in average predialysis serum phosphorus), and 7) clinical events (rate of non-access hospitalization or death). Hypertension and anemia are also main outcome domains, but without designation of single first priority outcomes.

Sequencher
type: Commercial Organization
type: NamedIndividual
has db xref: OMICS_01817
synonym: Sequencher sequence analysis software
IAO_0000115: Software for Next-Generation DNA sequencing, Sanger DNA analysis, and RNA sequencing. It contains sequence analysis tools which include reference-guided alignments, de novo assembly, variant calling, and SNP analyses. It has integrated the Cufflinks suite for in-depth transcript analysis and differential gene expression of RNA-Seq data.

HALT PKD
type: Resource
type: NamedIndividual
has db xref: nlx_152832
synonym: Polycystic Kidney Disease-Treatment Network
abbrev: HALT PKD
abbrev: HALT-PKD
IAO_0000115: Consortium established to design and implement clinical trials of treatments that might slow the progressive loss of renal function in Polycystic Kidney Disease (PKD). Two multicenter randomized, double-blind, placebo controlled clinical trials are running concurrently to study the efficacy of renin-angiotensin-aldosterone system blockade on the progression of cystic disease (kidney volume) and on the decline in renal function in autosomal dominant polycystic kidney disease (ADPKD). Study A is to study whether intensive ACE-I/ARB blockade decrease the progression of cystic disease compared to ACE-I monotherapy patients with early disease, relatively preserved renal function, and high-normal BP or hypertension. Study B is to study whether intensive ACE-I/ARB blockade as compared to ACE-I monotherapy slow the decline in kidney function, end-stage of renal disease, or death in the setting of standard blood pressure control in hypertensive patients with moderately advanced disease.

HEALTHY study
type: Resource
type: NamedIndividual
has db xref: nlx_152833
synonym: HEALTHY Intervention Program
synonym: HEALTHY Study Group
abbrev: HEALTHY
IAO_0000115: Primary prevention trial conducted in 42 middle schools at 7 locations across the US to impact risk factors for type 2 diabetes in adolescents. Students were recruited at the start of 6th grade (fall 2006) and followed to the end of 8th grade (spring 2009). Half of the schools were randomized to receive an intervention that integrated four components: the school nutrition environment, physical education class activities, behavior change initiatives, and educational and promotional communications activities.

Hepatitis B Research Network
type: Resource
type: NamedIndividual
has db xref: nlx_152834
abbrev: HBRN
IAO_0000115: Network that brings together clinical centers with expertise in caring for patients with chronic hepatitis B virus (HBV) infection to conduct research in order to better understand the physiological effects of the disease and develop effective treatment strategies with the currently available therapies. The web site is designed to inform the public of the research activities conducted by the Hepatitis B Research Network. It is also a portal to support communications for their researchers and participants in their studies. The Hepatitis B Research Network is currently seeking patients for a multi-center prospective study of the natural history of chronic hepatitis B. Within the next few months treatment trials for various patients with chronic hepatitis B will also begin enrolling patients. Details of the entry criteria for these studies can be obtained from the clinical centers outlined on the website's map.

ModelRun
type: Resource
type: NamedIndividual
has db xref: nlx_152893
IAO_0000115: Data set of output of neuron models through the Trestles supercomputer.

Kansas State University; Kansas; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100007765
has db xref: grid.36567.31
has db xref: ISNI:0000 0001 0737 1259
has db xref: nlx_62700
has db xref: Wikidata:Q31249
synonym: Kansas State University
abbrev: KSU
IAO_0000115: Public doctoral university located in Manhattan, Kansas that is involved with research, especially agricultural.

HALT-C Trial
type: Resource
type: NamedIndividual
has db xref: nlx_152835
synonym: Hepatitis C Antiviral Long-term Treatment against Cirrhosis
synonym: Hepatitis C Antiviral Long-term Treatment against Cirrhosis (HALT-C) Trial
synonym: Hepatitis C Antiviral Long-term Treatment against Cirrhosis Trial
abbrev: HALT-C
abbrev: HALT-C Trial
IAO_0000115: Multi-center, randomized controlled study designed to determine if continuing interferon long term over several years will suppress the Hepatitis C virus, prevent progression to cirrhosis, prevent liver cancer and reduce the need for liver transplantation. Patient enrollment began in 2000 and was completed in 2003 at 10 clinical centers, which were supported by a data coordinating center, virological testing center, and central sample repository. Patients with chronic hepatitis C and advanced fibrosis or cirrhosis on liver biopsy who failed to respond to a previous course of interferon alfa were enrolled in this study. Patients were initially treated with a 24-week course of peginterferon alfa-2a and ribavirin. Patients who remained hepatitis C virus RNA positive were then randomized to receive maintenance, low-dose peginterferon or to be followed on no treatment. Liver biopsies were done before enrollment and after 2 and 4 years of treatment or follow-up. The endpoints were development of cirrhosis, hepatic decompensation, hepatocellular carcinoma, death, or liver transplantation. 1050 patients were randomized and followed through the 4 year randomized phase of the trial and as long as 4 years off treatment. Serum samples collected at multiple time points, DNA and liver tissue are available for scientific investigation.

Immune Tolerance Network (ITN)
type: Resource
type: NamedIndividual
has db xref: nlx_152838
abbrev: ITN
IAO_0000115: International clinical research consortium dedicated to the clinical evaluation of novel tolerogenic approaches for the treatment of autoimmune diseases, asthma and allergic diseases, and the prevention of graft rejection. They aim to advance the clinical application of immune tolerance by performing high quality clinical trials of emerging therapeutics integrated with mechanism-based research. In particular, they aim to: * Establish new tolerance therapeutics * Develop a better understanding of the mechanisms of immune function and disease pathogenesis * Identify new biomarkers of tolerance and disease Their goals are to identify and develop treatment game changers for tolerance modulating therapies for the treatment of immune mediated diseases and disabling conditions, and to conduct high quality, innovative clinical trials and mechanistic studies not likely to be funded by other sources or to be conducted by private industry that advance our understanding of immunological disorders. In the Immune Tolerance Network's (ITN) unique hybrid academic/industry model, the areas of academia, government and industry are integral to planning and conducting clinical studies. They develop and fund clinical trials and mechanistic studies in partnership. Their development model is a unique, interactive process. It capitalizes on their wide-ranging, multidisciplinary expertise provided by an advisory board of highly respected faculty from institutions worldwide. This model gives investigators special insight into developing high quality research studies. The ITN is comprised of leading scientific and medical faculty from more than 50 institutions in nine countries worldwide and employs over 80 full-time staff at the University of California San Francisco (UCSF), Bethesda, Maryland and Benaroya Research Institute in Seattle, Washington.

Longitudinal Assessment of Bariatric Surgery
type: Resource
type: NamedIndividual
has db xref: nlx_152842
synonym: LABS consortium
synonym: Longitudinal Assessment of Bariatric Surgery (LABS) Consortium
synonym: Longitudinal Assessment of Bariatric Surgery Consortium
abbrev: LABS
IAO_0000115: Consortium comprised of six clinical centers and a data coordinating center to facilitate coordinated clinical, epidemiological, and behavioral research in the field of bariatric surgery, through the cooperative development of common clinical protocols and a bariatric surgery database that will collect information from participating clinical centers. LABS will help pool the necessary clinical expertise and administrative resources to facilitate the conduct of multiple clinical studies in a timely, efficient manner. Also, the use of standardized definitions, clinical protocols, and data-collection instruments will enhance the investigator's ability to provide meaningful evidence-based recommendations for patient evaluation, selection, and follow-up care. The consortium was funded in September 2003. The investigators have collaboratively developed a core database and clinical protocols, and subject enrollment began in early 2005. A repository of data and biological specimens for future research also will be collected by the centers participating in LABS. These will provide valuable resources for future study of obesity and its complications.

flowFP
type: Resource
type: NamedIndividual
has db xref: OMICS_05599
synonym: flowFP - Fingerprinting for Flow Cytometry
IAO_0000115: A Bioconductor software package for fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry.

National Center for Integrative Biomedical Informatics
type: Resource
type: NamedIndividual
has db xref: nif-0000-09660
synonym: NCIBI
IAO_0000115: The Center develops conceptual models, computational infrastructure, an integrated knowledge repository, and query and analysis tools that enable scientists to effectively access and integrate the wealth of biological data. The National Center for Integrative Biomedical Informatics (NCIBI) was founded in October 2005 and is one of seven National Centers for Biomedical Computing (NCBC) in the NIH Roadmap. NCIBI is based at the University of Michigan as a part of the Center for Computational Medicine and Biology (CCMB). NCIBI is composed of biomedical researchers, computational biologists, computer scientists, developers and human-computer interaction specialists organized into seven major core functions. They work in interdisciplinary teams to collectively develop tools that are not only computationally powerful but also biologically relevant and meaningful. The four initial Driving Biological Projects (prostate cancer progression, Type 1 and type 2 diabetes and bipolar disorder) provide the nucleation point from which tool development is informed, launched, and tested. In addition to testing tools for function, a separate team is dedicated to testing usability and user interaction that is a unique feature of this Center. Once tools are developed and validated the goal of the Center is to share and disseminate data and software throughout the research community both internally and externally. This is achieved through various mechanisms such as training videos, tutorials, and demonstrations and presentations at national and international scientific conferences. NCIBI is supported by NIH Grant # U54-DA021519.

RiVuR
type: Resource
type: NamedIndividual
has db xref: nlx_152848
synonym: Randomized Intervention for Children with Vesicoureteral Reflux
synonym: Randomized Intervention for Children With Vesicoureteral Reflux (RIVUR)
synonym: Randomized Intervention for Vesicoureteral Reflux
abbrev: RIVUR
IAO_0000115: Multicenter, randomized, double-blind, placebo-controlled trial is designed to determine whether daily antimicrobial prophylaxis is superior to placebo in preventing recurrence of urinary tract infection (UTI) in children with vesicoureteral reflux (VUR). The basic eligibility criteria are: (1) age at randomization of at least 2 months, but less than 6 years, (2) a diagnosed first febrile or symptomatic UTI within 42 days prior to randomization that was appropriately treated, and (3) presence of Grade I-IV VUR based on voiding cystourethrogram (VCUG). Patients will be randomly assigned to treatment for 2 years with daily antimicrobial prophylaxis (trimethoprim-sulfamethoxazole) or placebo. The study is designed to recruit 600 children (approximately 300 in each treatment group) over an 18-24 month period. The primary endpoint is recurrence of UTI. In addition, patients will be evaluated for secondary endpoints related to renal scarring and antimicrobial resistance. Scarring will be determined based on renal scintigraphy by 99mTc dimercaptosuccinic (DMSA) scan. Quality of life, compliance, safety parameters, utilization of health resources, and change in VUR will be assessed periodically throughout the study.

SEARCH for Diabetes in Youth
type: Resource
type: NamedIndividual
has db xref: nlx_152850
abbrev: SEARCH
abbrev: SEARCH Study
IAO_0000115: National multi-center study aimed at understanding more about diabetes among children and young adults in the United States less than 20 years of age in six geographically dispersed populations that encompass the ethnic diversity of the United States. SEARCH has been helping to find answers about the types of diabetes, its complications, and how having diabetes affects the lives of children and young adults. There are more than 20,000 study participants representing all different racial and ethnic backgrounds who have helped SEARCH determine the extent of diabetes in the community and its impact on different populations. The SEARCH Study invites Investigators interested in childhood Diabetes Research to collaborate on matters of interest to the field of childhood Diabetes.

Schizophrenia and Bipolar Disorder Genetics Blog
type: Resource
type: NamedIndividual
has db xref: nif-0000-10419
synonym: Genetics Blog
IAO_0000115: This resource aims to provide information for the general public on the background and current progress of scientific research into the role of genetics in these disorders. Additionally, it also aims to provide a forum for the discussion of aspects of psychiatric genetics open to members of the research community.

SISTEr
type: Resource
type: NamedIndividual
has db xref: nlx_152852
synonym: Stress Incontinence Surgical Treatment Efficacy Trial
abbrev: SISTEr
IAO_0000115: Clinical trial under the Urinary Incontinence Treatment Network to compare the treatment success for two surgical procedures that are frequently used and have similar cure rates, yet have not been compared directly to each other in a large, rigorously conducted randomized trial. The secondary aims of the trial are to compare other outcomes for the two surgical procedures, including quality of life, sexual function, satisfaction with treatment outcomes, complications, and need for other treatment(s) after surgery. Follow-up will be a minimum of two years and up to four years.

Urinary Incontinence Treatment Network
type: Resource
type: NamedIndividual
has db xref: nlx_152853
abbrev: UITN
IAO_0000115: Group of collaborating investigators who conduct long-term studies and clinical trials of the most commonly used surgical, pharmacological, and behavioral approaches for management of urinary incontinence in women diagnosed with stress and mixed incontinence.

Study of Nutrition in Acute Pancreatitis
type: Resource
type: NamedIndividual
has db xref: nlx_152854
abbrev: SNAP
IAO_0000115: Randomized multi-center clinical trial designed to test whether duodenojejunal (DJ) feeding is more effective than nasogastric (NG) feeding in providing enteral nutrition to patients with severe acute pancreatitis. SNAP will enroll participants with severe acute pancreatitis admitted to the intensive care unit at eight clinical centers. Upon enrollment, participants are assigned to NG or DJ feeding and managed for up to 28 days or until weaned on to solid food. Follow-up continues until participants are discharged from the hospital or for a maximum of 60 days. Outcomes relate to feeding tolerance and failure, nutritional status, risk for life-threatening pancreatic/systemic complications, and hospital mortality.

ChIPseeqer
type: Resource
type: NamedIndividual
has db xref: OMICS_00422
IAO_0000115: Software that provides a comprehensive framework for the analysis of ChIP-seq data.

TINSAL-T2D
type: Resource
type: NamedIndividual
has db xref: nlx_152855
synonym: Targeting INflammation using SALsalate for Type 2 Diabetes
synonym: Targeting Inflammation Using Salsalate for Type 2 Diabetes-stage II
abbrev: TINSAL-T2D
abbrev: TINSAL-T2D-II
IAO_0000115: Nationwide, randomized, double blind, multi-center research study to determine whether the drug salsalate, a member of the commonly used Non-Steroidal Anti-Inflammatory Drug (NSAID) class, is effective in lowering sugars in patients with type 2 diabetes. The study is conducted in two stages. The primary objective of the first stage is to select a dose of salsalate that is both well-tolerated and demonstrates a trend toward improvement in glycemic control. The primary objective of Stage 2 of the study is to evaluate the effects of salsalate on blood sugar control in diabetes; the tolerability of salsalate use in patients with type 2 diabetes (T2D); and the effects of salsalate on measures of inflammation, the metabolic syndrome, and cardiac risk.

Treatment Options for type 2 Diabetes in Adolescents and Youth
type: Resource
type: NamedIndividual
has db xref: nlx_152858
synonym: TODAY study
synonym: Treatment Options for type 2 Diabetes in Adolescents & Youth
abbrev: TODAY
IAO_0000115: Randomized, double blind, nationwide clinical trial to compare the efficacy and safety of three interventions to treat adolescents and youth with type 2 diabetes (T2D): (1) metformin alone, (2) metformin plus rosiglitazone, and (3) metformin plus an intensive lifestyle intervention called the TODAY Lifestyle Program (TLP). The secondary aims are to: compare and evaluate the safety of the three treatment arms; compare the effects of the three treatments on the pathophysiology of type 2 diabetes (T2D) with regards to beta cell function and insulin resistance, body composition, nutrition, physical activity and aerobic fitness, cardiovascular risk factors, microvascular complications, quality of life, and psychological outcomes; evaluate the influence of individual and family behaviors on treatment response; and compare the relative cost effectiveness of the three treatment arms. The study recruits patients over a three-year period and follows patients for a minimum of two years. Patients are randomized within two years of the diagnosis of T2D. Materials that were used for the study are made publicly available: * The TODAY Standard Diabetes Education (TSDE) program, developed especially for youth with type 2 diabetes. (All participants received the TSDE program) * The TODAY Lifestyle Program (TLP) that was among the treatments tested.

Karolinska Institute; Stockholm; Sweden
type: Organization
type: NamedIndividual
has db xref: nlx_41870
synonym: Karolinska Institutet
synonym: Karolinska University
abbrev: KI
IAO_0000115: Medical university in Stockholm, Sweden that offers more than fifty disciplines of medicine for study.

TOMUS
type: Resource
type: NamedIndividual
has db xref: nlx_152859
synonym: TOMUS-Trial Of Mid-Urethral Slings
synonym: Trial Of Mid-Urethral Slings
abbrev: TOMUS
IAO_0000115: Study that compared the outcomes of two minimally invasive surgical procedures to treat stress urinary incontinence in women. These procedures are called mid-urethral slings. The procedures insert a mesh sling or hammock to support the bladder neck so that urine does not leak. Both procedures have been approved by the FDA and have been shown to be safe and successful in treating stress urinary incontinence. However, it is not known if one is better than the other. This study answers that question. The secondary aims of the trial are to compare other outcomes for the two surgical procedures, including quality of life, sexual function, satisfaction with treatment outcomes, complications, and the need for other treatments(s) after surgery. Follow-up will be a minimum of two years. Stress urinary incontinence is the accidental leakage of urine during activities such as coughing, laughing, sneezing, or lifting heavy objects.

TRIGR
type: Resource
type: NamedIndividual
has db xref: nlx_152860
synonym: Trial to Reduce IDDM in the Genetically at Risk
synonym: TRIGR - Trial to Reduce IDDM in the Genetically at Risk
synonym: TRIGR trial
IAO_0000115: International, randomized, double-blinded trial to determine whether weaning to a casein hydrolysate formula during the first 6-8 months of life in place of cow milk based formula reduces the incidence of autoimmunity and type 1 diabetes in genetically susceptible newborn infants. 2160 eligible infants were randomized to test or control formulas when mothers decide to wean from exclusive breastfeeding. The participants will be monitored up to the age of 10 years for the appearance of diabetes-predictive autoantibodies and clinical type 1 diabetes. The TRIGR trial will determine whether delayed exposure to intact food proteins will reduce the chances of developing type 1 diabetes later in life. All babies in the study received the recommendation to breastfeed for at least the first six months of life. If a mother was unable to exclusively breastfeed before the baby was 8 months of age, her child was randomly assigned to one of two groups. One group of these babies received a trial formula based on extensively hydrolyzed protein; the other group received another trial formula containing a smaller amount of hydrolyzed protein. In the hydrolyzed formula, the big protein molecules have been split into very small fragments to provide a source of nutritional amino acids, but the fragments are likely too small to stimulate the immune system. The TRIGR trial will also be able to analyze whether exclusive breastfeeding per se can reduce the risk of the children to develop type 1 diabetes.

NeuroPedia
type: Resource
type: NamedIndividual
has db xref: nlx_152894
synonym: NeuroPedia: Neuropeptide database and spectra library
IAO_0000115: A neuropeptide encyclopedia of peptide sequences (including genomic and taxonomic information) and spectral libraries of identified MS/MS spectra of homolog neuropeptides from multiple species.

Karlsruhe Institute of Technology; Karlsruhe; Germany
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100009133
has db xref: grid.7892.4
has db xref: ISNI: 0000 0001 0075 5874
has db xref: nlx_48421
has db xref: Wikidata: Q309988
synonym: KIT
IAO_0000115: Public research university in Germany for engineering and natural sciences.

Viral Resistance to Antiviral Therapy of Chronic Hepatitis C
type: Resource
type: NamedIndividual
has db xref: nlx_152861
synonym: Study of Viral Resistance to Antiviral Therapy of Chronic Hepatitis C
synonym: Study of Viral Resistance to Antiviral Therapy of Chronic Hepatitis C (Virahep-C)
abbrev: Virahep-C
IAO_0000115: Study designed to test the hypothesis that African-Americans respond less well to combination pegylated interferon and ribavirin therapy than Caucasian-Americans who have chronic hepatitis C genotype 1 and who were not previously treated with either interferon or ribavirin. Reasons for differences in response, regardless of race, will be studied. All patients were treated with combination therapy of pegylated interferon and ribavirin for 48 weeks, and were followed for an additional 48 week safter cessation of therapy. 400 patients, half African-American and half Caucasian American, from 8 clinical centers with the goals of establishing rates of response to optimal current therapy in the two ethnic groups, identify factors predictive of response, establish patterns of viral kinetics in response to antiviral therapy, and test hypotheses concerning viral and host factors determining response to therapy. Four ancillary studies designed to elucidate biological and virological basis for non-response are also included in Virahep-C. Additionally, the study has central facilitates for pathology, the virological testing laboratory and a serum/tissue repository.

GenitoUrinary Development Molecular Anatomy Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-33426
has db xref: nlx_152871
synonym: Murine Atlas for Genitourinary Development
abbrev: GUDMAP
IAO_0000115: Project aggregates and provides experimental gene expression data from genito-urinary system. International consortium providing molecular atlas of gene expression for developing organs of GenitoUrinary (GU) tract. Mouse strains to facilitate developmental and functional studies within GU system. Experimental protocols and standard specifications. Tutorials describing GU organogenesis and primary data via database. Data are from large-scale in situ hybridization screens (wholemount and section) and microarray gene expression data of microdissected, laser-captured and FACS-sorted components of developing mouse genitourinary (GU) system.

Intestinal Stem Cell Consortium
type: Resource
type: NamedIndividual
has db xref: nlx_152862
synonym: ISCC - Intestinal Stem Cell Consortium
abbrev: ISCC
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Consortium to advance the understanding of intestinal epithelial stem cell biology during development, homeostasis, regeneration and disease. Its immediate goals are to isolate, characterize, culture and validate populations of intestinal stem cells; answer major questions in stem cell biology of the intestinal epithelium; and accelerate research by making information and resources available to the research community. Resources include data sets, protocols, and a resource catalog. Long-term goals include: 1) laying the ground work for therapeutic manipulation of the intestinal epithelium 2) contributing to the greater understanding of stem cell biology through knowledge of the intestine as a model stem cell-driven system. Research Projects are housed at 8 institutions across the nation: Oregon Health & Science University, Stanford University, Stowers Institute for Medical Research, University of California, Los Angeles School of Medicine (UCLA) (partnered with the VA Greater Los Angeles), University of North Carolina, Chapel Hill (UNC), University of Oklahoma, University of Pennsylvania, and University of Pittsburgh.

Medical Therapy of Prostatic Symptoms
type: Resource
type: NamedIndividual
has db xref: nlx_152863
synonym: Medical Therapy of Prostatic Symptoms (MTOPS)
abbrev: MTOPS
IAO_0000115: Multi-center double-masked, placebo-controlled randomized clinical trial designed to evaluate the long-term efficacy of finasteride, or doxazosin, or the combination of both, in delaying or preventing the clinical progression of symptomatic benign prostatic hyperplasia (BPH). MTOPS was the largest and longest study to test whether drug therapy can prevent or delay the noncancerous growth of the prostate. A unique feature of MTOPS that has not been done in prior studies of pharmacotherapy of BPH is the biopsy substudy. A total of 1,082 volunteers from the 2,931 participants randomized during the full-scale phase are currently participating in this substudy. Biopsies of the prostate will be obtained on these volunteers at predetermined times during the course of the trial to evaluate the status of the prostate at key event times. The purpose of the substudy was to provide additional information regarding the histopathobiology of BPH and to test existing biomarkers for their prognostic ability regarding response to drug therapy.

Type 1 Diabetes Genetics Consortium
type: Resource
type: NamedIndividual
has db xref: nlx_152867
synonym: Type 1 Diabetes Genetics Consortium (T1DGC)
abbrev: T1DGC
IAO_0000115: Data and biological samples were collected by this consortium organizing international efforts to identify genes that determine an individual risk of type 1 diabetes. It originally focused on recruiting families with at least two siblings (brothers and/or sisters) who have type 1 diabetes (affected sibling pair or ASP families). The T1DGC completed enrollment for these families in August 2009. They completed enrollment of trios (father, mother, and a child with type 1 diabetes), as well as cases (people with type 1 diabetes) and controls (people with no history of type 1 diabetes) from populations with a low prevalence of this disease in January 2010. T1DGC Data and Samples: Phenotypic and genotypic data as well as biological samples (DNA, serum and plasma) for T1DGC participants have been deposited in the NIDDKCentral Repositories for future research.

CisGenome
type: Resource
type: NamedIndividual
has db xref: biotools:cisgenome
has db xref: OMICS_00423
synonym: CisGenome v2.0
IAO_0000115: Integrated software tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis.

KESM brain atlas
type: Resource
type: NamedIndividual
has db xref: nlx_152869
synonym: KESMBA: Knife-Edge Scanning Microscope Brain Atlas
synonym: Knife-Edge Scanning Microscope Brain Atlas
abbrev: KESMBA
IAO_0000115: A web-based, light-weight 3D volume viewer that serves large volumes (typically the whole brain) of high-resolution mouse brain images (~1.5 TB per brain, ~1 um resolution) from the Knife-Edge Scanning Microscope (KESM), invented by Bruce H. McCormick. Currently, KESMBA serves the following data sets: * Mouse: Whole-brain-scale Golgi (acquired 2008 spring): neuronal morphology: Choe et al. (2009) * Mouse: Whole-brain India Ink (acquired 2008 spring): vascular network: Choe et al. (2009); Mayerich et al. (2011); * Mouse: Whole-brain Golgi (acquired 2011 summer): neuronal morphology: Choe et al. (2011); Chung et al. (2011); * Mouse: Whole-brain Nissl (acquired 2009-2010 winter): somata (Choe et al. 2010) (Coming soon) They will ship you the full data set on a hard drive if you provide them with the hard drive and shipping cost.

GlyProt
type: Resource
type: NamedIndividual
has db xref: biotools:glyprot
has db xref: nlx_152875
synonym: GlyProt - In Silico Glycosylation of Proteins
IAO_0000115: Web-based tool that enables meaningful N-glycan conformations to be attached to all the spatially accessible potential N-glycosylation sites of a known three-dimensional (3D) protein structure. The 3D structure of protein is required as input. Potential N-glysylations site are automatically detected. The attached glycan are constructed with SWEET-II, http://www.glycosciences.de/modeling/sweet2/doc/index.php

Distance Mapping
type: Resource
type: NamedIndividual
has db xref: nlx_152876
IAO_0000115: Web tool that allows drawing distances of equal r as a function of the appropriate F,Y coordinates using the nuclear Overhauser enhancement (NOE), which allows the detection of the proximity in space between protons that may be located in different, yet spatially neighboring residues of oligosaccharides. A single pair of contours drawn for the lower and upper limits of r for one NOE encloses a torus-like region which still covers an infinite number of F,Y conformations. Please note: This application only works if Java Script is activated in your web browser.

pdb-care
type: Resource
type: NamedIndividual
has db xref: nlx_152877
synonym: PDB CArbohydrate REsidue check
synonym: pdb-care: PDB CArbohydrate REsidue check
synonym: pdbcare
IAO_0000115: Tool that checks carbohydrate residues in pdb-files for errors, aiding experimentalists in detecting discrepancies in connectivities and nomenclature.

Neural Maestro
type: Resource
type: NamedIndividual
has db xref: nlx_153440
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. A C#.NET/C++.NET 4.0 API multi-threaded, parallel class library with CUDA kernels for EEG predictive analytics gleaned from the ModelMaker 2 application. This web service and component library offers functionality to do univariate and multivariate nonlinear time series and frequency based predictive analysis for EEG / Ecog / MEG signals for gaming applications. Neural Maestro works with both EEGLab / BCILab and eConnectome as well as other MATLAB and R packages. It enables one to build highly sophisticated neuroscience applications with little effort in Windows applications.

The Biomedical Research Foundation - Current Research
type: Resource
type: NamedIndividual
has db xref: nif-0000-10446
synonym: BRI Research
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This laboratory facilities contain core research space for monoclonal antibody production, oligonucleotide and peptide synthesis, gene cloning, DNA sequencing, high performance liquid chromatography, tissue culture, positron emission tomography, magnetic resonance spectroscopy and electron microscopy.

Colorado Assessment Tests - Repeat
type: Resource
type: NamedIndividual
has db xref: nif-0000-09822
synonym: Repeat
abbrev: CAT Repeat
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. This free neuropsychological evaluation software, Repeat, examines performance on a serial reaction time task thought to depend upon implicit memory. Participant's acquisition of a repeating stimulus sequence is assessed in this task. Repeat is a modification of procedures reported by Nissen and Bullemer (1987) and by Lewick, Hill and Bizot (1988). The computer screen is divided into quadrants. A single X, appears in one of the quadrants. The participant's task is either, depending on response modality, to strike as quickly as possible the key (4, 5, 1, 2 on the numeric keypad) corresponding to the quadrant in which the X appears or to position the mouse pointer over the quadrant and click it. The X then appears according to a repeating pre-programmed sequence in a different quadrant and the participant is required to respond as quickly as possible to that X. A trial is made up of a series of the repeating sequence. Sequence order and length and the number of iterations of the sequence are predetermined by the experimenter. CATs Repeat also allows for the interleaving of a randomly positioned X between each sequenced X. Alternatively a series of random presentations can be programmed to allow for assessment of the baseline speed of responding, that is a condition under which the participant can acquire no anticipatory information to enhance speed of responding. Repeat also contains a dual-task or split attention component modeled after a task reported by Nissen and Bullemer (1987). This task is identical to the one described above except that either a low or high tone is presented with each X presentation and the participant is asked to count the number of low tones they heard during a trial. The relative frequency of low tones is experimenter definable. Finally Repeat allows for the assessment of the explicit knowledge the participant may have acquired of the sequence. This component of the task is…

pdb2linucs
type: Resource
type: NamedIndividual
has db xref: nlx_152879
IAO_0000115: Service that automatically extracts carbohydrate information from pdb-files and displays it in LINUCS or IUPAC notation. Many pdb-files contain carbohydrate structures. Since there is not such a standard nomenclature like it exists for amino acids, it is difficult to find the carbohydrate information. Sometimes entire oligosaccharides are encoded in one single residue. Information about carbohydrate linkages is often missing, and if it is present, it is not in a unique format and therefore also difficult to find.

GlyVicinity
type: Resource
type: NamedIndividual
has db xref: nlx_152880
synonym: GlyVicinity: Analysis of Amino Acids in the Vicinity of Carbohydrate Residues contained in the Protein Data Bank (PDB)
IAO_0000115: Service to generate statistics about the amino acids present in the vicinity of carbohydrate residues. Besides the amino acids in sequential neighborhood of glycosylation sites (analysed by GlySeq), those in the spatial vicinity of carbohydrate residues determine the characteristics of glycoproteins. The latter ones are of special interest for the examination of carbohydrate-binding proteins. Since carbohydrate moieties are not covalently bound in these cases, sequence analysis comparable to that for glycosylation sites is not possible there. GlyVicinity performs statistical analyses on the types of amino acids around carbohydrate chains and on the atoms forming the closest contacts between protein and carbohydrate residues. Results are based on weekly updated datasets derived from the Protein Data Bank (PDB).

GlyTorsion
type: Resource
type: NamedIndividual
has db xref: nlx_152881
synonym: GlyTorsion: Analysis of Carbohydrate Torsion Angles found in the Protein Data Bank (PDB)
IAO_0000115: Service that performs a statistical analysis of carbohydrate torsion angles derived from the Protein Data Bank. Such as protein conformation can be described by the backbone torsion angles, a carbohydrate structure is mainly characterised by its linkage torsions. With the aid of pdb2linucs, a dataset of carbohydrate torsion angles was derived from from carbohydrate structures found in the PDB. This weekly updated dataset contains, besides linkage torsions, also ring torsions, omega torsions, N-acetyle group torsions and sidechain torsions of Asn residues involved in Glycan bonds. It can be queried by GlyTorsion.

GlySeq
type: Resource
type: NamedIndividual
has db xref: nlx_152882
synonym: GlySeq - Statistical Analysis of Glycoprotein Sequences
IAO_0000115: Service dedicated to statistically analyze the sequences around glycosylation sites. Glycosylation belongs to the most common and most important co- and postranslational modifications of proteins. Since it is often difficult to determine which potential glycosylation sites are in fact glycosylated, there is only few data available about glycoproteins. Sources from which such data can be retrieved are SwissProt and the Protein Data Bank (PDB). Data from the PDB is obtained using pdb2linucs and updated weekly. GlySeq is dedicated to statistically analyze these sequences, especially the areas around glycosylation sites.

NetNGlyc
type: Resource
type: NamedIndividual
has db xref: biotools:netnglyc
has db xref: nlx_153863
synonym: NetNGlyc Server
IAO_0000115: Server that predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons. NetNGlyc 1.0 is also available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for the most common UNIX platforms.

LINUCS
type: Resource
type: NamedIndividual
has db xref: nlx_152883
synonym: LInear Notation for Unique description of Carbohydrate Sequences
synonym: LINUCS: LInear Notation for Unique description of Carbohydrate Sequences
IAO_0000115: Service that directly converts the commonly used extended representation of complex carbohydrates into the preferred canonical description or into its inverted form. Input: A structure using the extended, non-graphic nomenclature (in ASCII writing) to describe complex carbohydrates as recommended by IUPAC. Output: A linear, unique notation. The source code (written in C), will be distributed so that software developers can easily implement their algorithm within their own application. LINUCS was chosen to fulfill to following conditions: * Input of extended, non-graphic nomenclature to describe carbohydrate structures. * Resulting linear code is closely related to notations and abbreviations recommended by IUPAC. * Number of additional rules to define the priority of the branches is low * Extended nomenclature of complex carbohydrates contains all information to define the hierarchy. * LINUCS is applicable to all types of carbohydrates (macrocyclic system are currently not implemented) . * Remaining unassigned linkage information are tolerated

sumo
type: Resource
type: NamedIndividual
has db xref: nlx_152885
synonym: SUgar MOtif search
synonym: sumo: SUgar MOtif search
IAO_0000115: Service that searches carbohydrate structures for motifs commonly used for carbohydrate classification, like N- and O-glycan cores, Lewis antigens, etc. Note: Sumo is currently under construction. Motif searches are a frequently used tool in proteomics. For carbohydrate structures, there are also many motifs classified in the literature, e.g. the Lewis antigens or the diverse O-glycan core structures. Sumo is a tool to locate such motifs in a carbohydrate structure given in LINUCS or in IUPAC nomenclature., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

GlycoFragment
type: Resource
type: NamedIndividual
has db xref: nlx_152886
synonym: GlycoFragments
synonym: Sugar Fragmentation
IAO_0000115: Service that calculates and displays the main fragments (Band C-, Z- and Y-, A- and X-ions) of oligosaccharides that should occur in MS-spectra. The extended ASCII nomenclature as recommended by IUPAC is used to input the sequence of complex oligosaccharides. However, some additional input rules have to be fulfilled. In case only the topology and composition of the oligosaccharide is known, a simpler way to input carbohydrate sequences is possible. Since the hydroxyl groups of synthetic carbohydrates are often the are protected they have included a way to indicate if sugar residue are persubstituted. Please have a look at the examples of valid input structures.

Glyco-CD
type: Resource
type: NamedIndividual
has db xref: nlx_152887
synonym: Glyco-CD databank
synonym: Glyco-CD database
synonym: GlycoCD database
abbrev: GlycoCD
IAO_0000115: Manually curated, comprehensive repository of clusters of differentiation (CDs) which are a) defined as distinct oligosaccharide sequences as part of either glycoproteins and/or glycosphingolipids and b) defined as proteins which have carbohydrate recognition sites (CRDs) or as carbohydrate binding lectins. The data base is generated by exhaustive search of literature and other online data banks related to carbohydrates and proteins. This data bank is the beginning of an effort to provide concise, relevant information of carbohydrate-related CDs in a user- friendly manner. For users convenience the data bank under menu browse of GlycoCD is arranged in two section namely carbohydrate recognition CDs (CRD CD) and glycan CD. The carbohydrate recognition CD part is the collection of proteins which recognize glycan structures by means of the CRDs. Glycan CD is the part in which CDs are summarized which characterize specific oligosaccharide structures. The GlycoCD databank has been developed with the aim to assist the immunologist, cell biologist as well as the clinician who wants to keep up with the present knowledge in this field of glycobiology.

Enrichr
type: Resource
type: NamedIndividual
has db xref: biotools:enrichr
has db xref: SciRes_000171
IAO_0000115: A web-based gene list enrichment analysis tool that provides various types of visualization summaries of collective functions of gene lists. It includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library, Data Driven Documents (D3). The software can also be embedded into any tool that performs gene list analysis. System-wide profiling of genes and proteins in mammalian cells produce lists of differentially expressed genes / proteins that need to be further analyzed for their collective functions in order to extract new knowledge. Once unbiased lists of genes or proteins are generated from such experiments, these lists are used as input for computing enrichment with existing lists created from prior knowledge organized into gene-set libraries.

Benaroya Research Institute: Neurological Diseases
type: Resource
type: NamedIndividual
has db xref: nif-0000-10379
synonym: Benaroya Research Institute Neurological Diseases Research
abbrev: BRI Neurological Diseases Research
IAO_0000115: BRI investigators study the molecular and genetic mechanisms which underlie some of the most devastating chronic neurological disorders, and conduct clinical trials for new innovative therapies. Neurological studies that are currently studied include Amyotrophic lateral sclerosis (ALS) or Lou Gehrig's Disease, Multiple Sclerosis, and Parkinson's Disease.

Neural Cipher
type: Resource
type: NamedIndividual
has db xref: nlx_153815
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. C#.NET 4.0 application that interfaces with the Neural Maestro class library to perform Classical and Bayesian logistic polynomial regression analysis for multiple trial and experimental neuroscience / electrophysiological datasets. The idea is to build a neural feature extractor to plug into a neural recognition network based on recordings from patch clamps and/or brain computer interfaces. Frequency based feature sets are collected from the simulation of neuronal cell assemblies and examined for inclusion in combinatorial regressions using the Neural Maestro API. Regressions are evaluated based on different metrics. The application interfaces with a R and MATLAB API and produces a compendium to be published on CRAN.

CGHcall
type: Resource
type: NamedIndividual
has db xref: OMICS_00709
IAO_0000115: Software that calls aberrations for array CGH data using a six state mixture model and several biological concepts. It is written in R.

EEG time series Data Sets
type: Resource
type: NamedIndividual
has db xref: nlx_153816
abbrev: EEG time series data
IAO_0000115: Five data sets containing quasi-stationary, artifact-free EEG signals both in normal subjects and epileptic patients were put in the web by Ralph Andrzejak from the Epilepsy center in Bonn, Germany. Each data set contains 100 single channel EEG segments of 23.6 sec duration.

Rodrigo Quian Quiroga EEG ERP and single cell recordings database
type: Resource
type: NamedIndividual
has db xref: nlx_153817
synonym: Rodrigo Quian Quiroga - EEG ERP and single cell recordings database
abbrev: EEG ERP and single cell recordings
IAO_0000115: 5 EEG, ERP and single cell recordings data sets where each file corresponds to the recording on a different subject in the left occipital electrode (O1), with linked earlobes reference. Each file contains several artifact-free trials, each of them containing 512 data points (256 pre- and 256 post-stimulation) stored with a sampling frequency of 250 Hz. Trials are stored consecutively in a 1 column file. Data was pre-filtered in the range 0.1-70Hz. All trials correspond to target stimulation with an oddball paradigm. STAR R based Data Sets Used * Dataset # 1: Human single-cell recording * Dataset # 2: Simulated extracellular recordings * Dataset # 3: EEG signals from rats * Dataset # 4: Pattern visual evoked potentials. * Dataset # 5: Tonic-clonic (Grand Mal) seizures.

EEG Database
type: Resource
type: NamedIndividual
has db xref: nlx_153818
synonym: EEG Database Data Set
IAO_0000115: Data set from a large study to examine EEG correlates of genetic predisposition to alcoholism. It contains measurements from 64 electrodes placed on the scalp sampled at 256 Hz (3.9-msec epoch) for 1 second. There were two groups of subjects: alcoholic and control. Each subject was exposed to either a single stimulus (S1) or to two stimuli (S1 and S2) which were pictures of objects chosen from the 1980 Snodgrass and Vanderwart picture set. When two stimuli were shown, they were presented in either a matched condition where S1 was identical to S2 or in a non-matched condition where S1 differed from S2. There were 122 subjects and each subject completed 120 trials where different stimuli were shown. The electrode positions were located at standard sites (Standard Electrode Position Nomenclature, American Electroencephalographic Association 1990). Zhang et al. (1995) describes in detail the data collection process. There are three versions of the EEG data set. * The Small Data Set (smni97_eeg_data.tar.gz) contains data for the 2 subjects, alcoholic a_co2a0000364 and control c_co2c0000337. For each of the 3 matching paradigms, c_1 (one presentation only), c_m (match to previous presentation) and c_n (no-match to previous presentation), 10 runs are shown. * The Large Data Set (SMNI_CMI_TRAIN.tar.gz and SMNI_CMI_TEST.tar.gz) contains data for 10 alcoholic and 10 control subjects, with 10 runs per subject per paradigm. The test data used the same 10 alcoholic and 10 control subjects as with the training data, but with 10 out-of-sample runs per subject per paradigm. * The Full Data Set contains all 120 trials for 122 subjects. The entire set of data is about 700 MBytes.

Bern-Barcelona EEG database
type: Resource
type: NamedIndividual
has db xref: nlx_153819
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented November 23, 2020; EEG data set, source code, and results from 7500 signal pairs from 5 epilepsy patients analyzed in the manuscript, Andrzejak RG, Schindler K, Rummel C. Nonrandomness, nonlinear dependence, and nonstationarity of electroencephalographic recordings from epilepsy patients. Phys. Rev. E, 86, 046206, 2012. All Matlab source codes are included in the file ASR_Sources_2012_10_16.zip. The clinical purpose of these recordings was to delineate the brain areas to be surgically removed in each individual patient in order to achieve seizure control.

rMAT
type: Resource
type: NamedIndividual
has db xref: OMICS_00810
IAO_0000115: Software package for normalizing and analyzing tiling arrays and ChIP-chip data. It is the R-version of a MAT program.

An efficient P300-based brain-computer interface for disabled subjects
type: Resource
type: NamedIndividual
has db xref: nlx_153820
IAO_0000115: A portal containing EEG datasets (in MATLAB format) and the MATLAB software that were used to produce the results in the paper named in the title of this resource. The files published can also be used as a basis for individual research on P300-based brain-computer interfaces. The system is based on the P300 evoked potential and is tested with five severely disabled and four able-bodied subjects. For four of the disabled subjects classification accuracies of 100% are obtained. The bitrates obtained for the disabled subjects range between 10 and 25 bits/min. The effect of different electrode configurations and machine learning algorithms on classification accuracy is tested.

Project BCI - EEG motor activity data set
type: Resource
type: NamedIndividual
has db xref: nlx_153822
IAO_0000115: EEG motor activity data sets used for Brain Computer Interface research project in Matlab MAT format. * Dataset 1 - 1D motion: This subject is a 21 year old, right handed male with no known medical conditions. The EEG consists of actual random movements of left and right hand recorded with eyes closed. Each row represents one electrode. The order of the electrodes is FP1 FP2 F3 F4 C3 C4 P3 P4 O1 O2 F7 F8 T3 T4 T5 T6 FZ CZ PZ. The recording was done at 500Hz using Neurofax EEG System which uses a daisy chain montage. The data was exported with a common reference using Eemagine EEG. AC Lines in this country work at 50 Hz. This info is also included in the MAT file. * Dataset 2 - 2D motion: This subject is a 21 year old, right handed male with no known medical conditions. The EEG consists of actual random movements of left and right hand recorded with eyes closed. Each row represents one electrode. The order of the electrodes is FP1 FP2 F3 F4 C3 C4 P3 P4 O1 O2 F7 F8 T3 T4 T5 T6 FZ CZ PZ. The recording was done at 500Hz using Neurofax EEG System which uses a daisy chain montage. The data was exported with a common reference using Eemagine EEG. AC Lines in this country work at 50 Hz. This data consists of the following movements # Three trials left hand forward movement # Three trials left hand backward movement # Three trials left hand forward movement # Three trials left hand forward movement # 1 trial imagined left hand forward movement # 1 trial imagined left hand backward movement # 1 trial imagined right hand forward movement # 1 trial imagined right hand backward movement # 1 trial left leg movement # 1 trial right leg movement

DEAPdataset
type: Resource
type: NamedIndividual
has db xref: nlx_153824
synonym: DEAP: A Dataset for Emotion Analysis using EEG Physiological and Video Signals
synonym: DEAPDataset: A Dataset for Emotion Analysis using EEG Physiological and Video Signals
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 12,2025. Multimodal dataset for emotion analysis using EEG, Physiological and Video Signals of human affective states. The electroencephalogram (EEG) and peripheral physiological signals of 32 participants were recorded as each watched 40 one-minute long excerpts of music videos. Participants rated each video in terms of the levels of arousal, valence, like/dislike, dominance and familiarity. For 22 of the 32 participants, frontal face video was also recorded. A novel method for stimuli selection was used, utilizing retrieval by affective tags from the last.fm website, video highlight detection and an online assessment tool. The dataset is made publicly available and other researchers are encouraged to use it for testing their own affective state estimation methods.

iBIOFind
type: Resource
type: NamedIndividual
has db xref: nlx_153829
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. C#.NET 4.0 WPF / OWL / REST / JSON / SPARQL multi-threaded, parallel desktop application enables the construction of biomedical knowledge through PubMed, ScienceDirect, EndNote and NIH Grant repositories for tracking the work of medical researchers for ranking and recommendations. Users can crawl web sites, build latent semantic indices to generate literature searches for both Clinical Translation Science Award and non-CTSA institutions, examine publications, build Bayesian networks for neural correlates, gene to gene interactions, protein to protein interactions and as well drug treatment hypotheses. Furthermore, one can easily access potential researcher information, monitor and evolve their networks and search for possible collaborators and software tools for creating biomedical informatics products. The application is designed to work with the ModelMaker, R, Neural Maestro, Lucene, EndNote and MindGenius applications to improve the quality and quantity of medical research. iBIOFind interfaces with both eNeoTutor and ModelMaker 2013 Web Services Implementation in .NET for eNeoTutor to aid instructors to build neuroscience courses as well as rare diseases. Added: Rare Disease Explorer: The Visualization of Rare Disease, Gene and Protein Networks application module. Cinematics for the Image Finder from Yale. The ability to automatically generate and update websites for rare diseases. Cytoscape integration for the construction and visualization of pathways for Molecular targets of Model Organisms. Productivity metrics for medical researchers in rare diseases. iBIOFind 2013 database now includes over 150 medical schools in the US along with Clinical Translational Science Award Institutions for the generation of biomedical knowledge, biomedical informatics and Researcher Profiles.

The Cromwell Workshop
type: Resource
type: NamedIndividual
has db xref: nlx_153830
synonym: Cromwell Workshop
abbrev: TCW
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. Statistical and biomedical informatics software studio that develops neuroscience applications and brain computer interface games. They are dedicated to the integration of medical research, neuroscience, time series analysis, computer programming, statistics, sensor technologies, graphics design, artificial intelligence and entertainment to build gaming systems for neuroscientific research and intelligent tutoring in the classroom and lab. The current focus of The Cromwell Workshop/Neuronal Architects is on theoretical neuroscience and experimental modeling of psychological and neural processes that involve attention, emotion, motivation and executive functions that are impaired by neurological diseases. The outcome of this work is to use these results in the design of multiple genre brain computer interface gaming systems that can be used in both clinical and at home settings. If you would like to explore any collaborative opportunities to use their software or enhance your existing statistical products with their .NET, Java, R and Matlab code bases, let them know.

TileMap
type: Resource
type: NamedIndividual
has db xref: OMICS_00812
synonym: TileMap Version 2
synonym: tilemapv2
IAO_0000115: Software tool for microarray tile mapping. It utilizes ChIP-chip peak calling to identify genomic loci that show transcriptional activities and transcription factor binding patterns of interest.

eNeoTutor
type: Resource
type: NamedIndividual
has db xref: nlx_153831
synonym: e-NeoTutor
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. ASP.NET AJAX .NET 4, Telerik controls enabled application designed to be used with the books presented, papers and web content to help with the acceleration of learning and software development for the neurosciences. All content developed at The Cromwell Workshop is intended to accelerate the implementation of biomedical knowledge, help with EEG clinical certifications and provide the opportunity for students, software developers, neuroscientists, neurologists and neurosurgeons to collaborate globally with knowledge content. e-NeoTutor relies on a subscription model to build software components in multiple languages and access book material. Tutor designed to complement free online course content in neuroscience, work with the Society of Neuroscience, The Human Connectome Project and assist researchers with CNIM certification, biomedical informatics, neuroinformatics and neuroscience training programs.

Clustal Omega
type: Resource
type: NamedIndividual
has db xref: biotools:clustalo
has db xref: nlx_153836
has db xref: OMICS_00972
has db xref: SCR_016062
abbrev: Clustalo
IAO_0000115: Software package as multiple sequence alignment tool that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. Accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/Clustal, GCG/MSF, RSF.

Waxholm Space
type: Resource
type: NamedIndividual
has db xref: nlx_153838
has db xref: nlx_155839
has db xref: SCR_009594
synonym: Mouse WHS atlas
synonym: Waxholm Space Atlas
synonym: Waxholm Standard Space
abbrev: WHS
abbrev: WSA
abbrev: WSS
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 1st, 2023. Coordinate based reference space for the mapping and registration of neuroanatomical data. Users can download image volumes representing the canonical Waxholm Space (WHS) adult C57BL/6J mouse brain, which include T1-, T2*-, and T2-Weighted MR volumes (generated at the Duke Center for In-Vivo Microscopy), Nissl-stained optical histology (acquired at Drexel University), and a volume of labels. All volumes are represented at 21.5μ isotropic resolution. Datasets are provided as gzipped NIFTI files.

BigBrain
type: Resource
type: NamedIndividual
has db xref: nlx_153840
has db xref: r3d100013950
synonym: BigBrain Database
synonym: BigBrain LORIS Database
synonym: BigBrain Project
synonym: BigBrain: An ultrahigh-resolution 3D human brain model
IAO_0000115: Ultrahigh resolution 3D human brain model at nearly cellular resolution of 20 micrometers, based on reconstruction of histological sections. Provides considerable neuroanatomical insight into human brain, thereby allowing extraction of microscopic data for modeling and simulation. Enables testing of hypotheses on optimal path lengths between interconnected cortical regions or on spatial organization of genetic patterning, redefining traditional neuroanatomy maps such as those of Brodmann and von Economo.

Human Brain Connectivity Database
type: Resource
type: NamedIndividual
has db xref: nlx_153841
IAO_0000115: Preliminary database of neuroanatomical connectivity reports specifically for the human brain, which have been manually curated. It includes details (based on manual literature curation) of tract tracing or related connectivity studies conducted in human brain tissue. This database and user interface will be expanded and improved in the near future.

HyperBrain
type: Resource
type: NamedIndividual
has db xref: nlx_153852
synonym: HyperBrain: A Resource for Learning NeuroAnatomy
synonym: HyperBrain: An Online Neuroanatomy Tutorial
IAO_0000115: An online tutorial for human neuroanatomy designed as a supplement to textbook and class learning or as a lab substitute when human specimens, slides and models are not available. HyperBrain includes thousand of images and hundreds of linked illustrated glossary terms, as well as movies, quizzes and interactive animations. Last updated 2012.

PD-DOC
type: Resource
type: NamedIndividual
has db xref: nif-0000-10109
synonym: Parkinson's Disease Data and Organizing Center
synonym: The Parkinson's Disease Data and Organizing Center
synonym: The Parkinson's Disease Data and Organizing Center (PD-DOC)
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on December 02, 2011. Notice: This domain name expired on 10/29/11 and is pending renewal or deletion PD-DOC is a portal and a database resource, hosting a database and linking to other databases and data sets of clinical and translational data. PD-DOC functions to organize and facilitate clinical and translational research in Parkinson's disease. The PD-DOC Database contains standardized data collected by user institutions on large numbers of patients with Parkinsons disease and other parkinsonian disorders. In some cases, data is obtained at a single point in time, while in others data is collected repeatedly over time. The PD-DOC Database is composed of the Core Data Set (CDS) which consists of those variables required to be gathered for each subject whose data is entered into the PD-DOC database. In 2005, working groups of Udall Center and invited experts deliberated to establish the components of each CDS section (e.g. General Clinical, Cognitive/Behavioral, Postmortem Brain Neuropathological Findings). The PD-DOC CDS was established and designed to optimize data analyses and data mining for large numbers of subjects participating in a variety of research studies. In most cases corresponding DNA samples are available form the NINDS Human Genetic Repository (at Coriell). Much of the website is publicly available for viewing. To request access to sections of the website dealing with downloading or requesting data, requesting a consultation, or submitting data or other information you will need to register. Before registering, you should read the PD-DOC Policies. Note that PD-DOC data can be used for research purposes only. Once your registration is successfully completed you will be automatically logged into the website.

Neurologychannel
type: Resource
type: NamedIndividual
has db xref: nif-0000-10380
synonym: neurologychannel
IAO_0000115: A topical portal which provides information about conditions that affect the nervous system (brain, spinal cord, nerves, and muscles), such as stroke (brain attack), Alzheimer's disease, and back pain. It is a physician developed and monitored source of neurology information for consumers. Additionally, it contains comprehensive condition and treatment information, as well as interactive tools.

BLASTN
type: Resource
type: NamedIndividual
has db xref: nlx_153932
has db xref: OMICS_00990
synonym: NCBI BLASTN
synonym: Nucleotide Blast
synonym: Standard Nucleotide BLAST
abbrev: BLASTn
IAO_0000115: Web application to search nucleotide databases using a nucleotide query. Algorithms: blastn, megablast, discontiguous megablast.

big-PI Predictor
type: Resource
type: NamedIndividual
has db xref: nlx_153855
synonym: big-PI Predictor: GPI Modification Site Prediction
IAO_0000115: Prediction tool locating potential GPI-modification sites in precursor sequences applied for large-scale protein sequence database searches. The composite prediction function (with separate parametrization for metazoan and protozoan proteins) consists of terms evaluating both amino acid type preferences at sequence positions near a supposed omega-site as well as the concordance with general physical properties encoded in multi-residue correlation within the motif sequence. The latter terms are especially successful in rejecting non-appropriate sequences from consideration. The algorithm has been validated with a self-consistency and two jack-knife tests for the learning set of fully annotated sequences from the SWISS-PROT database as well as with a newly created database big-Pi (more than 300 GPI-motif mutations extracted from original literature sources). The accuracy of predicting the effect of mutations in the GPI sequence motif was above 83 %.

DictyOGlyc
type: Resource
type: NamedIndividual
has db xref: biotools:dictyoglyc
has db xref: nlx_153856
IAO_0000115: Server that produces neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins.

CELDA Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_153858
synonym: Cell: Expression Localization Development Anatomy
synonym: CellFinder Ontology
abbrev: CELDA
IAO_0000115: Structured vocabulary to organize cell-associated data and to place these data in clearly defined semantic relations to other biological facts. It describes cell types, their properties and origin and links this information to other existing ontologies like the Cell Ontology (CL), Foundational Model of Anatomy (FMA), Gene Ontology (GO), Mouse Anatomy and others using the top-level ontology BioTop.

GlycoMod
type: Resource
type: NamedIndividual
has db xref: nlx_153859
synonym: GlycoMod Tool
IAO_0000115: A tool that can predict the possible oligosaccharide structures that occur on proteins from their experimentally determined masses. This is done by comparing the mass of the glycan to a list of pre-computed masses of glycan compositions. The program can be used with free or derivatised glycans and for glycopeptides where the peptide mass or protein is known. Compositional constraints can be applied to the output. Note: You can use GlycanMass to calculate the mass of an oligosaccharide structure from its oligosaccharide composition.

Visible Mouse Anatomy
type: Resource
type: NamedIndividual
has db xref: nlx_153861
synonym: Mouse Anatomy - The Visible Mouse
synonym: The Visible Mouse - Anatomy
IAO_0000115: Access to Quicktime movies of histologic mouse anatomy including heart / lung, kidney, mammary gland, lymph node, prostate, spleen, liver, salivary glands, and 3-D wire model based on MRI sections; a Quicktime mouse radiographic atlas of skeletal anatomy containing a series of radiographic images with color overlays and labels; and a table containing a comparison between mouse and human anatomy. Special topics include the virtual necroscopy. Anatomic systems cover the central nervous system, male genital-urinary tract, female genital-urinary tract, mammary, kidney, skeletal, cardiovascular, gastrointestinal, and respiratory systems. The pathology and imaging section includes anatomy, histology, comparative imaging, physiology, pathology, comparative mammary, comparative prostate, GEM, and an image archive. These pages were put together as a pilot demonstration by Dr. Robert Cardiff, UCD Center for Comparative Medicine with the collaboration of Dr. Michael Paulus, Oak Ridge National Laboratories,MicroCat Group, Dr. Allan Johnson, Duke University Center for In Vivo Microscopy, and Drs. Steve Griffey, Gary Henderson and Tom Jue, University of California, Davis. This is a work in progress and for demonstration purposes.

SeqScape Software
type: Commercial Organization
type: NamedIndividual
has db xref: OMICS_01819
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 28, 2017. A resequencing package designed for mutation detection and analysis, SNP discovery and validation, pathogen sub-typing, allele identification and sequence confirmation.

YinOYang
type: Resource
type: NamedIndividual
has db xref: biotools:yinoyang
has db xref: nlx_153865
IAO_0000115: Server that produces neural network predictions for O-beta-GlcNAc attachment sites in eukaryotic protein sequences. This server can also use NetPhos, to mark possible phosphorylated sites and hence identify Yin-Yang sites. YinOYang 1.2 is available as a stand-alone software package, with the same functionality. Ready-to-ship packages exist for the most common UNIX platforms.

NIDDK Information Network (dkNET)
type: Resource
type: NamedIndividual
has db xref: nlx_153866
has db xref: r3d100012845
synonym: DKnet
synonym: National Institute of Diabetes and Digestive and Kidney Disease Information Network
synonym: NIDDK Information Network
synonym: NIDDKInformation Network
abbrev: dkNET
IAO_0000115: The NIDDK Information Network (dkNET) is a community-based network to serve needs of basic and clinical investigators that includes large pools of data and research resources relevant to mission of National Institute of Diabetes and Digestive and Kidney Disease.

Drosophila anatomy and development ontologies
type: Resource
type: NamedIndividual
has db xref: nlx_153871
synonym: Drosophila anatomy & dev ontologies
abbrev: FBbt
IAO_0000115: A structured controlled vocabulary of the anatomy of Drosophila melanogaster. These ontologies are query-able reference sources for information on Drosophila anatomy and developmental stages. They also provide controlled vocabularies for use in annotation and classification of data related to Drosophila anatomy, such as gene expression, phenotype and images. They were originally developed by FlyBase, who continue to maintain them and have used them for over 200,000 annotations of phenotypes and expression. Extensive use of synonyms means that, given a suitably sophisticated autocomplete, users can find relevant content by searching with almost any anatomical term they find in the literature. These ontologies are developed in the web ontology language OWL2. Their extensive formalization in OWL can be used to drive sophisticated query systems.

Flannotator
type: Resource
type: NamedIndividual
has db xref: nlx_153872
IAO_0000115: Allows annotation of gene expression at all stages of development and tissue types (including sub cellular location) using standard Drosophila anatomy ontology. All methods of input use a controlled vocabulary to ensure data integrity.

Lifespan Observations Database
type: Resource
type: NamedIndividual
has db xref: nlx_153873
synonym: Sageweb Lifespan Observation Database
IAO_0000115: Database that collects published lifespan data across multiple species. The entire database is available for download in various formats including XML, YAML and CSV.

Teleost Anatomy Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_153876
abbrev: TAO
IAO_0000115: A multi-species anatomy ontology for teleost fishes. It was originally seeded from ZFA, but covers terms relevant to other taxa. The TAO uses terms from the Common Anatomy Reference Ontology (CARO) as a template for its upper level nodes, and the Vertebrate Skeletal Anatomy Ontology (VSAO) for general skeletal anatomy classes. Growth of the TAO is enabled by contributions from data curators and the ichthyological community. The TAO can be browsed by using the NCBO BioPortal and data annotated using TAO terms can be queried using the Phenoscape Knowedgebase.

Teleost Taxonomy Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_153877
abbrev: TTO
IAO_0000115: An ontology of taxonomic terms (names of taxonomic groups) used in the systematics of fish, including non-teleost groups such as Chondrichthys (sharks and rays), Sarcopterygii (lungfish and coelacanths), lampreys, and hagfish. It contains (as of August 2010) over 38,500 names, and over 44,000 taxonomic synonyms. A majority of the taxonomic names and synonyms were made available from the Catalog of Fishes. In July 2010 they added nearly 15,000 common names provided by Fishbase. Additional names and synonyms are added as a result of their curation activities. The ontology is being used to facilitate annotation of phenotypes, particularly for taxa that are not covered by NCBI because no submissions of molecular data have been made. Taxonomy ontologies can also be valuable in annotating legacy data, where authors make phenotype or ecological assertions (e.g., host-parasite associations) that refer to groups that are reorganized or no longer recognized. The taxonomy ontology serves as the source of taxa for their project's use for identifying evolutionary changes that match the phenotype of a zebrafish mutant.

AmphibiaWeb
type: Resource
type: NamedIndividual
has db xref: nlx_153878
has db xref: r3d100012518
IAO_0000115: Database of information on amphibian declines, natural history, conservation, and taxonomic information for every recognized species of amphibian in the world. Species accounts are being added regularly by specialists and volunteers and they contain species descriptions, life history information, conservation status, literature references, photos and range maps for many species. Some species have complete accounts; others as yet have only photographs or distributions. But all species can be queried for taxonomic, distributional and exact specimen data. AmphibiaWeb offers a powerful mapping tool by combining museum specimen data (via HerpNET) with expert opinion range maps (from Global Amphibian Assessment/IUCN) and overlaying these onto larger maps, allowing visualization in political, satellite, hybrid, or terrain map format. AmphibiaWeb currently (Aug 13, 2013) contains 7,160 species. They have 2,966 species accounts for 2,363 species, 6,517 literature references, 558 sound files, 109 video files, and 28,218 photos of 3,887 different amphibian species. These data come from numerous individuals--see acknowledgements. They have the ambitious goal of establishing a home page for every species of amphibian in the world. In order to accomplish this goal they encourage volunteers and specialists to help prepare species accounts. If you have special interest in a particular species, please contact them.

PhenoGen Informatics
type: Resource
type: NamedIndividual
has db xref: nlx_153879
has db xref: r3d100011596
has db xref: rid_000093
synonym: PhenoGen Informatics - The site for quantitative genetics of the transcriptome.
abbrev: PhenoGen
IAO_0000115: Website for analyzing microarray data. Software toolbox for storing, analyzing and integrating microarray data and related genotype and phenotype data. The site is particularly suited for combining QTL and microarray data to search for candidate genes contributing to complex traits. In addition, the site allows, if desired by the investigators, sharing of the data. Investigators can conduct in-silico microarray experiments using their own and/or shared data. There are five major sections of the site: Genome/Transcriptome Data Browser, Microarray Analysis Tools, Gene List Analysis Tools, QTL Tools, and Downloads. The genome/transcriptome data browser combines a genome browser with all the microarray, RNA-Seq, and Genomic Sequencing data. This provides an effective platform to view all of this data side by side. Source code is available on GitHub.

North American Conditional Mouse Mutagenesis Project
type: Resource
type: NamedIndividual
has db xref: nlx_153880
abbrev: NorCOMM
IAO_0000115: Large-scale research initiative focused on developing and distributing a library of mouse embryonic stem (ES) cell lines carrying single gene trapped or targeted mutations across the mouse genome. NorCOMM's large and growing archive of ES cells is publicly available on a cost-recovery basis from the Canadian Mouse Mutant Repository. As an international public resource, access to clones is unrestricted and nonexclusive. Through NorCOMM's affiliation with the Canadian Mouse Consortium (CMC), NorCOMM also provides clients with a single point of access to regional mouse derivation, phenotyping, genetic and archiving services across Canada. These value-added services can help your company harness NorCOMM's resources for drug discovery, target discovery and preclinical validation.

Texas A and M Institute for Genomic Medicine
type: Resource
type: NamedIndividual
has db xref: nlx_153881
synonym: Texas A&M Institute for Genomic Medicine
abbrev: TIGM
IAO_0000115: Resource for any researcher looking to obtain knockout mice and embryonic stem (ES) cells quickly and with favorable intellectual property (IP) terms. Our resources include the world’s largest gene trap library of ES cells in the C57BL/6N mouse strain and a constantly expanding repository of cryopreserved germplasm of knockout lines. TIGM provides both ES cell clones and mice as well as other transgenic core services including CRISPR/Cas9-based genome modifications within the Texas A&M system and to the public and private international research community.

Open Education Database
type: Resource
type: NamedIndividual
has db xref: nlx_153882
abbrev: OEDb
IAO_0000115: A collection of free open courses. Subjects include Arts, Business, Education, Engineering & Computer Science, Health & Medical, Liberal Arts, Math and Science.

BACContigEditor
type: Resource
type: NamedIndividual
has db xref: OMICS_00875
IAO_0000115: A simple sequence alignment editing tool, written in Java.

GTEx eQTL Browser
type: Resource
type: NamedIndividual
has db xref: nlx_153884
synonym: Genotype-Tissue Expression eQTL Browser
synonym: GTEx (Genotype-Tissue Expression) eQTL Browser
synonym: NCBI GTEx eQTL Browser
synonym: NCBI GTeX eQTL Browser
IAO_0000115: Database and browser that provides a central resource to archive and display association between genetic variation and high-throughput molecular-level phenotypes. This effort originated with the NIH GTEx roadmap project: however the scope of this resource will be extended to include any available genotype/molecular phenotype datasets.

Expression Patterns for C. elegans promoter GFP fusions
type: Resource
type: NamedIndividual
has db xref: nif-0000-25220
has db xref: nlx_153885
synonym: Caenorhabditis elegans Expression Patterns
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Database of expression patterns of C. elegans promoter::GFP constructs. A text description of the observed pattern is provided, indicating the stage(s) and tissue(s) in which GFP is expressed. Also available for some strains are the corresponding 2D and 3D images. Investigators may browse the entire list, search by gene name, tissue, stage, and pattern. Search results may be downloaded in .csv and .txt formats. All of the strains in the expression pattern database are displayed in the browse page. The records are organized by gene; information such as locus name, genomic location (WormBase), the presence of images and videos, and the actual expression pattern are shown in a tabular format.

ADInstruments - Data Acquisition Systems for Life Science
type: Organization
type: NamedIndividual
has db xref: nif-0000-10146
synonym: AD Instruments
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 19, 2018; A provider of computer-based data acquisition and analysis systems for life science. Products enable users to record and analyze life science data quickly and efficiently. ADInstruments product range is based on the PowerLab data acquisition system with LabChart software. The PowerLab system (also MacLab) is used in universities, hospitals, research institutes, pharmaceutical companies, contract research organizations and other private industry research sectors.

Human Gene Mutation Database
type: Resource
type: NamedIndividual
has db xref: biotools:hgmd
has db xref: nif-0000-10459
has db xref: nlx_153887
has db xref: OMICS_00281
has db xref: SCR_001888
synonym: The Human Gene Mutation Database
synonym: The Human Gene Mutation Database at the Institute of Medical Genetics in Cardiff
abbrev: HGMD
IAO_0000115: Curated database of known (published) gene lesions responsible for human inherited disease.

MATLAB
type: Resource
type: NamedIndividual
has db xref: nlx_153890
synonym: matlab
synonym: MATLAB -The Language of Technical Computing
synonym: matrix laboratory
IAO_0000115: Multi paradigm numerical computing environment and fourth generation programming language developed by MathWorks. Allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, Java, Fortran and Python. Used to explore and visualize ideas and collaborate across disciplines including signal and image processing, communications, control systems, and computational finance.

Ancora
type: Resource
type: NamedIndividual
has db xref: nlx_153891
synonym: Atlas of Noncoding Conserved Regions in Animals
IAO_0000115: Web resource that provides data and tools for exploring genomic organization of highly conserved noncoding elements (HCNEs) for multiple genomes. It includes a genome browser that shows HCNE locations and features novel HCNE density plots as a powerful tool to discover developmental regulatory genes and distinguish their regulatory elements and domains. They identify HCNEs as non-exonic regions of high similarity between genome sequences from distantly related organisms, such as human and fish, and provide tools for studying the distribution of HCNEs along chromosomes. Major peaks of HCNE density along chromosomes most often coincide with developmental regulatory genes. Their aim with this site is to aid discovery of developmental regulatory genes, their regulatory domains and their fundamental regulatory elements.

AnimalTFDB
type: Resource
type: NamedIndividual
has db xref: biotools:animal_tfdb
has db xref: nlx_153892
has db xref: OMICS_01856
synonym: Animal Transcription Factor Database
IAO_0000115: A comprehensive transcription factor (TF) database in which they identified and classified all the genome-wide TFs in 50 sequenced animal genomes (Ensembl release version 60). In addition to TFs, it also collects transcription co-factors and chromatin remodeling factors of those genomes, which play regulatory roles in transcription. Here they defined the TFs as proteins containing a sequence-specific DNA-binding domain (DBD) and regulating target gene expression. Currently, the AnimalTFDB classifies all the animal TFs into 72 families according to their conserved DBDs. Gene lists of transcription factors, transcription co-factors and chromatin remodeling factors of each species are available for downloading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

asSeq
type: Resource
type: NamedIndividual
has db xref: biotools:asseq
has db xref: nlx_153893
has db xref: OMICS_01948
IAO_0000115: Software that establishes a statistical framework for future developments of eQTL (expression quantitative trait locus) mapping methods using RNA-seq data (e.g., linkage-based eQTL mapping), and the joint study of multiple genetic markers and/or multiple genes. This R package has been submitted to R/bioconductor. It will be available on bioconductor soon. It is recommended to install this R package from bioconductor. You can also install this R package from the source code by yourself. Since the R package contains C code, a C complier is required for installation. With both R and appropriate c complier installed, this R package can be installed using the following command (in Mac Terminal window or Windows command window) R CMD INSTALL asSeq

Shiny
type: Resource
type: NamedIndividual
has db xref: nlx_153894
IAO_0000115: Open source R package that provides web framework for building web applications using R. Used to create interactive web apps in native R, without needing to use HTML, CSS, or JavaScript.

vIST/e
type: Resource
type: NamedIndividual
has db xref: nlx_153923
synonym: DTITool
IAO_0000115: Open source, platform-independent application for the visualization and analysis of complex, high-dimensional imaging data such as Diffusion Tensor Imaging (DTI) and High Angular Resolution Diffusion Imaging (HARDI). It has a plugin-based architecture which allows third parties to develop new plugins to extend the tool. Overview of the many features: * vIST/e is programmed in C++. It uses the Visualization Toolkit for visualization and pipelined data processing, as well as the cross-platform toolkit Qt Framework for an easy-to-use Graphical User Interface. * vIST/e introduces a powerful new plugin system, which allows for modular development with increased extensibility and stability. * Powerful GPU-based visualization techniques allow for smooth, real-time visualization of large data sets. Using custom ray tracing algorithms created with OpenGL, vIST/e can render DTI ellipsoids and HARDI spherical harmonics glyphs up to 4th order. The high frame rates offered by modern GPU technology allows for interactive exploration of this complex data. * Diffusion Tensor Imaging data can be visualized and interactively explored in a number of ways, including multiple cross-sections, volume rendering, and tensor glyphs. Derived scalar volumes, including various different anisotropy measures, can be computed and visualized. Data from other modalities, such as structural MRI, can be shown alongside the DTI data. * Various fiber tracking methods allow for fast and accurate reconstruction of fiber pathways. Interactively defined Regions of Interest (ROIs) can be used for seeding and filtering of fibers. Fibers are visualized either as lines, optionally using a powerful, GPU-based lighting engine, or as 3D structures such as tubes. * Scalar volumes, glyphs, and fibers can be colored using a wide array of coloring option. Customizable color loop-up tables allow for highly flexible visualization of scalar data. * Visualization and processing of various different HARDI formats is suppor…

Sherlock
type: Resource
type: NamedIndividual
has db xref: nlx_153895
IAO_0000115: Service to discover disease genes in GWAS using eQTL signature matching by simply submitting your list of GWAS associations (SNPs and p-values). It is important to upload all SNPs in your association study, not just the top hits. Sherlock may be able to group multiple lower-confidence SNPs to discover functionally-important genes.

MirSNP
type: Resource
type: NamedIndividual
has db xref: nlx_153896
IAO_0000115: Database of human SNPs in predicted miRNA-mRNA binding sites, based on information from dbSNP135 and mirBASE18. MirSNP is highly sensitive and covers most experiments confirmed SNPs that affect miRNA function. MirSNP may be combined with researchers' own GWAS or eQTL positive data sets to identify the putative miRNA-related SNPs from traits/diseases associated variants. They aim to update the MirSNP database as new versions of mirBASE and dbSNP database become available.

Ensembl Variation
type: Resource
type: NamedIndividual
has db xref: nlx_153897
synonym: ensembl variation
IAO_0000115: Public database that stores areas of genome that differ between individual genomes (variants) and, where available, associated disease and phenotype information. Different types of variants for several species: single nucleotide polymorphisms (SNPs), short nucleotide insertions and/or deletions, and longer variants classified as structural variants (including CNVs). Effects of variants on the Ensembl transcripts and regulatory features for each species are predicted. You can run same analysis on your own data using Variant Effect Predictor. These data are integrated with other data sources in Ensembl, and can be accessed using the API or website. For several different species in Ensembl, they import variation data (SNPs, CNVs, allele frequencies, genotypes, etc) from a variety of sources (e.g. dbSNP). Imported variants and alleles are subjected to quality control process to flag suspect data. In human, they calculate linkage disequilibrium for each variant, by population.

NIF Web Services
type: Resource
type: NamedIndividual
has db xref: nlx_153899
synonym: Neuroscience Information Framework Web Services
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Representational State Transfer (REST) model based service for accessing a set of Neuroscience Information Framework (NIF) data through a fixed set of operations. They are defined by a WADL file which allows clients to automatically generate code for these services. The services (AnnotateService, FederationService, LdaService, LexicalService, LiteratureService, QueryService, SummaryService, VocabularyService) include the ability to: * Retrieve a federation summary, e.g., http://nif-services.neuinfo.org/servicesv1/v1/summary?q=* * Retrieve data records from a NIF federation source for a search, e.g., http://nif-services.neuinfo.org/servicesv1/v1/federation/data/nif-0000-00007-1?q=purkinje * Retrieve registry data records from NIF, e.g., http://nif-services.neuinfo.org/servicesv1/v1/federation/data/nlx_144509-1?q=miame * Retrieve a complete search summary, e.g., http://nif-services.neuinfo.org/servicesv1/v1/federation/search?q=cortex * Retrieve NIF auto-complete suggestions, e.g., http://nif-services.neuinfo.org/servicesv1/v1/vocabulary?prefix=hippo * Use the NIF annotator for arbitrary text, e.g., http://nif-services.neuinfo.org/servicesv1/v1/annotate?content=The%20cerebellum%20is%20a%20wonderful%20thing These services are documented for developers in the WADL file (and client stubs should have the comments embedded in them). Visit, http://nif-services.neuinfo.org/servicesv1/ for more information

VentDB
type: Resource
type: NamedIndividual
has db xref: nlx_154725
has db xref: r3d100011536
IAO_0000115: Database contating hydrothermal spring geochemistry that hosts and serves the full range of compositional data acquired on seafloor hydrothermal vents from all tectonic settings. It can accommodate published historical data as well as legacy and new data that investigators contribute.

Research Services Branch National Institutes of Mental Health
type: Resource
type: NamedIndividual
has db xref: nlx_156832
synonym: Research Services Branch National Institutes of Mental Health National Institutes of Neurological Disorders and Stroke
abbrev: RSB
IAO_0000115: Portal for NIH, NIMH, and NINDS scientific and computer resources including Mac sites, PC sites, Linux sites, intramural programs, intranet and the NIH JumpStart and Directory.

Human Gene Trap Mutant Collection
type: Resource
type: NamedIndividual
has db xref: nlx_153909
IAO_0000115: Collection of isogenic human cell lines that are deficient for the expression of single genes. The current collection is based on the human cell line KBM-7 (Kotecki et al. Experimental Cell Research 1999), which is haploid for all chromosomes except chromosome 8 and a small part of chromosome 15. In these cells, genes are disrupted by the means of a retroviral gene trap. The collection is being expanded to cover the majority of expressed genes. The Human Gene Trap Mutant Collection is generated as a public-private partnership between CeMM (the Research Center for Molecular Medicine of the Austrian Academy of Sciences) and Haplogen.

WTCHG Genome Scan Viewer
type: Resource
type: NamedIndividual
has db xref: nlx_153902
synonym: Genome Scan Database
synonym: Genome Scan Viewer
synonym: Wellcome Trust Centre for Human Genetics Genome Scan Viewer
abbrev: GSCANDB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database / display tool of genome scans, with a web interface that lets the user view the data. It does not perform any analyses - these must be done by other software, and the results uploaded into it. The basic features of GSCANDB are: * Parallel viewing of scans for multiple phenotypes. * Parallel analyses of the same scan data. * Genome-wide views of genome scans * Chromosomal region views, with zooming * Gene and SNP Annotation is shown at high zoom levels * Haplotype block structure viewing * The positions of known Trait Loci can be overlayed and queried. * Links to Ensembl, MGI, NCBI, UCSC and other genome data browsers. In GSCANDB, a genome scan has a wide definition, including not only the usual statistical genetic measures of association between genetic variation at a series of loci and variation in a phenotype, but any quantitative measure that varies along the genome. This includes for example competitive genome hybridization data and some kinds of gene expression measurements.

openSNP
type: Resource
type: NamedIndividual
has db xref: nlx_153904
IAO_0000115: Database of raw data from people who have shared their direct-to-customer (DTC) genetic results from 23andMe, deCODEme or FamilyTreeDNA. Logged-In users can search the database for users with specific phenotypes and mass-download all corresponding SNP-datasets. This allows you to get datasets like All genotyping files of openSNP-users that have Alzheimer and the corresponding control group. They are currently working on providing API-access. You can also use JSON to get access to openSNP-data and some other ways: If you want to automate the file-downloads for a given phenotype the RSS-feeds could help you. Inside the RSS-XML there are 2 flags you could use to automatically create correct genotype-groups: gives you the variation of this user at the phenotype you are looking at and gives you the download link. If you were genotyped by 23andMe, deCODEme or FamilyTreeDNA (contact them regarding others) you can upload the raw genotype data which you can download from your DTC test provider. The data will then be openly available for the world to see and download. They also parse these SNPs and annotate them. For annotation they include the manually curated SNPedia and find Open Access primary publications which appear in the journals of The Public Library of Science (PLoS), an Open Access publishing group. Additionally they screen Mendeley, a crowd-sourced repository of scientific publications. You can also publish some of your phenotypes so some day it might get possible to associate some SNPs with phenotypes. You can also share your knowledge about SNPs and phenotypes with other users and can socialize.

Diffusion MRI of Traumatic Brain Injury
type: Resource
type: NamedIndividual
has db xref: nlx_153906
abbrev: Diffusion MRI of TBI
IAO_0000115: Project to define a roadmap for diffusion MR imaging of traumatic brain imaging and design an infrastructure to implement the recommendations and tested to ensure feasibility, disseminate results, and facilitate deployment and adoption. The research roadmap and infrastructure development will concentrate on three areas: 1) standardization of diffusion imaging methodology, 2) trial design and patient selection for acute or chronic therapy, and 3) development of multi-center collaborations and repositories for evaluating whether advanced diffusion imaging does improve decision making and TBI patients' outcomes. # DTI MRI reproducability: One of the major areas of investigation in this project is to study the reproducibility of data acquisition and image analysis algorithms. Understanding reproducibility defines a base level of deviation from which scans can be analyzed with statistical significance. As part of this work they are also developing site qualification criteria with the intention of setting limits on the MR system minimal performance for acceptable use in TBI evaluation. # Infrastructure for image storage, analysis and visualization: There is a continuing need to refine and extend software methods for diffusion MRI data analysis and visualization. Not only to translate tools into clinical practice, but also to encourage continuation of the innovation and development of new tools and techniques. To deliver upon these goals they are designing and implementing a storage and computational infrastructure to provide access to shared datasets and intuitive interfaces for analysis and visualization through a variety of tools. A strong emphasis has been placed on providing secure data sharing and the ability to add community defined common data elements. The infrastructure is built upon a Software-as-a-Service model, in which tools are hosted and managed remotely allowing users access through well-defined interfaces. The final service will also facilitate compositio…

Camino
type: Resource
type: NamedIndividual
has db xref: nlx_153907
synonym: UCL Camino Diffusion MRI Toolkit
IAO_0000115: Free, open-source, object-oriented software package for analysis and reconstruction of Diffusion MRI data, tractography and connectivity mapping. The toolkit implements standard techniques, such as diffusion tensor fitting, mapping fractional anisotropy and mean diffusivity, deterministic and probabilistic tractography. It also contains more specialized and cutting-edge techniques, such as Monte-Carlo diffusion simulation, multi-fibre and HARDI reconstruction techniques, multi-fibre PICo, compartment models, and axon density and diameter estimation. Camino has a modular design to enable construction of processing pipelines that include modules from other software packages. The toolkit is primarily designed for unix platforms and structured to enable simple scripting of processing pipelines for batch processing. Most users use linux, MacOS or a unix emulator like cygwin running under windows. However, the core code is written in Java and thus is simple to call from other platforms and programming environments, such as matlab running under unix or windows.

Brainspell
type: Resource
type: NamedIndividual
has db xref: nlx_153908
abbrev: brainspell
IAO_0000115: Crowdsourcing site for annotating neuroimaging literature. Brainspell also allows for search across the literature.

University of California Davis Center for Neuroscience
type: Organization
type: NamedIndividual
has db xref: nif-0000-02314
synonym: UC Davis Center of Neuroscience
abbrev: UCD Center of Neuroscience
IAO_0000115: Recognizing the importance of research in Neuroscience and its great promise, as well as the importance of educating the neuroscientists of the future, the University of California, Davis, in 1990, established The Center for Neuroscience. The Center has now become the focus of interdisciplinary studies in Cellular, Molecular, Systems, Cognitive and Translational Neuroscience, with a Faculty made up of world leaders in brain research. The Center occupies facilities especially designed to promote and foster interactions among the resident faculty, associated faculty, postdoctoral fellows, and graduate students, with state-of-the-art lab space and associated facilities such as cellular and molecular imaging, functional imaging of the human brain and extensive databasing facilities. The Center provides an attractive setting for seminar series that feature distinguished National and International guest speakers as well as speakers from the UC Davis community of scientists. The Center is home to a number of visiting scholars each year and enjoys a lively intellectual atmosphere.

DTI and Fibertools Software Package
type: Resource
type: NamedIndividual
has db xref: nlx_153913
synonym: DTI & Fibertools
abbrev: DTI and Fibertools
abbrev: DTI&FiberTools
IAO_0000115: Implemented under MATLAB, this DTI image processing toolbox provides import-filters for several MR file standards, a processing unit to calculate the diffusion tensors; several GUI based tools to calculate fiber tracks and to evaluate the DTI dataset. The results can be filed as images with 3D impression or can be logged in formatted ASCII files. Tools and features: * DTI Processing Unit: Calculates the diffusion tensors and their eigenvalues and eigenvectors. Different file formats are supported (like DICOM, Bruker, binary files, Matlab structures). The standard SIEMENS and GE diffusion encoding schemes are supported; other schemes have to be defined in a separate text, .m or .mat file. * FiberTracking: ** Fiber tracking is realized by using the FACT algorithm (Mori et al., Annal. Neurol 1999). ** Probabilistic tracking realized by using the PiCo (Parker et al., JMRI 2003) approach but with DTI data as basis. It is possible to extract pathways between two seeds by combining two maps (Kreher et al., NeuroImage 2008). ** Global Fiber Tracking on basis of HARDI or DTI data. The method is based on the approach reported in (Marco Reisert et al: Global fiber reconstruction becomes practical. NeuroImage 54(2):955-62) * FiberViewer: ** Visualization and Navigation through different data modalities like DTI maps, fiber tracks, diffusion main directions. ** Supports different kinds of DTI maps (e.g. FA, Trace, lambda images ) ** Creation and manipulation of mask based ROIs. ** Selection of streamline fibers ** Visualization of probabilistic fiber tracking results ** Documentation by logging statistics of ROIs and fiber tracks into text files. ** Import/Export from/to ANALYZE or Nifti * 3D Visualizer: Visualization of map slices, ROIs, and fiber tracks with 3D impression. * Batch Editor: Automatic processing of high amounts of data. Possibility to link processing with SPM8 easily.

Diffusion Tensor Imaging ToolKit
type: Resource
type: NamedIndividual
has db xref: nlx_153914
abbrev: DTI-TK
IAO_0000115: A spatial normalization and atlas construction toolkit optimized for examining white matter morphometry using DTI data with special care taken to respect the tensorial nature of the data. It implements a state-of-the-art registration algorithm that drives the alignment of white matter (WM) tracts by matching the orientation of the underlying fiber bundle at each voxel. The algorithm has been shown to both improve WM tract alignment and to enhance the power of statistical inference in clinical settings. A 2011 study published in NeuroImage ranks DTI-TK the top-performing tool in its class. Key features include: * open standard-based file IO support: NIfTI format for scalar, vector and tensor image volumes * tool chains for manipulating tensor image volumes: resampling, smoothing, warping, registration & visualization * pipelines for WM morphometry: spatial normalization & atlas construction for population-based studies * built-in cluster-computing support: support for open source Sun Grid Engine (SGE) * Interoperability with other popular DTI tools: AFNI, Camino, FSL & DTIStudio * Interoperability with ITK-SNAP: support multi-modal visualization and segmentation

ExploreDTI
type: Resource
type: NamedIndividual
has db xref: nlx_153916
synonym: Explore DTI
IAO_0000115: A graphical toolbox developed in Matlab for exploratory diffusion (tensor) MRI and fiber tractography. It includes diffusion reconstruction approaches, analysis and visualization tools for fiber tractography, atlas based segmentation, and connectivity networks. It also provides a wide range of quality assessment and pre-processing tools. Main features: * Visualization of scalar and vector maps of various diffusion tensor properties * Display of principal diffusion vectors, cuboids, and ellipsoids with several color-encodings * Deterministic (streamline) and 'probabilistic' (wild-bootstrap) fiber tractography * Clustering of fiber tracts * Data quality assessment tools * HARDI reconstructions (Q-ball and spherical deconvolution imaging) * Tract-specific measurements * Tract-segment analysis * Motion / distortion correction (with B-matrix rotation!) * Other cool stuff... (see publication link)

Connectome Mapping Toolkit
type: Resource
type: NamedIndividual
has db xref: nlx_153920
IAO_0000115: A Python-based open source toolkit for magnetic resonance connectome mapping, data management, sharing, visualization and analysis. The toolkit includes the connectome mapper (a full DMRI processing pipeline), a new file format for multi modal data and metadata, and a visualization application.

TORTOISE
type: Resource
type: NamedIndividual
has db xref: nlx_153921
synonym: Tolerably Obsessive Registration and Tensor Optimization Indolent Software Ensemble
IAO_0000115: An integrated and flexible software package for processing of DTI data, and in general for the correction of diffusion weighted images to be used for DTI and potentially for high angular resolution diffusion imaging (HARDI) analysis. It can be run on both Linux and Mac platforms. It is composed of two modules named DIFF PREP and DIFF CALC. * DIFF_PREP - software for image resampling, motion, eddy current distortion and susceptibility induced EPI distortion corrections, and for re-orientation of data to a common space * DIFF_CALC - software for tensor fitting, error analysis, color map visualization and ROI analysis In addition, TORTOISE contains additional Utilities, such as a tool for the analysis of multi-center phantom data.

An Integrated Multiple Structure Visualization and Multiple Sequence Alignment Application
type: Resource
type: NamedIndividual
has db xref: biotools:friend
has db xref: nif-0000-10149
synonym: FRIEND
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities such as: structure visualization with different rendering and coloring, sequence alignment, and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including: structural alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions, and protein super-families. Friend is also useful for the functional annotation of proteins, protein modeling, and protein folding studies. Friend provides three levels of usage; 1) an extensive GUI for a scientist with no programming experience, 2) a command line interface for scripting for a scientist with some programming experience, and 3) the ability to extend Friend with user written libraries for an experienced programmer. The application is linked and communicates with local and remote sequence and structure databases.

Cuffdiff
type: Resource
type: NamedIndividual
has db xref: biotools:cuffdiff
has db xref: OMICS_01969
synonym: Cuffdiff 2
IAO_0000115: Software that estimates expression at transcript-level resolution and controls for variability evident across replicate libraries.

Mammalian Brain Methylomes
type: Resource
type: NamedIndividual
has db xref: nlx_153926
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Datasets described in the manuscript: "Global Epigenomic Reconfiguration During Mammalian Brain Development" (Science, 2013 - DOI: 10.1126/science.1237905. This study provides genome-wide composition, patterning, cell specificity, and dynamics of DNA methylation at single-base resolution in human and mouse frontal cortex throughout their lifespan. Widespread methylome reconfiguration occurs during fetal to young adult development, coincident with synaptogenesis.

UW-Madison Neuroscience Resources
type: Resource
type: NamedIndividual
has db xref: nlx_153927
synonym: UW Madison Neuroscience Resources
synonym: UW-Madison Neuroscience Resource Page
abbrev: UW Neuroanatomy Resources
abbrev: UW Neuroscience Resources
IAO_0000115: Training materials including Web edition modules of the neuroanatomy coursebooks used by first-year medical students at the University of Wisconsin Medical School (UWMS), videos, and images. Topics include spinal cord, brain stem, Cerebellum, Thalamus, Cranial Nerves and National Board Review practice questions.

EMBASE
type: Resource
type: NamedIndividual
has db xref: nlx_153929
synonym: EMBASE (Excerpta Medica Database)
synonym: Embase: Biomedical Database
synonym: EMBASE: Excerpta Medica
synonym: Excerpta Medica Database
abbrev: Embase
IAO_0000115: Comprehensive international bibliographic biomedical database that enables users to track and retrieve precise information on drugs and diseases from pre-clinical studies to searches on critical toxicological information. It contains bibliographic records with citations, abstracts and indexing derived from biomedical articles in peer reviewed journals, and is especially strong in its coverage of drug and pharmaceutical research. Embase can help with everything from clinical trials research to pharmacovigilance and is updated online daily and weekly. Its broad biomedical scope covers the following areas: * Drug therapy and research, including pharmaceutics, pharmacology and toxicology * Clinical and experimental (human) medicine * Basic biological science relevant to human medicine * Biotechnology and biomedical engineering, including medical devices * Health policy and management, including pharmacoeconomics * Public, occupational and environmental health, including pollution control * Veterinary science, dentistry, and nursing The Embase Application Programming Interface supports export, RSS feeds, and integration services, making it possible to share data with a wide range of systems.

NIF Blog
type: Resource
type: NamedIndividual
has db xref: nlx_153930
synonym: Neuroscience Information Framework blog
IAO_0000115: Blog put out by the Neuroscience Information Framework covering a variety of neuroscience related topics including topics encountered by the Neuroscience Information Framework as a project.

Melvin Yahr International Parkinson's Disease Foundation
type: Resource
type: NamedIndividual
has db xref: nif-0000-11666
synonym: Melvin Yahr Foundation
synonym: The Melvin Yahr International Parkinson's Disease Foundation
abbrev: MYIPDF
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 28, 2017. Foundation that helps junior physicians and neuroscientists continue their research on Parkinson's Disease and related disorders, with financial support for professional and intellectual development. It promotes an international community of researchers, focusing on the young enthusiastic investigators and clinicians who might otherwise be forced to abandon their ideas and efforts.

BLASTX
type: Resource
type: NamedIndividual
has db xref: nlx_153933
has db xref: OMICS_00992
synonym: Translated BLAST
synonym: Translated BLAST: blastx
IAO_0000115: Web application to search protein databases using a translated nucleotide query. Translated BLAST services are useful when trying to find homologous proteins to a nucleotide coding region. Blastx compares translational products of the nucleotide query sequence to a protein database. Because blastx translates the query sequence in all six reading frames and provides combined significance statistics for hits to different frames, it is particularly useful when the reading frame of the query sequence is unknown or it contains errors that may lead to frame shifts or other coding errors. Thus blastx is often the first analysis performed with a newly determined nucleotide sequence and is used extensively in analyzing EST sequences. This search is more sensitive than nucleotide blast since the comparison is performed at the protein level.

First Nerve
type: Resource
type: NamedIndividual
has db xref: nlx_153935
IAO_0000115: Blog by Avery Gilbert, a sensory psychologist, taking a scientific sniff at the culture of smell. His specialty is olfaction --the strange and wonderful world of smell. He's worked in academia and the corporate world, published research in scientific journals, and written a book on the science of smell.

Annual Reviews: A Nonprofit Scientific Publisher
type: Resource
type: NamedIndividual
has db xref: nif-0000-10150
synonym: Annual Reviews
IAO_0000115: Annual Reviews offers comprehensive, timely collections of critical reviews written by leading scientists. It publishes authoritative, analytic reviews in 37 focused disciplines within the Biomedical, Life, Physical, and Social Sciences. The mission of Annual Reviews is to provide systematic, periodic examinations of scholarly advances in a number of fields of science through critical authoritative reviews. The comprehensive critical review not only summarizes a topic but also roots out errors of fact or concept and provokes discussion that will lead to new research activity. The critical review is an essential part of the scientific method. Sponsors: Annual Reviews is a non-profit organization created and managed by scientists to serve science by publishing reviews in 40 different scientific fields.

Sample of Science
type: Resource
type: NamedIndividual
has db xref: nlx_153937
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Free access service resource dedicated to connect researchers creating scientific samples with scientists who need samples for their experiments. With Sample of Science researchers can submit samples, or contact scientists proposing sample for dissemination. Each disseminated sample also gets its description published in Sample of Science Bulletin, a dedicated open access journal. It acquires a Digital Object Identifier (DOI) and becomes a fully citable item. Because both adequate sample descriptions and mutually-agreed dissemination conditions are key factors for a fruitful dissemination that respects mutual interest, Sample of Science provides tools to elaborate, communicate, discuss, and refine both sample description and dissemination conditions. This process, termed peer-adoption process, results in the publication of disseminated sample descriptions in Sample of Science Bulletin, a dedicated open access publication. The publication in Sample of Science Bulletin is useful to provide adequate recognition to Sample Authors who contribute to the development of science by offering visibility to their disseminated samples. To the adopter it provides experimental details regarding the sample under the form of a citable reference useful for any future publications involving this sample. To a larger scientific community interested in material science, it provides a useful tool to stay abreast the activity of sample providers in their respective field of expertise.

The Book of GENESIS
type: Resource
type: NamedIndividual
has db xref: nlx_153938
synonym: Book of GENESIS
abbrev: BoG
IAO_0000115: Book with a downloadable version of the second edition of a practical introduction to the interdisciplinary field of computational neuroscience through the use of the GENESIS simulator. It is designed to be a step-by-step tutorial for professionals, researchers and students working in fields ranging from neuroscience to bioengineering, medicine, artificial neural networks and the cognitive sciences. Part I of the book teaches concepts in neuroscience and neural modeling by means of interactive computer tutorials on subjects ranging from neuronal membrane properties to cortical networks. These chapters, written by several contributors, allow the student to perform realistic simulations and experiments on model neural systems and provide the necessary background for understanding and using the tutorials. The simulations are user-friendly with on-line help and may be used without any prior knowledge of the GENESIS simulator or computer programming. Part II is intended to teach the use of the GENESIS script language for the construction of one's own simulations. This part will be useful for self-study by researchers who wish to do neural modeling, as well as students. It follows approximately the same sequence of topics as Part II, and uses parts of the tutorial simulations as examples of GENESIS programming. Several of these are based on recent research simulations which have been published in the neuroscience literature, but which have not been previously available for use outside the laboratories of the original researchers. Thus, the reader may modify these simulations and use them as a starting point for the development of original simulations. In addition to many revisions and additions to existing chapters, this second edition includes two new chapters on the modeling of biochemical signaling pathways and on the use of GENESIS on parallel computers and networks of workstations. Other new additions include a section describing ways to implement synaptic modificati…

IPython
type: Resource
type: NamedIndividual
has db xref: nlx_153939
synonym: IPython Interactive Computing
abbrev: IP(y)
IAO_0000115: A web-based interactive computational environment where you can combine code execution, text, mathematics, plots and rich media into a single document. It offers a comprehensive library on top of which more sophisticated systems can be built. The project provides an enhanced interactive environment that includes support for data visualization and facilities for distributed and parallel computation.

Kasetsart University; Bangkok; Thailand
type: Organization
type: NamedIndividual
has db xref: nlx_72794
IAO_0000115: Public university in the capital of Thailand. Originally created to promote agricultural sciences, it now offers degrees in a range of fields including engineering, social sciences, business administration, and education.

Diabetes Disease Portal
type: Resource
type: NamedIndividual
has db xref: nlx_153942
IAO_0000115: An integrated resource for information on genes, QTLs and strains associated with diabetes. The portal provides easy acces to data related to both Type 1 and Type 2 Diabetes and Diabetes-related Obesity and Hypertension, as well as information on Diabetic Complications. View the results for all the included diabetes-related disease states or choose a disease category to get a pull-down list of diseases. A single click on a disease will provide a list of related genes, QTLs, and strains as well as a genome wide view of these via the GViewer tool. A link from GViewer to GBrowse shows the genes and QTLs within their genomic context. Additional pages for Phenotypes, Pathways and Biological Processes provide one-click access to data related to diabetes. Tools, Related Links and Rat Strain Models pages link to additional resources of interest to diabetes researchers.

Functional Anatomy of the Cerebro-Cerebellar System (FACCS)
type: Resource
type: NamedIndividual
has db xref: nif-0000-02317
synonym: Functional Anatomy of the Cerebro-Cerebellar System
abbrev: FACCS
IAO_0000115: Public neuroscience database providing a collection of published data describing structure and structure-function relationships in one of the largest projection systems of the brain: the cerebro-cerebellar system. It also gives access to a suite of tools that allow the user to visualize and analyze any selected combination of data sets. Contact them if you are interested in contributing data. The overall goal is to improve communication of results and permit re-use of previously published data in new contexts. FACCS is a part of the Rat Brain WorkBench, a new research and development project funded by The Research Council of Norway, the Centre for Molecular Biology and Neuroscience, and the European Union. The project is directed by Jan G. Bjaalie, Centre for Molecular Biology and Neuroscience & Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway.

Reliable detection of directional couplings using rank statistics
type: Resource
type: NamedIndividual
has db xref: nlx_153987
IAO_0000115: Source code that allows you to calculate the different measures used in Chicharro D, Andrzejak RG (2009): Reliable detection of directional couplings using rank statistics. Physical Review E, 80, 026217.

Characterizing unidirectional couplings between point processes and flows
type: Resource
type: NamedIndividual
has db xref: nlx_153988
IAO_0000115: Source code that allows you to calculate the different measures used in Andrzejak and Kreuz 2011, http://iopscience.iop.org/0295-5075/96/5/50012

Detecting event-related time-dependent directional couplings
type: Resource
type: NamedIndividual
has db xref: nlx_153989
IAO_0000115: Source code that allows you to calculate the different measures used in Andrzejak et al 2006, http://iopscience.iop.org/1367-2630/8/1/006

Nonlinear time series analysis in a nutshell
type: Resource
type: NamedIndividual
has db xref: nlx_153990
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. Source code that allows you to calculate the different measures used in Andrzejak RG (2011): Nonlinear time series analysis in a nutshell, http://www.dtic.upf.edu/~ralph/Kansas3.pdf. In: Osorio I, Zaveri H, Frei M, Arthurs S (eds.) Epilepsy: The Intersection of Neurosciences, Biology, Mathematics, and Engineering. CRC Press, Taylor & Francis Group, 125-138. http://www.taylorandfrancis.com/books/details/9781439838853/ The files allow you to calculate the nonlinear prediction error from some time series, you can generate a time series of an autoregressive process of order one and integrate the differential equation of the Lorenz dynamics.

Homology Maps Page
type: Resource
type: NamedIndividual
has db xref: nif-0000-25559
synonym: Homology
IAO_0000115: This page provides quick access to the Comparative mapping functions available in the Map Viewer. Currently, comparative maps are calculated using HomoloGene orthology predictions. Once the gene pairs have been established, blocks of conserved syteny can be established using the positions of each gene object in their respective builds. Sponsors: This resource is supported by NCBI.

Time-resolved and time-scale adaptive measures of spike train synchrony
type: Resource
type: NamedIndividual
has db xref: nlx_153991
IAO_0000115: Source code that allows you to calculate the different measures used in Kreuz T, Chicharro D, Greschner M, Andrzejak RG (2011): Time-resolved and time-scale adaptive measures of spike train synchrony, http://www.sciencedirect.com/science/article/pii/S0165027010006564. Journal of Neuroscience Methods,195, 92-106 & Kreuz T, Chicharro D, Andrzejak RG, Haas JS, and Abarbanel HDI (2009) Measuring multiple spike train synchrony. Journal of Neuroscience Methods 183:287-299 http://www.sciencedirect.com/science/article/pii/S0165027009003616

SLqPCR
type: Resource
type: NamedIndividual
has db xref: OMICS_04010
synonym: SLqPCR - Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH
IAO_0000115: Software functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH.

Association of American Medical Colleges
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100005435
has db xref: grid.414000.1
has db xref: ISNI: 0000 0000 8652 9597
has db xref: nif-0000-10157
has db xref: Wikidata: Q4809610
abbrev: AAMC
IAO_0000115: Not-for-profit association representing all 141 accredited U.S. and 17 accredited Canadian medical schools; nearly 400 major teaching hospitals and health systems, including 51 Department of Veterans Affairs medical centers; and 90 academic and scientific societies. Through these institutions and organizations, the AAMC represents 128,000 faculty members, 75,000 medical students, and 110,000 resident physicians. Through its programs and services, it strengthens the world's most advanced medical care by supporting the entire spectrum of education, research, and patient care activities conducted by member institutions. The AAMC and its members are dedicated to the communities they serve and steadfast in their desire to earn and keep the public's trust for the role they play in improving the nation's health. The vision of the AAMC and its members is a healthy nation and world in which: - America's system of medical education, through continual renewal and innovation, prepares physicians and scientists to meet the nation's evolving health needs. - The nation's medical students, biomedical graduate students, residents, fellows, faculty, and the health care workforce are diverse and culturally competent. - Advances in medical knowledge, therapies, and technologies prevent disease, alleviate suffering, and improve quality of life. - The nation's health system meets the needs of all. - Concern for compassion, quality, safety, efficacy, accountability, affordability, professionalism, and the public good guide the health care community.

Ataxia-Telangiectasia Childrens Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-10158
synonym: A-T Children's Project
IAO_0000115: The Ataxia Telangiectasia Children's Project, better known as the A-T Children's Project, was founded in late 1993 by a family in Florida with two young sons who have A-T. It is a public, tax-exempt, non-profit organization pursuant to Section 501(c)(3) of the Internal Revenue Code, and all gifts and donations to the Project are tax deductible. The A-T Children's Project was formed to raise funds through events and contributions from corporations, foundations and friends. These funds are then used to accelerate first-rate, international scientific research aimed at finding a cure and improving the lives of all children with ataxia-telangiectasia. - To encourage and support excellent laboratory research which will accelerate the discovery of a cure or possible therapies for ataxia-telangiectasia by: - awarding competitive research grants to top scientists using a peer-review board comprised of top scientists and physicians, - organizing and sponsoring workshops and symposiums in order to encourage cooperation among laboratories and to generate new research strategies, and - working with Congress and the National Institutes of Health to encourage the funding of active research on A-T by agencies of the U.S. government. - To improve the accurate and timely diagnosis of A-T patients by increasing public awareness and by educating physicians. - To develop and maintain an international patient registry of A-T patients with objective, neutral oversight, while leaving ultimate control in the hands of treating physicians, so that up-to-date clinical information about A-T patients can be obtained for researchers and so that when a treatment is developed, all patients can be reached through their physicians. - To support and oversee a clinical center and information clearinghouse at a top-rated, world-class medical center for the evaluation of A-T patients by a multidisciplinary team of specialists, and for the accumulation of experience in managing the many facets of A-T such…

ATCC
type: Organization
type: NamedIndividual
has db xref: grid.281196.5
has db xref: ISNI: 0000 0001 2161 7948
has db xref: nif-0000-10159
has db xref: Wikidata: Q2843042
synonym: American Type Culture Collection
synonym: ATCC(dna)
synonym: ATCC(in host)
synonym: ATCC: The Global Bioresource Center
IAO_0000115: Global nonprofit biological resource center (BRC) and research organization that provides biological products, technical services and educational programs to private industry, government and academic organizations. Its mission is to acquire, authenticate, preserve, develop and distribute biological materials, information, technology, intellectual property and standards for the advancement and application of scientific knowledge. The primary purpose of ATCC is to use its resources and experience as a BRC to become the world leader in standard biological reference materials management, intellectual property resource management and translational research as applied to biomaterial development, standardization and certification. ATCC characterizes cell lines, bacteria, viruses, fungi and protozoa, as well as develops and evaluates assays and techniques for validating research resources and preserving and distributing biological materials to the public and private sector research communities.

Speed BioSystems
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_152465
IAO_0000115: Commercial antibody supplier based in Maryland.

NIDAG: Neuroimaging Data Access Group
type: Resource
type: NamedIndividual
has db xref: nif-0000-10161
synonym: Neuroimaging Data Access Group
abbrev: NIDAG
IAO_0000115: An international working group dedicated to improving access to neuroimaging results in a free and open-access manner. It seeks to establish a universal coordinate database, including both past papers and future studies. Their current project involves the creation of a comprehensive database of neuroimaging results searchable based on standardized coordinates. Once complete, this will allow anyone to find all of the articles that report a coordinate, or set of coordinates, easily and without cost. Eventually, they hope to expand this database to include not only coordinates, but statistical parametric maps as well. Formation of such a database will increase the likelihood of relevant papers being found and cited, and also be a very useful tool for those interested in meta-analysis, and hopefully clarify structure-function relationships. They are interested in hearing from people who might be willing to contribute to their projects, particularly those with programming experience. The number of published neuroimaging studies is increasing rapidly and it is not feasible to read them all. If a computer database could store key information from published fMRI papers and make that information easier to search or share, this would have substantial benefits for the neuroimaging community. Projects like AMAT, Brainmap, Brede and SumsDB have started to tackle this problem. NIDAG wants to formalize and improve these databases so that they meet the needs of the neuroimaging community. Formal meta-analysis of published data is a valuable way to assess the consistency and reliability of experimental results. A database of neuroimaging results would facilitate meta-analyses, in conjunction with tools like GingerALE and Multi-level Kernel Density Analysis.

Genes to Cognition - Biological Resources
type: Resource
type: NamedIndividual
has db xref: nif-0000-10163
synonym: G2C - Biological Resources
synonym: G2C Biological Resources
synonym: G2C Mice Resources
synonym: G2C-Biological Resources
IAO_0000115: Biological resources, including gene-targeting vectors, ES cell lines, antibodies, and transgenic mice, generated for its phenotyping pipeline as part of the Genes to Cognition research program are freely-available to interested researchers. Available Transgenic Mouse Lines: *Hras1 (H-ras) knockout,C57BL/6J *Dlg4 (PSD-95) knockout,129S5 *Dlg4 (PSD-95) knockout,C57BL/6J *Dlg3 (SAP102) knockout with hprt mutation,129S5 *Dlg3 (SAP102) knockout (wild-type for hprt,C57BL/6J *Syngap1 (SynGAP) knockout (from 8.24 clone), C57BL/6J *Dlg4 (PSD-95) guanylate kinase domain deletion, C57BL/6J *Ptk2 (FAK) knockout,C57BL/6J

Virtual Health Library
type: Resource
type: NamedIndividual
has db xref: nif-0000-10164
synonym: VHL
IAO_0000115: VHL is a library, a decentralized and dynamic information-source collection, designed to provide equitable access to scientific knowledge on health. This collection operates as an Internet network of products and services, structured to progressively meet the need for information on health on the part of authorities, administrators, researchers, professors, students, professionals, the media and the general public. It sets itself apart from other information sources available on the Internet due to its selection criteria and quality control. The Virtual Health Library is envisioned as the broad of scientific and technical knowledge based in health-entered, organized, and stored in electronic format in the countries of the Region, universally accessible on the Internet and compatible with international databases. The VHL is a common space shared by information users, producers and intermediaries. It is based on the information paradigm set by the Internet, where users may interact with networks of information sources and with other users. The most important consequence of this paradigm is the convergence of functions and activities of production, intermediation and use of information sources. It will also be possible to enrich, schedule, reformulate, and/or translate the basic information sources into new information products and services, with value added, in order to meet more efficiently the information needs of users from specific communities. BIREME has established a plan of action to implement the Virtual Health Library based on 5 lines of action: promotion and marketing; realignment of traditional products and services; production of electronic publications; development of tools for integrating and locating information; and development of other Virtual Health Library components. Sponsors: VHL is supported by the Latin-American and Caribbean Center on Health Sciences Information.

Ribosomal Mutation Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02522
synonym: The Ribosomal Mutation Database
IAO_0000115: This is a database of 16S and 23S ribosomal RNA mutations reported in literature, expanded to include mutations in ribosomal proteins and ribosomal factors. Access to the expanded versions of the 16S and 23S Ribosomal RNA Mutation Databases has been improved to permit searches of the lists of alterations for all the data from (1) one specific organism, (2) one specific nucleotide position, (3) one specific phenotype, or (4) a particular author. Please send bibliographic citations for published work to be included in The Ribosomal Mutation Database to the curator via email. The database currently consists of 1024 records, including 485 16S rRNA records from Escherichia coli, 37 16S-like rRNA records from other organisms, 421 23S rRNA records from E. coli, and 81 23S-like records from other organisms. The numbering of positions in all records corresponds to the numbering in E. coli. We welcome any suggested revisions to the database, as well as information about newly characterized 16S or 23S rRNA mutations. The expanded database will be renamed to The Ribosomal Mutation Database and will include mutations in ribosomal proteins and ribosomal factors.

Proteome 2D-PAGE Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02523
abbrev: 2D-PAGE
IAO_0000115: The Proteome 2D-PAGE Database system for microbial research is a curated database for storing and investigating proteomics data. Software tools are available and for data submission, please contact the Database Curator. Established at the Max Plank Institution for Infection Biology, this system contains four interconnected databases: i.) 2D-PAGE Database: Two dimensional electrophoresis (2-DE) and mass spectrometry of diverse microorganisms and other organisms. This database currently contains 4971 identified spots and 1228 mass peaklists in 44 reference maps representing experiments from 24 different organisms and strains. The data were submitted by 84 Submitters from 24 Institutes and 12 nations. It also contains various software tools that are important in formatting and analyzing gels and mass peaks; software include: *TopSpot: Scanning the gel, editing the spots and saving the information *Fragmentation: Fragmentation of the gel image into sections *MS-Screener: Perl script to compare the similarity of MALDI-PMF peaklists *MS-Screener update: MS-Screener can be used to compare mass spectra (MALDI-MS(/MS) as well as ESI-MS/MS spectra) on the basis of their peak lists (.dta, .pkm, .pkt, or .txt files), to recalibrate mass spectra, to determine and eliminate exogenous contaminant peaks, and to create matrices for cluster analyses. *GelCali: Online calibration of the Mr- and pI-axis of 2-DE gels with mathematical regression methods ii.)Isotope Coded Affinity Tag (ICAT)-LC/MS database: Isotope Coded Affinity Tag (ICAT)-LC/MS data for Mycobacterium tuberculosis strain BCG versus H37Rv. iii.) FUNC_CLASS database: Functional classification of diverse microorganism. This database also integrates genomic, proteomic, and metabolic data. iv.) DIFF database: Presentation of differently regulated proteins obtained by comparative proteomic experiments using computerized gel image analysis.

Biocatalogue - The Life Science Web Services Registry
type: Resource
type: NamedIndividual
has db xref: biotools:biocatalogue
has db xref: nif-0000-10167
synonym: Biocatalog
abbrev: BioCatalogue
IAO_0000115: Crowd-curated catalog of life sciences Web services with over 2400 service entries, thereby enabling users (people and programs) to discover and use these services easily. It provides a platform with several (standardized) interfaces and a suite of tools for registration of services by the community of users as well as empowers the community to extend and enhance the system. BioCatalogue provides a centralized biological web services market place which is accessible to the world as it is searchable and indexable to search engines. Additionally, it provides a quality of service standard for biological web services thereby enabling services to be classified and checked for availability, reliability and other quality measures. Primary goals: * Provide a single registration point for Web Service providers and a single search site for scientists and developers. * Providers, Expert curators and Users will provide oversight, monitor the catalog and provide high quality annotations for services. * BioCatalogue is a place where the community can find contacts and meet the experts and maintainers of these services.

5 prime end Serial Analysis of Gene Expression Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02525
synonym: 5'end Serial Analysis of Gene Expression Database
synonym: 5end Serial Analysis of Gene Expression Database
abbrev: 5'SAGE
abbrev: 5SAGE
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on October 30, 2012. A database that displays the observed frequencies of individual 5' end SAGE tags and previously unknown transcription start sites in the promoter regions, introns and intergenic regions of known genes. 5'SAGE will be useful for analyzing promoter regions and start site variation in different tissues, and is freely available.

Biological Pathways Exchange
type: Resource
type: NamedIndividual
has db xref: nif-0000-10171
has db xref: nlx_157327
synonym: BioPAX
synonym: BioPAX: Biological Pathways Exchange
IAO_0000115: Community standard for pathway data sharing. Standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Supports data exchange between pathway data groups and thus reduces complexity of interchange between data formats by providing accepted standard format for pathway data. Open and collaborative effort by community of researchers, software developers, and institutions. BioPAX is defined in OWL DL and is represented in RDF/XML format.Uses W3C standard Web Ontology Language, OWL.

Internet Archive
type: Resource
type: NamedIndividual
has db xref: nif-0000-10172
synonym: The Internet Archive
abbrev: IA
IAO_0000115: An Internet library offering the general public access to historical collections that exist in digital format including texts, audio, moving images, and software. Additionally it provides archived web pages in their collections, and specialized services for adaptive reading and information access for the blind and other persons with disabilities. Founded in 1996 and located in San Francisco, the Archive has been receiving data donations from Alexa Internet and others. In late 1999, the organization started to grow to include more well-rounded collections.

rSeqDiff
type: Resource
type: NamedIndividual
has db xref: OMICS_01968
synonym: rSeqDiff: Detecting differential isoform expression from RNA-Seq data using hierarchical likelihood ratio test
IAO_0000115: An R package that can detect differential gene and isoform expressions from RNA-seq data of multiple biological conditions. The approach considers three cases for each gene: 1) no differential expression, 2) differential expression without differential splicing and 3) differential splicing.

MRI CVPR
type: Resource
type: NamedIndividual
has db xref: nlx_155662
IAO_0000115: Tools processing MRI data with a number of techniques from cvpr conference, including segmentation, matching, features, and classification.

Brain Dynamics Centre
type: Resource
type: NamedIndividual
has db xref: nif-0000-10177
synonym: BDC
IAO_0000115: The Brain Dynamics Centre (BDC) is a network of centers and units. It achieves a unique exploration of the healthy brain and disorders of brain function. It translates these insights into new ways to tailor treatments to the individual. There approach is: "integrative neuroscience" - bringing together clinical observations, theory, and modern imaging technologies. And it's theoretical framework derives from linking physiology, psychology and evolution. Additionally, BDC also actively researches ADHD and conduct disorder, stress and trauma-related problems, depression and anxiety, anorexia nervosa, psychosis (including early onset) and conversion disorders. The research facilities DBC include assessment, rooms, two cognition-brain function laboratories, genotyping and an MRI Suite with 1.5 and 3T GE systems. BDC is the coordinating site for an international network - BRAINnet. It has over 180 members, and coordinates access to the first standardized database on the human brain for scientific purposes: Brain Resource International Database.

ezDICOM
type: Resource
type: NamedIndividual
has db xref: nif-0000-00296
synonym: ezDICOM DICOM Viewer
IAO_0000115: Software designed to display most medical images, including MRI, CT, X-ray, and ultrasound. All versions of ezDICOM can automatically detect the format of a medical image and display it on the screen. The software is easy to use, mature, and can view a wide range of medical images including proprietary formats as well as images in the DICOM standard. The software will also automatically recognize and display Analyze, GE (LX, Genesis), Interfile, Siemens (Magnetom, Somatom) and NEMA images.

Conrad Prebys Center for Chemical Genomics
type: Resource
type: NamedIndividual
has db xref: nif-0000-10180
synonym: CPCCG
IAO_0000115: The Conrad Prebys Center for Chemical Genomics (CPCCG) uses advanced screening technologies to identify high level chemical probes that interact with proteins involved in cellular processes. Optimization of these probes using medicinal chemistry and informatics will form the basis of a new generation of medicines. CPCCG is 1 of 4 Comprehensive Centers chosen nationally to be a part of the Molecular Libraries Probe Program (MLP), which established the Molecular Libraries Probe Production Centers Network (MLPCN). The goal is to produce small molecule probes that allow research into health and disease on the cellular level. CPCCG core services span a range of biochemical and cell-based screens for obtaining hits and provide chemistry resources for optimizing hits into probes or drug development. - Full scale screening capabilities and technology which can provide rapid screening on a broad diversity of assays and detection platforms - Several fully-integrated industrial-scale high-throughput screening (HTS) workstations - HTS microscopy/HCS and novel algorithm development for image analysis - Full hit-to-probe chemistry and exploratory pharmacology - Powerful NMR based Chemical Fragment Screening - Highly integrated informatics infrastructure and efficient data mining capabilities - Protein production facility - Cell production facility for scale-up tissue culture The CPCCG Screening Core can screen 96, 384 or 1536 well formats using either biochemical or cell-based assays, and can process over 300,000 wells per day. Total throughput capacity will climb to over 2 million compounds per day following the opening of Burnhams east coast campus in Lake Nona, Florida.

Sanford-Burnham Neuroscience and Aging Research Center
type: Resource
type: NamedIndividual
has db xref: nif-0000-10181
synonym: Burnham Institute NASCR
synonym: Del E. Webb Neuroscience Aging and Stem Cell Research Center
synonym: NASCR
synonym: Neuroscience and Aging Research Center
synonym: Sanford-Burnham Del E. Webb Neuroscience Aging and Stem Cell Research Center
synonym: Sanford-Burnham NASCR
abbrev: NARC
IAO_0000115: Center that translates basic science discoveries into new treatments to extend lifespan and to combat degenerative disorders associated with aging or development. Their researchers are discovering the etiological pathways as well as small-molecule and stem cell-based treatments to address the clinical unmet need of these patients. The Center uses a team based approach to apply their expertise in stem cells to develop therapies for new treatments for stroke and Parkinson's disease. They are also performing high-throughput screens to identify new molecules to protect the synapses of nervesthe connections between nerves that mediate movement, memory and cognition for Alzheimer's, Parkinson's and autism. By studying the links between Down syndrome and Alzheimer's disease, they are exploring new treatments to improve cognition in both disorders. Their collaborations with clinical partners enable them to test new discoveries in human trials, with a goal to improve the lives of patients and families affected by neurodegenerative disease and aging disorders.

Functional Image Processing software Computational Olio
type: Resource
type: NamedIndividual
has db xref: nif-0000-00298
abbrev: FIASCO
IAO_0000115: Collection of software designed to analyze fMRI data using a series of processing steps. The input is the raw data, and the outputs are statistical brain maps showing regions of neural activation. Corrections for different systematic variations in the k-space (raw) data obtained from an fMRI session (head motion, ghosting, etc) are performed first. The image is then reconstructed (using the Fast Fourier Transform) and statistical analyses run. The user has a great deal of flexibility in choosing which corrections and statistics are executed. FIASCO emphasizes correct statistical models, for example for group comparisons.

AffinDB
type: Resource
type: NamedIndividual
has db xref: nif-0000-02536
has db xref: OMICS_01897
synonym: AffinDB - Affinity Database For Protein-Ligand Complexes
synonym: Affinity Database
IAO_0000115: Database of affinity data for protein-ligand complexes of the Protein Data Bank (PDB) providing direct and free access to the experimental affinity of a given complex structure. Affinity data are exclusively obtained from the scientific literature. As of Thursday, May 01st, 2014, AffinDB contains 748 affinity values covering 474 different PDB complexes. More than one affinity value may be associated with a single PDB complex, which is most frequently due to multiple references reporting affinity data for the same complex. AffinDB provides access to data in three different forms: # Summary information for PDB entry # Affinity information window # Tabular reports

Four-dimensional Ascidian Body Atlas
type: Resource
type: NamedIndividual
has db xref: nif-0000-02529
synonym: FABA: Four-dimensional Ascidian Body Atlas
abbrev: FABA
IAO_0000115: Image resource including ascidian's three-dimensional (3D) and cross-sectional images through the developmental time course. These images were reconstructed from more than 3,000 high-resolution real images collected by confocal laser scanning microscopy (CLSM) at newly defined 26 distinct developmental stages (stages 1-26) from fertilized egg to hatching larva, which were grouped into six periods named the zygote, cleavage, gastrula, neurula, tailbud, and larva periods. The data set will be helpful in standardizing developmental stages for morphology comparison as well as for providing guidelines for several functional studies of a body plan in chordate.

Archaeal and Bacterial ABC Transporter Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02530
synonym: Archaeal and Bacterial ABC Systems database
abbrev: ABCdb
IAO_0000115: ABCdb is a public resource devoted to the ATP-binding Cassette (ABC) transporters encoded by completely sequenced prokaryotic genomes. In order to establish, in a complete genome, the repertory of ABC systems, we have to: i) identify the different partners, ii) assemble the partners in putative systems, and iii) classify the system into the correct functional subfamily (Quentin et al., 2002). The main pitfalls were the identification of loosely conserved domains and the assembly of partners encoded by genes dispersed over the chromosome. In order to face the avalanche of newly sequenced genomes, we decided to also feed into the database the raw prediction issued by this automatic procedure, before time consuming review by an expert occurs. Therefore, the database comprises two sections: CleanDb, for data checked by an expert and AutoDb for raw data. The ABC proteins are involved in a wide variety of physiological processes in Archaea, Bacteria and Eucaryota where they are encoded by large families of paralogous genes. The majority of ABC domains energize the transport of compounds across membranes. In bacteria, ABC transporters are involved in the uptake of a wide variety of molecules, as well as in mechanisms of virulence and antibiotic resistance. In eukaryotes, most of them are involved in drug resistance and in human cell, many are associated with diseases. Sequence analysis reveals that members of the ABC superfamily can be organized into sub-families, and suggests that they have diverged from common ancestral forms. A typical ABC transporter system is composed of an assembly of protein domains that serve different functions: i) two Nucleotide Binding Domains (NBD) that energize transport via ATP hydrolysis, ii) two Membrane Spanning Domains (MSD) that act as a membrane channel for the substrate, and iii) for the importer, a Solute Binding Protein (SBP) that confers substrates specificity on the transporter. The different partners of an ABC system are generally…

Enriched Domain Detector
type: Resource
type: NamedIndividual
has db xref: OMICS_03964
synonym: EDD - Enriched Domain Detector
abbrev: EDD
IAO_0000115: A ChIP-seq peak caller for detection of megabase domains of enrichment.

A Classification of Mobile genetic Elements
type: Resource
type: NamedIndividual
has db xref: biotools:aclame
has db xref: nif-0000-02533
has db xref: OMICS_01528
synonym: ACLAME: A CLAssification of Mobile genetic Elements
abbrev: ACLAME
IAO_0000115: A database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. In addition to provide information on the full genomes and genetic entities, it aims at building a comprehensive classification of the functional modules of MGE's at the protein, gene, and higher levels. Prophinder, a tool dedicated to the detection of prophages in sequenced bacterial genomes, is available on ACLAME.

PELICAN
type: Resource
type: NamedIndividual
has db xref: nlx_154035
has db xref: OMICS_00215
synonym: Pedigree Editor for LInkage Computer ANalysis
IAO_0000115: Software utility for graphically editing the pedigree data files used by programs such as FASTLINK, VITESSE, GENEHUNTER and MERLIN. It can read in and write out pedigree files, saving changes that have been made to the structure of the pedigree. Changes are made to the pedigree via a graphical display interface. The resulting display can be saved as a pedigree file and as a graphical image file.

IDRISI
type: Resource
type: NamedIndividual
synonym: IDRISI Selva
IAO_0000115: Geospatial software for monitoring and modeling the Earth system. Includes tools for GIS, image processing, surface analysis, vertical applications for land change analysis and earth trends exploration, and more.

Cold Spring Harbor Protocols: Collected Resources - Behavioral Assays
type: Resource
type: NamedIndividual
has db xref: nif-0000-10198
synonym: Cold Spring Harbor Protocols - Behavioral Assays
abbrev: CSH Protocols - Behavioral Assays
IAO_0000115: A bibliography of published Behavioral Assays by Cold Spring Harbor Protocols. Cold Spring Harbor Protocols is an interdisciplinary journal providing a definitive source of research methods in cell, developmental and molecular biology, genetics, bioinformatics, protein science, computational biology, immunology, neuroscience and imaging. Each monthly issue details multiple essential methods - a mix of cutting-edge and well-established techniques. Newly commissioned protocols and unsolicited submissions are supplemented with articles based on Cold Spring Harbor Laboratorys renowned courses and manuals. All protocols are up-to-date and presented in a consistent, easy-to-follow format.

Kent State University; Ohio; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100010254
has db xref: grid.258518.3
has db xref: ISNI:0000 0001 0656 9343
has db xref: nlx_65248
has db xref: Wikidata:Q1473615
synonym: Kent State
abbrev: KSU
IAO_0000115: Public university in Ohio providing undergraduate and graduate degrees, as well as access to various institutes.

Cerebellar Gene Regulation in Time and Space Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-10192
synonym: Cb GRiTS Database
abbrev: Cb GRiTS
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Time-series data sets spanning twelve time-points between E12-P9 for exploring cerebellar development of the mouse in time and space. The database contains a number of mutant / wildtype microarray datasets including two complete wildtype microarray time-series (C57BL/6 and DBA/2J). The dataset also includes in situ hybridization and bioinformatic analyses. Exploration of this dataset will allow the investigator to assess differential gene expression profiles from a developing mutant cerebella, to assess the temporal changes in gene expression in the wildtype, and to verify the cellular expression of these genes in images from our in situ hybridization library. Using the database, the investigator can explore the developmental expression or differential expression patterns of a particular gene, or create lists of similarly expression genes by building simple search algorithms. These lists can then be mined across all the datasets in both space and time. Cb GRiTS's current datasets represent gene expression analyses from multiple cerebellar mutant and wildtype single time-point and developmental series.

Cerebellar Platform
type: Resource
type: NamedIndividual
has db xref: nif-0000-10193
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented January 13, 2022. Digital research archive for cerebellar research including mini-reviews of contemporary cerebellar research, list of papers and mathematical models for cerebellar operation.

Chemistry Structures and 3D Molecules at 3Dchem.com
type: Resource
type: NamedIndividual
has db xref: nif-0000-10194
synonym: 3D chem
synonym: 3Dchem
synonym: A to Z Index of Structures at 3Dchem.com
synonym: Chemistry Structures 3D Molecules (at) 3Dchem.com
synonym: Chemistry Structures & 3D Molecules (at) 3Dchem.com
synonym: Chemistry Structures and 3D Molecules
abbrev: 3Dchem.com
IAO_0000115: A database that provides various information about more than 400 drugs, structures and molecules. Links are available for Molecules of the Month, A to Z Index of Structures, Top 50 Prescription Medicines, Gallery, Library of Inorganic Structures (over 1600 structures), Interactive 3D Periodic Table, 3D Stereo Glasses, Desktop Wallpaper, Medical advice and Search 3Dchem.com.

nondetects
type: Resource
type: NamedIndividual
has db xref: biotools:nondetects
has db xref: OMICS_03938
synonym: nondetects - Non-detects in qPCR data
IAO_0000115: Software R package to model and impute non-detects in results of qPCR experiments.Used to directly model non-detects as missing data.

rlsim
type: Resource
type: NamedIndividual
has db xref: OMICS_01965
synonym: rlsim - a package for simulating RNA-seq library preparation with parameter estimation
IAO_0000115: Software package for simulating RNA-seq library preparation with parameter estimation.

vuTools
type: Resource
type: NamedIndividual
has db xref: nlx_156025
IAO_0000115: VUIIS (Vanderbilt University Institute of Imaging Science) Image and Data Analysis Core's data processing tools written for MATLAB and, unless stated otherwise, capable of processing 2D/3D images (matrices). These tools are written for ease of use from within MATLAB.

Chilibot: Gene and Protein relationships from MEDLINE
type: Resource
type: NamedIndividual
has db xref: biotools:chilibot
has db xref: nif-0000-10196
has db xref: OMICS_01176
synonym: Chilibot - Mining PubMed for relationships
abbrev: Chilibot
IAO_0000115: Data analysis service that searches PubMed literature database (abstracts) about specific relationships between proteins, genes, or keywords using a NLP-based text-mining approach. The results are returned as a graph. The synonym database used in Chilibot is available, without fee, for academic use only. Several different search methods are supported including: * searching for relationship between two genes, proteins or keywords * searching for relationships between many genes, proteins, or keywords * searching for relationships between two lists of genes, proteins, or keywords Advanced options include: * Automated hypothesis generation (graph) * Restricting context using keywords * Providing your own synonyms * Modifying synonyms provided by Chilibot * Color coding nodes with gene expression values * Special search: modulation

unifiedWMWqPCR
type: Resource
type: NamedIndividual
has db xref: biotools:unifiedwmwqpcr
has db xref: OMICS_03937
synonym: unifiedWMWqPCR - Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
IAO_0000115: Software package that implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data.

Phelan-McDermid Syndrome Foundation
type: Resource
type: NamedIndividual
has db xref: nif-0000-10203
abbrev: PMSF
IAO_0000115: The Phelan-McDermid Syndrome Foundation, established in 2002, is a 501(c)3 nonprofit group that provides support services for those who have family members affected by 22q13 Deletion Syndrome / Phelan-McDermid Syndrome. It also raises money to further awareness of the syndrome through research and sponsoring an international conference every two years that brings together families, researchers and therapists. The Foundation facilitates connections between families through networking, communications and support services. We also build alliances with other rare diseases groups to expand our reach and exposure. The syndrome, which affects families worldwide, is a rare genetic occurrence and is the result of a damaged or missing protein on the 22nd chromosome. Our Foundation works with researchers who are looking into the cause and possible cure for the syndrome. PMSF's grants and fellowships program is intended to encourage research projects that will advance the development of treatments and cures for PMS. Our mission is to bring together everyone affected by 22q13 Deletion Syndrome/Phelan-McDermid Syndrome to help them through the challenges they face every day and to raise awareness in the medical and research communities.

Database of Cellular Morphologies
type: Resource
type: NamedIndividual
has db xref: nif-0000-10204
IAO_0000115: Database that provides 3-dim reconstructions of thalamic and neocortical neurons. These cells were reconstructed from 80-micron serial sections using a computerized tracing system, as well as a Neurolucida tracing system. The dendritic morphology and diameters were reconstructed in 3-dim using a X 100 objective and correction for tissue shrinkage was included, leading to a theoretical accuracy of 0.1 microns on dendritic diameters. The morphology and the modeling of these cells is described in the references given for each cell. The NEURON geometry of these cells are also available. Anyone is welcome to use these geometries in models.

Depression Alliance
type: Resource
type: NamedIndividual
has db xref: nif-0000-10206
synonym: DA
IAO_0000115: DA works to relieve and to prevent depression by providing information and support services to those who are affected by it via their publications, supporter services and network of self-help groups for people affected by depression. Depression Alliances services help people to understand, work with and recover from symptoms associated with depression. Depression Alliance believes that the stigma and lack of accurate information surrounding depression continues to prevent people from seeking and finding appropriate and vital help when it is required. Early intervention and information are crucial in enabling those affected by depression to recover quickly and critically in preventing further episodes. Informed by the experiences of people with depression and by research, DA works extensively with government agencies and healthcare professionals to improve the service provision for those affected by depression. DA also campaigns to raise awareness amongst the general public about the realities of this severe and enduring illness by organizing a variety of events and initiatives.

HAPLOPAINTER
type: Resource
type: NamedIndividual
has db xref: biotools:haplopainter
has db xref: nlx_154062
has db xref: OMICS_00209
abbrev: HaploPainter
IAO_0000115: A pedigree drawing program, suitable in processing haplotype outputs from GENEHUNTER, ALLEGRO, MERLIN, and SIMWALK (entry from Genetic Analysis Software)

German Collection of Microorganisms and Cell Cultures
type: Resource
type: NamedIndividual
has db xref: DOI:10.13145
has db xref: DOI:10.17616/R3G88X
has db xref: nif-0000-10209
has db xref: r3d100010219
synonym: Leibniz Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
synonym: Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures
abbrev: DSMZ
IAO_0000115: The DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (German Collection of Microorganisms and Cell Cultures) is the most comprehensive biological resource center in Europe. With more than 18.000 microorganisms, 1.200 plant viruses, 600 human and animal cell lines, 770 plant cell cultures and more than 7.100 cultures deposited for the purposes of patenting, DSMZ has demonstrated their obligation to serve science for decades. Main functions of DSMZ are: - to collect, maintain and store microorganisms and cell lines, as well as other biological material of relevance for applied biology, biotechnology, microbiology, teaching and other areas of research and general application; - to keep the scientific and industrial community informed on the contents of the collections by the means of catalogs, special lists, databases or electronic media; - to supply scientists and institutions with DSMZ cultures, in accordance with national and international laws such as the Infektionsschutzgesetz (Act dealing with protection against infection), the Genetic Engineering Act, the Foreign Trade Laws, the Convention on Biological Diversity as well as the DSMZ terms of supply; - to function as an internationally recognized collection center for the deposit of microorganisms, cell lines, and other biological material which have been cited in scientific literature or which are used in national or international test procedures (e.g. type strains, reference strains for national and international quality control regulations or susceptibility tests, strains with special properties, such as the production of enzymes, degradation of pollutants, host strains for plasmids, etc.); - to act as an International Depositary Authority (IDA) for the deposit of biological material for patent purposes according to the Budapest Treaty; - to act, in a confidential manner, as a center for the safe deposit of biological material; - to act as an advisory center for the scientific community and t…

Duke University of North Carolina Brain Imaging and Analysis Center Core Facility
type: Resource
type: NamedIndividual
has db xref: nif-0000-10210
synonym: Brain Imaging and Analysis Center
synonym: Brain Imaging and Analysis Center (BIAC)
synonym: Duke University of North Carolina Brain Imaging and Analysis Center
abbrev: BIAC
abbrev: Duke-UNC BIAC
IAO_0000115: BIAC strives for excellence in its dual mission of research and service. BIAC faculty members are leaders in imaging methodology development, in analysis techniques, as well as in their application in cognitive and clinical neurosciences. In addition, BIAC offers imaging service to other imaging faculty members on campus and at the University of North Carolina in Chapel Hill.

CAMRD
type: Resource
type: NamedIndividual
has db xref: nif-0000-10211
synonym: Center for Advanced Magnetic Resonance Development
synonym: Department of Radiology: Center for Advanced Magnetic Resonance Development
synonym: Duke Center for Advanced Magnetic Resonance Development
synonym: Duke University Medical Center
synonym: DUMC CAMRD
synonym: DUMC Center for Advanced Magnetic Resonance Development
IAO_0000115: Research facility of the Department of Radiology at the Duke University Medical Center (DUMC) providing access to a whole-body, commercially manufactured 3 Tesla (Trio, Siemens Medical Systems) MR Imaging and Spectroscopy System with full research capability. The Center is fully equipped to perform clinical and research MR imaging or spectroscopy studies on humans or large animals. A full range of monitoring, anesthesia, RF coil development, computer and instrumental control facilities as well as MR research technologists and physics/chemistry consultation are available to Department of Radiology researchers and their collaborators.

HOMOZYGOSITYMAPPER
type: Resource
type: NamedIndividual
has db xref: biotools:homozygositymapper
has db xref: nlx_154069
has db xref: OMICS_00123
abbrev: HomozygosityMapper
IAO_0000115: A web-based approach of homozygosity mapping that can handle tens of thousands markers. User can upload their own SNP genotype files to the database. Intuitive graphic interface is provided to view the homozygous stretches, with the ability of zooming into single chromosomes or user-defined chromosome regions. The underlying genotypes in all samples are displayed. The software is also integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. (entry from Genetic Analysis Software)

QuasiSeq
type: Resource
type: NamedIndividual
has db xref: OMICS_01963
IAO_0000115: Software package to apply the QL, QLShrink and QLSpline methods to quasi-Poisson or quasi-negative binomial models for identifying differentially expressed genes in RNA-seq data.

Duke University Medical Center: Duke Image Analysis Laboratory
type: Resource
type: NamedIndividual
has db xref: nif-0000-10213
synonym: DMC DIAL
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Duke Image Analysis Laboratory (DIAL) is committed to providing comprehensive imaging support in research studies and clinical trials to various agencies. The capabilities of the lab include protocol development, site training and certification, and image archival and analysis for a variety of modalities including magnetic resonance imaging, magnetic resonance spectroscopy, computed tomography and nuclear medicine. DIAL uses the latest technologies to analyze Magnetic Resonance Imaging (MRI) data sets of the brain. Currently the lab is engaged in measurement of the hippocampus, amygdala, caudate, ventricular system, and other brain regional volumes. Each of these techniques have undergone a rigorous validation process. The measurements of brain structures provide a useful means of non-invasively testing for changes in the brain of the patient. Changes over time in the brain can be detected, and evaluated with respect to the treatment that the patient is receiving. Magnetic Resonance Spectroscopy (MRS) allows DIAL to obtain an accurate profile of the chemical content of the brain. This sensitive technique can detect small changes in the metabolic state of the brain; changes that vary in response to administration of therapeutic agents. The ability to detect these subtle shifts in brain chemistry allows DIAL to identify changes in the brain with more sensitivity than allowed by image analysis. In this respect, NMR spectroscopy can provide early detection of changes in the brain, and serves to compliment the data obtained from image analysis. Additionally, DIAL also contains SQUID (Scalable Query Utility and Image Database). It is an image management system developed to facilitate image management in research and clinical trials: SQUID offers secure, redundant image storage and organizational functions for sorting and searching digital images for a variety of modalities including MRI, MRS, CAT …

eBioNews - A Subsidiary of eBioCenter
type: Resource
type: NamedIndividual
has db xref: nif-0000-10216
synonym: eBioNews
IAO_0000115: eBioNews specializes in online information services and resource exchanges in the fields of life sciences and biotechnology. By applying its knowledge database and content management system (CMS), eBioNews offers readers and customers the organized and comprehensive information. eBioNews also provides a membership-based service to assist our customers in information and data search, processing, storage, and sharing. Generally, eBioNews covers the following areas: - life science frontiers - news and discussions - features and specials - resources and sourcing - career development - academic and industry - training and education Additionally, eBioNews information is organized into the following two clusters: - News Center: 1. Headlights 2. Research Frontiers 3. General Research 4. Clinical Development 5. Enterprise & Industry 6. Products & Services 7. Investment & Financials 8. Features 9. Newsletter The News Center consists of the elements and mechanisms that enable collecting, organizing, displaying, and delivering life science related information, data, and knowledge. - Resource Center: 1. eBioResources 2. Cooperation 3. Events 4. Human Resources 5. Intellectual Property 6. Finance & Legal 7. Operations 8. Organization 9. Publication The Resource Center is a system that hosts and facilitates the resource-related information between and among multiple parties, especially for promoting cooperation, collaboration, consortium, partnering, joint venture, licensing, out-sourcing, and trading. Sponsors: This resource is supported by eBioCenter Corporation.

Kent State University School of Biomedical Sciences; Ohio; USA
type: Organization
type: NamedIndividual
has db xref: nlx_60057
synonym: KSU School of Biomedicine
abbrev: KSUSBS
IAO_0000115: Graduate school in biomedical sciences at Kent State University with programs in neurosciences, physiology, biological anthropology, cellular molecular, and pharmacology.

sSeq
type: Resource
type: NamedIndividual
has db xref: OMICS_01962
synonym: sSeq - Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size
IAO_0000115: Software package to discover the genes that are differentially expressed between two conditions in RNA-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial (NB) distribution using a shrinkage approach for dispersion estimation. The method of moment (MM) estimates for dispersion are shrunk towards an estimated target, which minimizes the average squared difference between the shrinkage estimates and the initial estimates. The exact per-gene probability under the NB model is calculated, and used to test the hypothesis that the expected expression of a gene in two conditions identically follow a NB distribution.

GERMLINE
type: Resource
type: NamedIndividual
has db xref: biotools:germline
has db xref: nlx_154080
has db xref: OMICS_00202
IAO_0000115: Software application for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

MCMC.qpcr
type: Resource
type: NamedIndividual
has db xref: OMICS_03934
synonym: MCMC.qpcr: Bayesian analysis of qRT-PCR data
IAO_0000115: Software package that implements generalized linear mixed model analysis of qRT-PCR data based on lognormal-Poisson model fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). Also implemented are the lognormal model for higher-abundance data and a classic model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results.

Arabidopsis GeneNet Supplementary DataBase
type: Resource
type: NamedIndividual
has db xref: nif-0000-02539
abbrev: AGNS
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 5, 2017.

CNVrd2
type: Resource
type: NamedIndividual
has db xref: OMICS_03924
synonym: CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data
IAO_0000115: A software package that uses next-generation sequencing data to measure human gene copy number for multiple samples, indentify SNPs tagging copy number variants and detect copy number polymorphic genomic regions.

Experimental Network for Functional Integration: A European Network of Excellence for Data Integration and Systems Biology
type: Resource
type: NamedIndividual
has db xref: nif-0000-10224
synonym: ENFIN
IAO_0000115: ENFIN is a virtual institute to enable systems-level integration of experimental results. It is committed to provide a Europe-wide integration of computational approaches in systems biology. Its objectives are: - To develop a shared approach between traditionally dry and traditionally wet researchers in the area of systems-level interpretation of experimental results - To develop a distributed computational platform this integration and analysis of experimental data - To directly prove that such an approach has scientific value - To encourage and participate in the critical assessment of systems-level approaches - To disseminate knowledge and techniques to other academic researchers worldwide - To disseminate knowledge and techniques to commercial researchers, in particular European SMEs - To train young European researchers from a variety of backgrounds in system-level informatics techniques. The ENFIN Network runs four major platforms: A Joint Research Program covering the fields of Discrete Function Prediction, Network Reconstruction, Systems-Level Modeling, a Provision of Analysis Tools - EnSUITE, a Platform for Data Integration - EnCORE, and training Courses and Workshops on Systems Biology. Sponsors: The ENFIN project is funded by the European Commission within its FP6 Programme, under the thematic area Life sciences, genomics and biotechnology for health,contract number LSHG-CT-2005-518254.

FunDO
type: Resource
type: NamedIndividual
has db xref: nif-0000-10225
synonym: FunDO - Exploring Genes Using Functional Disease Ontology Annotations
IAO_0000115: Tool that takes a list of genes and finds relevant diseases based on statistical analysis of the Disease Ontology annotation database. It accepts Entrez gene ids or gene symbols, separated by tabs, newlines, or commas. This list of genes can be obtained by microarray, proteomics, sequencing or other high-throughput screening methods.

TaLasso
type: Resource
type: NamedIndividual
has db xref: OMICS_00417
IAO_0000115: Tool for quantification of human miRNA-mRNA Interactions. TaLasso is also available as Matlab or R code.

MatrixDB
type: Resource
type: NamedIndividual
has db xref: biotools:matrixdb
has db xref: nif-0000-10226
has db xref: r3d100010672
synonym: Extracellular Matrix Interactions Database
synonym: MatrixDB: Extracellular Matrix Interactions Database
IAO_0000115: Freely available database focused on interactions established by extracellular proteins and polysaccharides, taking into account the multimeric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers). MatrixDB is an active member of the International Molecular Exchange (IMEx) consortium and has adopted the PSI-MI standards for annotating and exchanging interaction data. It includes interaction data extracted from the literature by manual curation, and offers access to relevant data involving extracellular proteins provided by the IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database. The database reports mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules. Interactions with lipids and cations are also reported. MatrixDB is focused on mammalian interactions, but aims to integrate interaction datasets of model organisms when available. MatrixDB provides direct links to databases recapitulating mutations in genes encoding extracellular proteins, to UniGene and to the Human Protein Atlas that shows expression and localization of proteins in a large variety of normal human tissues and cells. MatrixDB allows researchers to perform customized queries and to build tissue- and disease-specific interaction networks that can be visualized and analyzed with Cytoscape or Medusa. Statistics (2013): 2283 extracellular matrix interactions including 2095 protein-protein and 169 protein-glycosaminoglycan interactions.

Farsight Toolkit
type: Resource
type: NamedIndividual
has db xref: nif-0000-10227
synonym: FARSIGHTWiki
abbrev: FARSIGHT
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. A collection of software modules for image data handling, pre-processing, segmentation, inspection, editing, post-processing, and secondary analysis. These modules can be scripted to accomplish a variety of automated image analysis tasks. All of the modules are written in accordance with software practices of the Insight Toolkit Community. Importantly, all modules are accessible through the Python scripting language which allows users to create scripts to accomplish sophisticated associative image analysis tasks over multi-dimensional microscopy image data. This language works on most computing platforms, providing a high degree of platform independence. Another important design principle is the use of standardized XML file formats for data interchange between modules.

Adobe FormsCentral
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_156027
synonym: Adobe Forms Central
abbrev: FormsCentral
IAO_0000115: Service to create PDF and web forms.

ALFRED
type: Resource
type: NamedIndividual
has db xref: nif-0000-02541
has db xref: r3d100012700
synonym: ALlele FREquency Database
synonym: The ALlele FREquency Database
IAO_0000115: A public curated compilation of allele frequency data on anthropologically defined human population samples linked to the molecular genetics-human genome databases. Only data on well defined population samples that are large enough to yield reasonably accurate frequencies and for polymorphisms sufficiently defined to be replicable can be included in ALFRED. Researchers wishing to have their data entered into ALFRED should contact them. Initially, ALFRED contained primarily data generated in the laboratories of K.K. and J.R. Kidd in the Department of Genetics at Yale, including extensive unpublished data. Data from the published literature are being entered into ALFRED in a systematic way, with a focus on polymorphisms studied in many different populations. ALFRED is distinct from such databases as dbSNP, which catalogs sequence variation. ALFRED's focus is on allele frequencies in diverse anthropologically defined populations. It is not a compendium of human DNA polymorphisms but of frequencies of selected polymorphisms with an emphasis on those that have been studied in multiple populations. All of the data in ALFRED are considered to be in the public domain and available for use in research and teaching. ALFRED provides easy searching options including versatile "Keyword search" and also has numerous summary tables providing quick overviews of contents by chromosome, population, average heterozygosity, Fst and others, all available under various tabs from the ALFRED homepage.

Generic Model Organism Database Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-10234
synonym: Generic Model Organism Database
abbrev: GMOD
IAO_0000115: A collection of open source software tools for creating and managing genome-scale biological databases. GMOD is made up databases, applications, and adaptor software that connects these components together. You can use it to create a small laboratory database of genome annotations, or a large web-accessible community database. At first GMOD just featured model organisms but now any organism with any kind of sequence associated with it is a good candidate as a subject for a GMOD database. There are GMOD databases with just protein sequence in them, with EST sequence only, those that are concerned primarily with gene expression, and even those dedicated to collections of RNA sequence. They have also heard of GMOD databases for oligonucleotides and plasmids.

Harvard Medical School, Department of Systems Biology: The Megason Lab - MegaCapture Software
type: Resource
type: NamedIndividual
has db xref: nif-0000-10242
synonym: MegaCapture
IAO_0000115: MegaCapture is a VisualBasic macro developed for automating the acquisition of in toto image sets. It is useable on Zeiss microscopes using LSM v4.x software (pre-Zen). MegaCapture can automatically acquire image sets across any combination of dimensions including x, y, z, time, color, x-tile, y-tile, row, and column. Images are exported on the fly and can be compressed allowing very large (100,000 images) image sets to be captured. Sponsors: MegaCapture is supported by Harvard University.

UKU Neuroscience and Neurology Links
type: Resource
type: NamedIndividual
has db xref: nif-0000-00099
synonym: UKU Neurology Links
synonym: UKU Neuroscience Links
IAO_0000115: Portal of neuroscience and neurology resources pertaining to the University of Eastern Finland.

AlterORF
type: Resource
type: NamedIndividual
has db xref: nif-0000-02543
synonym: Alternate Open Reading Frame
synonym: Alternate ORF
synonym: AlternateORF
IAO_0000115: Some of the alternate ORFs predicted to be genes by automatic annotation programs are subsequently culled by human curators; however, many escape even expert curation. AlterORF provides a database of such potentially mis-annotated ORFs. It has warehoused all alternate ORFs in fully sequenced microbial genomes that have significant hits with one or more of the protein features described in CDD, COG, KOG, PFAM, PRK and SMART in which the corresponding annotated genes that have been deposited in the databases have no such characteristics Some of the alternate ORFs that have significant protein features (CDD, COG, etc.) are associated with annotated genes that also have significant protein features, making it moot which is the real gene. Some of these instances are potentially dual function genes in which both ORFs may be expressed (e.g. ref). AlterORF identifies these possibilities for further computational and experimental investigation. All data present in AlterORF and database files and tables can be download in a compressed file. Please take in account that the complete database has ~ 300 GB. AlterORF operate 132 cpu cluster contributed by Microsoft as part of a sponsored research program. The Center for Bioinformatics and Genome Biology is a member of the Ibero- Latin American Bioinformatics Network (RIB), the Virtual Institute for Integrative Biology (VIIB) and the E-science Infrastructure Shared Between Europe and Latin America (EELA-2).

Sea Urchin Genome Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-10253
synonym: HGSC Sea Urchin Genome Project
synonym: Sea Urchin
IAO_0000115: Provides informationa about Genome of California Purple Sea Urchin, one species (Strongylocentrotus purpuratus) of which has been sequenced and annotated by Sea Urchin Genome Sequencing Consortium led by HGSC. Reports sequence and analysis of genome of sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology.

Altmetric API
type: Resource
type: NamedIndividual
has db xref: nlx_156028
synonym: The Altmetric API
IAO_0000115: Application programming interface that gives one programmatic access to the article level metrics data associated with articles and datasets collected by Altmetric. It extracts, disambiguates and collates mentions of scholarly works online, allowing one to focus on one's core product.

Genome Network Platform
type: Resource
type: NamedIndividual
has db xref: nif-0000-10237
abbrev: GNP
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Integrated database of experiment data generated by participating research institutes and public databases relating to: 1) transcription starting position of human genes in the human genome, 2) conjunction to control region on transcriptional factors and the human genome 3) protein-protein interaction with a central focus on transcription factors organized for use in genome level research. Gene Search is the function to search the integrated database by using keywords and public IDs. The search results can be visualized by: * Genome Explorer : provides annotation of landmarks (genes, transcription start sites, etc.) aligned in accordance with their genome locations. * PPI Network : provides a graphical view of protein-protein interaction (PPI) network from the experimental data generated under the project and the public datasets. * Expression Profile : clusters genes by expression pattern and display the result with heatmap. The function provides genes which have relation of coregulation and anti-coregulation. * Comparison Viewer : This function gives the view to compare the genomic regions between human and mouse homologous genes. The viewer shows the distribution of transcription start sites (TSS) as the way of separable by tissues or time points with other landmarks on genome region. * Gene Stock : This is the function to save the gene list that you are interested until the session is closed.

pairedBayes
type: Resource
type: NamedIndividual
has db xref: OMICS_01958
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10th,2023. An R code for Bayesian modeling of paired RNA-seq experiments.

RNASeqBias
type: Resource
type: NamedIndividual
has db xref: OMICS_01957
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10th,2023. An R software package for detecting and correcting biases in RNA-Sequencing data.

LAMP
type: Resource
type: NamedIndividual
has db xref: nlx_154103
synonym: Linkage and Association Modeling in Pedigrees
IAO_0000115: Software for linkage and association modeling in pedigrees that uses a maximum likelihood model to extract information on genetic linkage and association from samples of unrelated individuals, sib pairs, trios and larger pedigrees (Li et al, 2005; Li et al, 2006). It provides estimates of genetic model parameters and powerful tests of association in settings where population stratification is not a concern.

George Mason University: Krasnow Institute for Advanced Study
type: Resource
type: NamedIndividual
has db xref: nif-0000-10239
synonym: GMU Kransnow
IAO_0000115: The Krasnow Institute seeks to expand understanding of mind, brain, and intelligence by conducting research at the intersection of the separate fields of cognitive psychology, neurobiology, and the computer-driven study of artificial intelligence and complex adaptive systems. These separate disciplines increasingly overlap and promise progressively deeper insight into human thought processes. The Institute also examines how new insights from cognitive science research can be applied for human benefit in the areas of mental health, neurological disease, education, and computer design. It is this informed access to mind and brain that is the core of the mission of The Krasnow Institute. While their goals and tools are scientific, they also are fully cognizant of the applications of the results for the benefit of mankind, in areas like mental health, neurological diseases, and computer design. In asking the major questions they realized the necessity of being flexible, innovative, and trans-disciplinary. Therefore, they became dedicated to bringing together scholars from a wide variety of specialties and providing a milieu where they can be both productive and interactive. This institute will provide these researchers with the tools required to move ahead and create an environment of optimal scientific integrity coupling innovation with risk taking. The Krasnow institute is especially attuned to the deep insights from evolutionary biology, which is at the root of understanding all organismic functions including cognition; computer studies of complex systems, which present a revolution in our ability to deal with the world of interactive agents; and a long history of cognitive psychology, which provides a huge data base of human abilities and responses. It also continues to develop its long-term research program based on the contributions of George Mason University faculty holding joint appointments at Krasnow and other GMU academic departments. Additionally, the Krasno…

Hanchuan Peng Shared Software
type: Resource
type: NamedIndividual
has db xref: nif-0000-10241
IAO_0000115: Online portal of the software resources provided by Hanchuan Peng's lab. Program functions include 3D image rendering, MATLAB toolboxs, image annotator, and cell explorer atlas and building tools.

plateCore
type: Resource
type: NamedIndividual
has db xref: OMICS_05641
synonym: plateCore - Statistical tools and data structures for plate-based flow cytometry
IAO_0000115: Software that provides basic S4 data structures and routines for analyzing plate based flow cytometry data.

King's College London; London; United Kingdom
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100009360
has db xref: grid.13097.3c
has db xref: ISNI:0000 0001 2322 6764
has db xref: nlx_60659
has db xref: Wikidata:Q245247
synonym: King's College
abbrev: KCL
IAO_0000115: Public research university located in London, United Kingdom that offers undergraduate, graduate, and professional degree programs in medicine, economics, social sciences, etc.

Internet Atlas of Histology
type: Resource
type: NamedIndividual
has db xref: nif-0000-10251
synonym: UICU Histology Atlas
IAO_0000115: This portal leads to the Internet Atlas of Histology. This atlas allows you to explore the complete set of histological specimens that features many excellent plastic sections prepared by Aulikki Kokko-Cunningham, M.D. Also called University of Illnois at Urbana-Champaign, the College of Medicine: Internet Atlas of Histology Over 1000 labeled histological features are labeled and have accompanying functional descriptions. All of this information is accessible though an alphabetical index and a search engine. This resource has images categorized in: - Slides: Links to all of the specimens - Objects:Index of histological features Sponsors: This resource is supported by UIUC.

Kidney and Urinary Pathway Knowledge Base
type: Resource
type: NamedIndividual
has db xref: nlx_154134
synonym: Kidney & Urinary Pathway Knowledge Base
abbrev: KUPKB
IAO_0000115: A collection of omics datasets (mRNA, proteins and miRNA) that have been extracted from PubMed and other related renal databases, all related to kidney physiology and pathology giving KUP biologists the means to ask queries across many resources in order to aggregate knowledge that is necessary for answering biological questions. Some microarray raw datasets have also been downloaded from the Gene Expression Omnibus and analyzed by the open-source software GeneArmada. The Semantic Web technologies, together with the background knowledge from the domain's ontologies, allows both rapid conversion and integration of this knowledge base. SPARQL endpoint http://sparql.kupkb.org/sparql The KUPKB Network Explorer will help you visualize the relationships among molecules stored in the KUPKB. A simple spreadsheet template is available for users to submit data to the KUPKB. It aims to capture a minimal amount of information about the experiment and the observations made.

Neurological Disorder Resources
type: Resource
type: NamedIndividual
has db xref: nif-0000-00100
IAO_0000115: Online portal resource with hierarchically-organized list of links to web resources concerning neurological disorders.

Animal QTLdb
type: Resource
type: NamedIndividual
has db xref: nif-0000-02550
has db xref: r3d100010744
synonym: Animal QTL database
synonym: Animal Quantitative Trait Loci (QTL) database
synonym: Animal Quantitative Trait Loci database
synonym: AnimalQTLdb
IAO_0000115: Database of trait mapping data, i.e. QTL (phenotype / expression, eQTL), candidate gene and association data (GWAS) and copy number variations (CNV) mapped to livestock animal genomes, to facilitate locating and comparing discoveries within and between species. New data and database tools are continually developed to align various trait mapping data to map-based genome features, such as annotated genes. QTLdb is open to house QTL/association date from other animal species where feasible. Most scientific journals require that any original QTL/association data be deposited into public databases before paper may be accepted for publication. User curator accounts are provided for direct data deposit. Users can download QTLdb data from each species or individual chromosome.

cPath
type: Resource
type: NamedIndividual
has db xref: nif-0000-10292
synonym: cPath2
IAO_0000115: Data management software that runs the Pathway Commons web service. It makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Main features: * Import pipeline capable of aggregating pathway and interaction data sets from multiple sources, including: MINT, IntAct, HPRD, DIP, BioCyc, KEGG, PUMA2 and Reactome. * Import/Export support for the Proteomics Standards Initiative Molecular Interaction (PSI-MI) and the Biological Pathways Exchange (BioPAX) XML formats. * Data visualization and analysis via Cytoscape. * Simple HTTP URL based XML web service. * Complete software is freely available for local install. Easy to install and administer. * Partly funded by the U.S. National Cancer Institute, via the Cancer Biomedical Informatics Grid (caBIG) and aims to meet silver-level requirements for software interoperability and data exchange.

AntiJen
type: Resource
type: NamedIndividual
has db xref: nif-0000-02551
synonym: AntiJen - A Kinetic
synonym: AntiJen Database
synonym: AntiJen Database v2.0
synonym: AntiJen v2.0
synonym: Thermodynamic and Cellular Database
IAO_0000115: Database with quantitative binding data for peptides binding to various cells including MHC Ligand, TCR-MHC complexes, T-cell epitopes, TAP, B-cell, and immunological protein-protein interactions. Information in each entry includes peptide libraries, copy numbers, and diffusion coefficient data.

Medical Image Processing and Visualization in Virtual Environments
type: Resource
type: NamedIndividual
has db xref: nlx_155663
IAO_0000115: This resouce will centralize development of tools for interaction with medical imaging data in immersive virtual environments (based on the Vizard platform).

Sheep Brain Atlas
type: Resource
type: NamedIndividual
has db xref: nif-0000-00102
synonym: The Navigable Atlas of the Sheep Brain
IAO_0000115: Online portal and image database of coronal sections of the sheep brain. Each image contains stained sections of cell bodies and myelinated fibers; nuclei and tracts are labeled.

Database for Antisense Oligonucleotides Selection and Design
type: Resource
type: NamedIndividual
has db xref: nif-0000-02552
synonym: AOBase
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. AOBase is a database for antisense oligonucleotides (AOs) selection and design. AOBase is a database developed to facilitate Antisense Oligonucleotides (ODNs) selection for gene expression modulation and to provide a free data source for computer aided ODNs design. Information about valid and invalid ODNs reported in literature are collected and stored in the database, including oligo sequences, target sequences, secondary structures of the target sites, oligo activity measured, and the assay type used for activity measurement. The details on target RNA molecules and reference literature can be explored through the hyperlinks linked to GenBank and PubMed respectively. Each record can be searched for via two web retrieval interfaces: 1) TargetSearch interface, which allows users to query ODNs by name, accession number, or only imprecise descriptions of its target RNA; 2) AOSearch interface, which allows users to search ODNs with several parameters combined, such as oligo activity measured, oligo concentration applied, and motifs involved in oligo sequences. With these two retrieval interfaces, AOBase can be used to select effective ODNs for gene function exploration without expensive in vitro screening experiments, and contribute to mining rules for rational ODNs design. A user friendly interface to encourage data submission is provided.

Dynamic Brain Platform
type: Resource
type: NamedIndividual
has db xref: nif-0000-10262
has db xref: nif-0000-10377
has db xref: SCR_001812
synonym: Dynamic Brain PF
synonym: Neuro-Imaging Platform
abbrev: DBPF
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19. 2022. Platform to promote studies on dynamic principles of brain functions through unifying experimental and computational approaches in cellular, local circuit, global network and behavioral levels. Provides services such as data sets, popular research findings and articles and current developments in field. This site has been archived since FY2019 and is no longer updated.

International Neuroinformatics Coordinating Facility: Blue Gene/L Access
type: Resource
type: NamedIndividual
has db xref: nif-0000-10263
synonym: INCF Blue Gene/L Access
IAO_0000115: Through this site, INCF provides he neuroinformatics community with access to an IBM Blue Gene/L supercomputer. INCF owns a share of a BlueGene/L (BG/L) supercomputer located at the Parallel Computer Center (PDC) at The Royal Institute of Technology (KTH) in Stockholm. Allocations are now available through the INCF Secretariat. During an initial evaluation phase, a limited numbers of large-scale computing projects will be selected, based on the suitability of the project for supercomputing. Research groups with limited access to supercomputers at their home institutions are given priority. Approved projects are regularly re-evaluated. New projects are approved based on availability and usage load of the BG/L. The Blue Gene/L supercomputer project is aimed at expanding the horizon of high-performance computing to unprecedented levels of scale and performance. Blue Gene/L is the first supercomputer in the Blue Gene family. The full Blue Gene/L consists of 64 racks containing 65,536 high-performance compute nodes. Each node (nodes and chips are the same in the Blue Gene system) contains two embedded 32-bit PowerPC processors. Furthermore, the same chip that is used for compute nodes is also used for the 1,024 I/O nodes. A three-dimensional torus network and a collective network are used to interconnect all nodes. The full system contains 33 terabytes of main memory; it is designed to achieve 183.5 teraflops peak performance using one of the processors of each node for computation and the other processor for communication, and 367 teraflops using both processors for computation. Another key architectural feature of this supercomputer is the link chip component and five Blue Gene/L networks, the PowerPC 440 core and floating-point enhancements, the on-chip and off-chip distributed memory system, the node- and system-level design for high reliability, and the comprehensive approach to fault isolation. One of the key objectives in Blue Gene/L design is to achieve cost/perf…

MUlti SImulation Coordinator
type: Resource
type: NamedIndividual
has db xref: nif-0000-10265
synonym: INCF MUSIC simulator
abbrev: MUSIC
IAO_0000115: Software that allows large scale neuron simulators to communicate during runtime. It allows exchange of data among parallel applications in a cluster environment, interconnects large-scale neuronal network simulators with each other or with other tools, participates in multi-simulations, and is continuously developed and extended. Three simulators currently have MUSIC interfaces: Moose, NEURON and NEST. Three applications execute in parallel while exchanging data via MUSIC. The software interface promotes interoperability by allowing models written for different simulators to be simulated together in a larger system. It enables re-usability of models or tools by providing a standard interface. As data are distributed over a number of processors, it is non-trivial to coordinate data transfer so that it reaches the correct destination at the correct time. Current and future simulators can make use of MUSIC - compliant general purpose tools and participate in multi-simulations, for example when: * Different parts of a complex nervous system model are optimally implemented in different simulators, and need to communicate with each other. * Post-processing of generated data is needed, where the amounts of data are too large for intermediate storage, and requires the simulator to pass the data directly to the post-processing module. A standard interface enables straight-forward independent third-party development and community sharing of interoperable software tools for parallel processing. * Library and utilities are written in C++, uses MPI. * It is possible to add a MUSIC interface to existing simulators. * Works independently, no assumptions are made about other applications to facilitate development of general purpose tools. * Performance Data transport with high bandwidth and low latency.

PLINK
type: Resource
type: NamedIndividual
has db xref: nlx_154200
has db xref: OMICS_00206
has db xref: SCR_021271
synonym: PLINK 1.9
synonym: plink - Whole genome association analysis toolset
synonym: PLINK/SEQ
IAO_0000115: Open source whole genome association analysis toolset, designed to perform range of basic, large scale analyses in computationally efficient manner. Used for analysis of genotype/phenotype data. Through integration with gPLINK and Haploview, there is some support for subsequent visualization, annotation and storage of results. PLINK 1.9 is improved and second generation of the software.

King Abdullah University of Science and Technology; Makkah Province; Saudi Arabia
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100004052
has db xref: grid.45672.32
has db xref: ISNI:0000 0001 1926 5090
has db xref: nlx_156708
has db xref: Wikidata:Q1463036
synonym: King Abdullah University of Science and Technology
abbrev: KAUST
IAO_0000115: Private research university in Thuwal, Saudi Arabia that offers undergraduate and graduate degree programs in Biological and Environmental Science and Engineering (BESE), Computer, Electrical, and Mathematical Science and Engineering (CEMSE), and Physical Science and Engineering (PSE).

MACH 1.0
type: Resource
type: NamedIndividual
has db xref: nlx_154202
has db xref: OMICS_00064
synonym: MArkov Chain Haplotyper MINIMAC
synonym: MArkov Chain Haplotyping
IAO_0000115: A Markov Chain based software tool for haplotyping, genotype imputation and disease association analysis that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.

International Union of Physiological Sciences: Physiome Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-10266
synonym: IUPS Physiome
IAO_0000115: The Physiome Project is a worldwide public domain effort to provide a computational framework for understanding human and other eukaryotic physiology. It aims to develop integrative models at all levels of biological organization, from genes to the whole organism via gene regulatory networks, protein pathways, integrative cell function, and tissue and whole organ structure/function relations. Additionally, an important goal of the project is to develop applications for teaching physiology. Current projects include the development of: - ontologies to organize biological knowledge and access to databases - markup languages to encode models of biological structure and function in a standard format for sharing between different application programs and for re-use as components of more comprehensive models - databases of structure at the cell, tissue and organ levels - software to render computational models of cell function such as ion channel electrophysiology, cell signaling and metabolic pathways, transport, motility, the cell cycle, etc. in 2 & 3D graphical form - software for displaying and interacting with the organ models which will allow the user to move across all spatial scales Sponsors: This project is supported by the International Union of Physiological Sciences (IUPS), the IEEE Engineering. in Medicine and Biology (EMBS), and the International Federation for Medical and Biological Engineering (IFMBE)

Brainstorm
type: Resource
type: NamedIndividual
has db xref: nif-0000-10267
synonym: brainstorm3
IAO_0000115: Software as collaborative, open source application dedicated to analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and animal invasive neurophysiology. User-Friendly Application for MEG/EEG Analysis.

MetaBase
type: Resource
type: NamedIndividual
has db xref: biotools:metabase
has db xref: nif-0000-10293
synonym: MetaBase (MB)
abbrev: MB
IAO_0000115: User-contributed list of biological databases available on the internet. Currently there are 1,801 entries, each describing a different database. The databases are described in a semi-structured way by using templates and entries can carry various user comments and annotations. Entries can be searched, listed or browsed by category. The site uses the same MediaWiki technology that powers Wikipedia, The Mediawiki system allows users to participate on many different levels, ranging from authors and editors to curators and designers. MetaBase aims to be a flexible, user-driven (user-created) resource for the biological database community. The main focuses of MetaBase are: * As a basic requirement, MB contains a list of databases, URLs and descriptions of the most commonly used biological databases currently available on the internet. * The system should be flexible, allowing users to contribute, update and maintain the data in different ways. * In the future we aim to generate more communication between the database developer and user communities.

PennSeq
type: Resource
type: NamedIndividual
has db xref: biotools:pennseq
has db xref: OMICS_01946
IAO_0000115: Software for isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution. Instead of making parametric assumptions, they give adequate weight to the underlying data by the use of a non-parametric approach. The rationale is that regardless what factors lead to non-uniformity, whether it is due to hexamer priming bias, local sequence bias, positional bias, RNA degradation, mapping bias or other unknown reasons, the probability that a fragment is sampled from a particular region will be reflected in the aligned data. This empirical approach thus maximally reflects the true underlying non-uniform read distribution.

Intute: The Best Web Resources For Education and Research
type: Resource
type: NamedIndividual
has db xref: nif-0000-10268
synonym: Intute
IAO_0000115: Intute is a free online service that helps you to find the best web resources for your studies and research. It was created in response to users' needs and the changing Internet information environment. With millions of resources available on the Internet, it can be difficult to find useful material. The Intute subject specialists review and evaluate thousands of resources to help you choose the key websites in your subject. Intute can also help you develop your Internet research skills through our Virtual Training Suite tutorials, written by lecturers and librarians from universities across the UK. The discipline focus of their service is delivered through four new subject groups: * Science, Engineering and Technology (including geography) * Arts and Humanities * Social Sciences * Health and Life Sciences Intute is created by a consortium of seven universities, working together with a whole host of partners. The Intute consortium includes: * University of Birmingham * University of Bristol * Heriot-Watt University * The University of Manchester * Manchester Metropolitan University * University of Nottingham * University of Oxford Sponsors: Intute is funded by the Joint Information Systems Committee (JISC).

APHIDBASE
type: Resource
type: NamedIndividual
has db xref: nif-0000-02554
synonym: Aphid Genome Database
synonym: The Aphid Genome Database
abbrev: AphidBase
IAO_0000115: Aphid genome database. Facilitates community annotation of pea aphid genome by International Aphid Genomics Consortium (IAGC). It aims to store recently acquired genomic resources on aphids and compare them to other insect resources as functional annotation tools. AphidBase Information System designed to organize and distribute genomic data and annotations for large international community was constructed using open source software tools from Generic Model Organism Database (GMOD).

JENA: A Semantic Web Framework for Java
type: Resource
type: NamedIndividual
has db xref: nif-0000-10271
synonym: Apache Jena
abbrev: Jena
IAO_0000115: Java framework for building Semantic Web applications, it provides a collection of tools and Java libraries to help you to develop semantic web and linked-data apps, tools and servers. It provides extensive Java libraries for helping developers develop code that handles RDF, RDFS, RDFa, OWL and SPARQL in line with published W3C recommendations. Jena includes a rule-based inference engine to perform reasoning based on OWL and RDFS ontologies, and a variety of storage strategies to store RDF triples in memory or on disk. The Jena Framework includes: * an API for reading, processing and writing RDF data in XML, N-triples and Turtle formats; * an ontology API for handling OWL and RDFS ontologies; * a rule-based inference engine for reasoning with RDF and OWL data sources; * stores to allow large numbers of RDF triples to be efficiently stored on disk; * a query engine compliant with the latest SPARQL specification * servers to allow RDF data to be published to other applications using a variety of protocols, including SPARQL In April 2012, Jena graduated from the Apache incubator process and was approved as a top-level Apache project.

FACTA+.
type: Resource
type: NamedIndividual
has db xref: biotools:facta_plus
has db xref: nif-0000-10272
has db xref: OMICS_01181
synonym: Finding Associated Concepts with Text Analysis
abbrev: FACTA+
IAO_0000115: Text mining tool to discover associations between biomedical concepts from MEDLINE articles. Use the service from your browser or via a Web Service. The whole MEDLINE corpus containing more than 20 million articles is indexed with an efficient text search engine, and it allows you to navigate such associations and their textual evidence in a highly interactive manner - the system accepts arbitrary query terms and displays relevant concepts immediately. A broad range of important biomedical concepts are covered by the combination of a machine learning-based term recognizer and large-scale dictionaries for genes, proteins, diseases, and chemical compounds. There is also a FACTA+ visualization service that can be found here: http://www.nactem.ac.uk/facta-visualizer/

Prediction of Amyloid Structure Aggregation
type: Resource
type: NamedIndividual
has db xref: biotools:pasta
has db xref: OMICS_03861
synonym: PASTA 2.0
synonym: Prediction of amyloid structure aggregation
abbrev: PASTA
IAO_0000115: Online interface that utilizes an algorithm to predict the most aggregation-prone portions and the corresponding beta-strand inter-molecular pairing for a given input sequence. Users can paste the sequence into the interface and output the appropriate sequence.

Journal of Cerebral Blood Flow and Metabolism
type: Resource
type: NamedIndividual
has db xref: nif-0000-10274
abbrev: JCBFM
IAO_0000115: The Journal of Cerebral Blood Flow & Metabolism stands at the interface between basic and clinical neurovascular research, and features timely and relevant research highlighting experimental, theoretical, and clinical aspects of brain circulation, metabolism and imaging. The journal is relevant to any physician or scientist with an interest in brain function, cerebrovascular disease, cerebral vascular regulation and brain metabolism, including neurologists, neurochemists, physiologists, pharmacologists, anesthesiologists, neuroradiologists, neurosurgeons, neuropathologists and neuroscientists. On this website, you will find the full text of articles published online weekly, in advance of print, the current issue and an archive of previous issues. You can also find general information about the journal, and more detailed information for readers, authors, referees, librarians, advertisers, and journalists. Most articles are published online before they appear in print. New papers are uploaded weekly to the Advance online publication (AOP) page. The online publication date is specified for each paper; these versions are identical to the printed version in every respect and may be cited using the digital object identifier (DOI).

TANGO
type: Resource
type: NamedIndividual
has db xref: biotools:tango
has db xref: OMICS_03859
IAO_0000115: A computer algorithm to predict aggregation nucleating regions in proteins as well the effect of mutations and environmental conditions on the aggregation propensity of these regions.

DNACLUST
type: Resource
type: NamedIndividual
has db xref: OMICS_01955
synonym: DNAClust
IAO_0000115: Software program for clustering large number of short similar DNA sequences. It was originally designed for clustering targeted 16S rRNA pyrosequencing reads.

InterMine
type: Resource
type: NamedIndividual
has db xref: biotools:intermine
has db xref: OMICS_03840
IAO_0000115: An open source data warehouse system built for the integration and analysis of complex biological data that enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding data. InterMine includes a user-friendly web interface that works "out of the box" and can be easily customized for specific needs, as well as a powerful, scriptable web-service API to allow programmatic access to data.

MSClust
type: Resource
type: NamedIndividual
has db xref: OMICS_01954
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10th,2023. An M software package for Clustering 16S rRNA sequences into operational taxonomic units (OTUs). The download link contain the package and some benchmark data sets.

ReCount - A multi-experiment resource of analysis-ready RNA-seq gene count datasets
type: Resource
type: NamedIndividual
has db xref: OMICS_01953
abbrev: ReCount
IAO_0000115: RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, they combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward.

Neurolucida
type: Resource
type: NamedIndividual
has db xref: nif-0000-10294
synonym: MBF Neurolucida
IAO_0000115: Neurolucida is advanced scientific software for brain mapping, neuron reconstruction, anatomical mapping, and morphometry. Since its debut more than 20 years ago, Neurolucida has continued to evolve and has become the worldwide gold-standard for neuron reconstruction and 3D mapping. Neurolucida has the flexibility to handle data in many formats: using live images from digital or video cameras; stored image sets from confocal microscopes, electron microscopes, and scanning tomographic sources, or through the microscope oculars using the patented LucividTM. Neurolucida controls a motorized XYZ stage for integrated navigation through tissue sections, allowing for sophisticated analysis from many fields-of-view. Neurolucidas Serial Section Manager integrates unlimited sections into a single data file, maintaining each section in aligned 3D space for full quantitative analysis. Neurolucidas neuron tracing capabilities include 3D measurement and reconstruction of branching processes. Neurolucida also features sophisticated tools for mapping delineate and map anatomical regions for detailed morphometric analyses. Neurolucida uses advanced computer-controlled microscopy techniques to obtain accurate results and speed your work. Plug-in modules are available for confocal and MRI analysis, 3D solid modeling, and virtual slide creation. The user-friendly interface gives you rapid results, allowing you to acquire data and capture the full 3D extent of neurons and brain regions. You can reconstruct neurons or create 3D serial reconstructions directly from slides or acquired images, and Neurolucida offers full microscope control for brightfield, fluorescent, and confocal microscopes. Its added compatibility with 64-bit Microsoft Vista enables reconstructions with even larger images, image stacks, and virtual slides. Adding the Solid Modeling Module allows you to rotate and view your reconstructions in real time. Neurolucida is available in two separate versions Standard and Works…

Living Links: Center for the Advanced Study of Ape and Human Evolution
type: Resource
type: NamedIndividual
has db xref: nif-0000-10280
synonym: Living Links
IAO_0000115: The primary mission of the Living Links Center is to study human evolution by investigating our close genetic, anatomical, cognitive, and behavioral similarities with great apes. The Living Links Center was established for primate studies that shed light on human behavioral evolution. It is an integrated part of the Yerkes National Primate Research Center, which is the nation's oldest and largest primate center. The Living Links Center is home to two socially housed groups of chimpanzees and two socially housed groups of capuchin monkeys. The research conducted in this center is broken down into four categories: - Chimpanzees: Chimpanzee research at the Living Links Center is conducted at the Yerkes Field Station, which is home to two socially housed chimpanzee groups known as FS1 and FS2. Each mixed gender group of 12 individuals lives in a large outdoor enclosure with wooden climbing structures and play objects attached to an indoor sleeping area. FS1 and FS2 can hear, but not see each other because their enclosures are ~200m apart and separated by a small hill. Chimpanzee research is conducted on a volunteer basis with members of each group. - Elephants: This newly found presence of mirror self-recognition in elephants, previously predicted due to their well-known social complexity, is thought to relate to empathetic tendencies and the ability to distinguish oneself from others. As a result of this study, the elephant now joins a cognitive elite among animals commensurate with its well-known complex social life and high level of intelligence. Although elephants are far more distantly related to us than the great apes, they seem to have evolved similar social and cognitive capacities making complex social systems and intelligence part of this picture. These parallels between humans and elephants suggest a convergent cognitive evolution possibly related to complex sociality and cooperation. - Capuchin Monkeys: Though there are several different species of capuchin …

RSVSim
type: Resource
type: NamedIndividual
has db xref: OMICS_03822
synonym: RSVSim: an R/Bioconductor package for the simulation of structural variations
IAO_0000115: A software package for the simulation of deletions, insertions, inversions, tandem duplications and translocations of various sizes in any genome available as FASTA-file or data package in R. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates.

ApiDots
type: Resource
type: NamedIndividual
has db xref: nif-0000-02556
IAO_0000115: Note: ApiDots is currently unavailable. For data on apicomplexan EST assemblies, please see EuPathDB ApiDots is a database integrating mRNA/EST sequences from numerous Apicomplexan parasites. ESTs and mRNAs were clustered and further assembled to generate consensus sequences. These consensus sequences were then subjected to database searches against protein sequences and protein domain sequences. The underlying relational structure of this database allows researchers to analyze these data and pose biologically interesting questions.

TCC
type: Resource
type: NamedIndividual
has db xref: OMICS_01952
synonym: Tag Count Comparison
synonym: TCC: Differential expression analysis for tag count data with robust normalization strategies
IAO_0000115: An R package that provides a series of functions for differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES). The basic idea of DEGES is that potential differentially expressed genes or transcripts (DEGs) among compared samples should be removed before data normalization to obtain a well-ranked gene list where true DEGs are top-ranked and non-DEGs are bottom ranked. This can be done by performing a multi-step normalization strategy (called DEGES for DEG elimination strategy). A major characteristic of TCC is to provide the robust normalization methods for several kinds of count data (two-group with or without replicates, multi-group/multi-factor, and so on) by virtue of the use of combinations of functions in other sophisticated packages (especially edgeR, DESeq, and baySeq).

SAMstrt
type: Resource
type: NamedIndividual
has db xref: OMICS_01951
IAO_0000115: Software package that provides the significance analysis of sequencing data with spike-in normalization. The statistical backgrounds and the benefits depend on SAMseq of the samr package.

Aptamer Database - The Ellington Lab
type: Resource
type: NamedIndividual
has db xref: nif-0000-02558
synonym: Aptamer Database
synonym: Ellington Lab Aptamer Database
IAO_0000115: The Aptamer Database is a comprehensive, annotated repository for information about aptamers and in vitro selection. This resource is provided to collect, organize and distribute all the known information regarding aptamer selection. Aptamers are DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules. Aptamers have been selected which bind nucleic acid, proteins, small organic compounds, and even entire organisms.

pRESTO
type: Resource
type: NamedIndividual
has db xref: OMICS_03443
synonym: REpertoire Sequencing TOolkit
IAO_0000115: Software toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires.

MEME Suite - Motif-based sequence analysis tools
type: Resource
type: NamedIndividual
has db xref: biotools:meme_suite
has db xref: nif-0000-10298
has db xref: OMICS_08103
synonym: The MEME Suite
abbrev: MEME Suite
IAO_0000115: Suite of motif-based sequence analysis tools to discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences; search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN; compare a motif to all motifs in a database of motifs; associate motifs with Gene Ontology terms via their putative target genes, and analyze motif enrichment using SpaMo or CentriMo. Source code, binaries and a web server are freely available for noncommercial use.

PoissonSeq
type: Resource
type: NamedIndividual
has db xref: OMICS_01950
synonym: PoissonSeq: Significance analysis of sequencing data based on a Poisson log linear model
IAO_0000115: Software package that implements a method for normalization, testing, and false discovery rate estimation for RNA-sequencing data.

Mount Sinai School of Medicine: In-Vivo Molecular Imaging Laboratory
type: Resource
type: NamedIndividual
has db xref: nif-0000-10299
synonym: MSSM IMIL
IAO_0000115: The In-Vivo Molecular Imaging Laboratory (IMIL) is a MSSM shared resource facility serving the research community of Mount Sinai with equipment and imaging expertise. State-of-the-art bioluminescent as well as fluorescent imaging modalities are supported for in-vivo monitoring of cellular and genetic activity. Investigators are provided with cutting edge imaging technologies as well as analysis techniques. The long-term goal is to establish a comprehensive SRF for in-vivo molecular imaging using micro-MRI, micro-PET and other modalities. IMIL houses a Xenogen IVIS-200 Series imaging system with the integrated fluorescent imaging options. Simultaneous dual reporter in-vivo imaging is possible with bioluminescence and fluorescence probes. The imaging chamber has a gas anesthesia manifold that can accommodate up to 5 mice for simultaneously image acquisition. Selectable field of views allow in-plane (X,Y) imaging resolutions of up to 60-microm. Integrated spectra filters allow for the determination of signal source depth (Z). IMIL will provide data acquisition services as well as analysis. IMIL has a dedicated imaging technologist for data acquisition. Investigators will bring their prepared animal to the lab and an IMIL imaging technologist will assist in sedating the animals and acquire imaging data. Typical imaging sessions last about an hour. Certified users who are trained in the use of the software will be able to perform their own analysis at the console. Usage of the imaging device is charged by the hour ($100/hour). Structural Imaging The IVIS-200 has the built-in capability of obtaining an image of the surface topography of the animal for 2D and 3D localization. If additional true 3D imaging data is required, micro MRI is available through the Imaging Science Laboratories (ISL). Image Analysis The IVIS-200 has an integrated image acquisition and analysis software (Living Image Software 2.50). Comprehensive data quantification is possible with this software. R…

CQN
type: Resource
type: NamedIndividual
has db xref: biotools:cqn
has db xref: OMICS_01949
synonym: Conditional Quantile Normalization
IAO_0000115: A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method.

GLiMMPS
type: Resource
type: NamedIndividual
has db xref: OMICS_01947
IAO_0000115: Software to characterize the genetic variation of alternative splicing using a robust statistical method for detecting splicing quantitative trait loci (sQTLs) from RNA-seq data. It takes into account the individual variation in sequencing coverage and the noise prevalent in RNA-seq data.

TEMP
type: Resource
type: NamedIndividual
has db xref: biotools:temp
has db xref: OMICS_03821
IAO_0000115: Software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data.

BEAGLE
type: Resource
type: NamedIndividual
has db xref: nlx_154238
has db xref: OMICS_00052
has db xref: OMICS_00201
synonym: BEAGLE Genetic Analysis Software Package
IAO_0000115: Software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples. BEAGLE can * phase genotype data (i.e. infer haplotypes) for unrelated individuals, parent-offspring pairs, and parent-offspring trios. * infer sporadic missing genotype data. * impute ungenotyped markers that have been genotyped in a reference panel. * perform single marker and haplotypic association analysis. * detect genetic regions that are homozygous-by-descent in an individual or identical-by-descent in pairs of individuals. Beagle can also be used in conjunction with PRESTO, a program for fast and flexible permutation testing. PRESTO can compute empirical distributions of order statistics, analyze stratified data, and determine significance levels for one-stage and two-stage genetic association studies. BEAGLE is written in Java and runs on any computing platform with a Java version 1.6 interpreter (e.g. Windows, Unix, Linux, Solaris, Mac).

SPP
type: Resource
type: NamedIndividual
has db xref: biotools:spp
has db xref: OMICS_00425
synonym: SPP Package
IAO_0000115: R analysis and processing package for Illumina platform Chip-Seq data.

MouseCyc
type: Resource
type: NamedIndividual
has db xref: nif-0000-10303
synonym: Mouse Genome Informatics: MouseCyc database
synonym: MouseCyc database
IAO_0000115: A manually curated database of both known and predicted metabolic pathways for the laboratory mouse. It has been integrated with genetic and genomic data for the laboratory mouse available from the Mouse Genome Informatics database and with pathway data from other organisms, including human. The database records for 1,060 genes in Mouse Genome Informatics (MGI) are linked directly to 294 pathways with 1,790 compounds and 1,122 enzymatic reactions in MouseCyc. (Aug. 2013) BLAST and other tools are available. The initial focus for the development of MouseCyc is on metabolism and includes such cell level processes as biosynthesis, degradation, energy production, and detoxification. MouseCyc differs from existing pathway databases and software tools because of the extent to which the pathway information in MouseCyc is integrated with the wealth of biological knowledge for the laboratory mouse that is available from the Mouse Genome Informatics (MGI) database.

Arabidopsis Hormone Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02559
synonym: Arabidopsis Hormone Database 2.0
abbrev: AHD
abbrev: AHD2.0
IAO_0000115: Database providing a systematic and comprehensive view of morphological phenotypes regulated by plant hormones, as well as regulatory genes participating in numerous plant hormone responses. By integrating the data from mutant studies, transgenic analysis and gene ontology annotation, genes related to the stimulus of eight plant hormones were identified, including abscisic acid, auxin, brassinosteroid, cytokinin, ethylene, gibberellin, jasmonic acid and salicylic acid. Another pronounced characteristics of this database is that a phenotype ontology was developed to precisely describe all kinds of morphological processes regulated by plant hormones with standardized vocabularies. To increase the coverage of phytohormone related genes, the database has been updated from AHD to AHD2.0 adding and integrating several pronounced features: (1) added 291 newly published Arabidopsis hormone related genes as well as corrected information (e.g. the arguable ABA receptors) based on the recent 2-year literature; (2) integrated orthologues of sequenced plants in OrthoMCLDB into each gene in the database; (3) integrated predicted miRNA splicing site in each gene in the database; (4) provided genetic relationship of these phytohormone related genes mining from literature, which represents the first effort to construct a relatively comprehensive and complex network of hormone related genes as shown in the home page of our database; (5) In convenience to in-time bioinformatics analysis, they also provided links to a powerful online analysis platform Weblab that they have recently developed, which will allow users to readily perform various sequence analysis with these phytohormone related genes retrieved from AHD2.0; (6) provided links to other protein databases as well as more expression profiling information that would facilitate users for a more systematic analysis related to phytohormone research. Please help to improve the database with your contributions.

Arabidopsis Nucleolar Protein Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02562
synonym: AtNoPDB Database
abbrev: AtNoPDB
IAO_0000115: Database of proteins found in the nucleoli of Arabidopsis, identified through proteomic analysis. The Arabidopsis Nucleolar Protein database (AtNoPDB) provides information on the plant proteins in comparison to human and yeast proteins, and images of cellular localizations for over a third of the proteins. A proteomic analysis was carried out of nucleoli purified from Arabidopsis cell cultures and to date 217 proteins have been identified. Many proteins were known nucleolar proteins or proteins involved in ribosome biogenesis. Some proteins, such as spliceosomal and snRNP proteins, and translation factors, were unexpected. In addition, proteins of unknown function which were either plant-specific or conserved between human and plant, and proteins with differential localizations were identified.

BIRDSUITE
type: Resource
type: NamedIndividual
has db xref: nlx_154245
has db xref: OMICS_00705
abbrev: Birdsuite
IAO_0000115: Open-source set of tools to detect and report SNP genotypes, common Copy-Number Polymorphisms (CNPs), and novel, rare, or de novo CNVs in samples processed with the Affymetrix platform. While most of the components of the suite can be run individually (for instance, to only do SNP genotyping), the Birdsuite is especially intended for integrated analysis of SNPs and CNVs.

myExperiment
type: Resource
type: NamedIndividual
has db xref: biotools:myexperiment
has db xref: nif-0000-10309
has db xref: r3d100010473
synonym: my experiment
IAO_0000115: Community repository and virtual research environment where scientists can safely publish their workflows and experiment plans, share them with groups and find and use those of others. Workflows, other digital objects and collections (called Packs) can be swapped, sorted and searched. It supports Linked data, has a SPARQL Endpoint and REST API and is based on an open source Ruby on Rails codebase. Scientific workflows in various formats can be uploaded. Specific support is provided for Taverna workflows for which the system displays relevant metadata, components and visual previews, that are retrieved directly from workflow files. Version history for workflows is collected. This feature allows the contributor to keep previous versions of the workflow available, when the latest one is uploaded. This brings additional benefit for the users by allowing them to view the development stages of the workflow towards its latest implementation.

National Center for e-Social Science: Obesity e-Lab
type: Resource
type: NamedIndividual
has db xref: nif-0000-10310
synonym: NCeSS: Obesity e-Lab
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Obesity e-Lab is a unique, secure environment for producing, sharing, communicating and finding obesity research between epidemiologists, public health researchers and social scientists. Features of e-Lab: - Tools to share: it enables social and biomedical researchers to share data, information and analytical tools for obesity research. First, it will create a portal to provide access to the platform and facilitate social networking. - Navigation tools: Second, it will generate search and navigation tools for researchers in academic, NHS or local government organizations to find data from administrative and secure data services, via social science views of health datasets, and health science views of social datasets. Within the NHS, e-Lab links records from a variety of administrative and health (and social) care sources for broadly-specified obesity research, and make pseudonymised extracts of NHS-linked datasets available via the portal. - Analytical tools: Third, it will develop analytical tools, focused on: i) easy, reliable and privacy-protecting transformation of geo-codes in health records to other geographies and area-based social and economic measures; ii) epidemiological extensions to geographical information systems; iii) growth-standardization of child obesity measures. The tool-building will employ as much existing software as possible, focusing on the provision of simple, intuitive interfaces to proven software to make it easy for social or biomedical researchers to use collaboratively.

NASTIseq
type: Resource
type: NamedIndividual
has db xref: OMICS_01945
IAO_0000115: Software for integrated detection of natural antisense transcripts using strand-specific RNA sequencing data.

EarLab
type: Resource
type: NamedIndividual
has db xref: nif-0000-00101
synonym: A Digital Warehouse of Auditory Models and Data
synonym: EarLab (at) Boston University
synonym: EarLab at Boston University
synonym: EarLab: A Digital Warehouse of Auditory Models and Data
synonym: EarLab: A Digital Warehouse of Auditory Models Data
synonym: EarLab: A Virtual Hearing Laboratory
IAO_0000115: Freely-accessible auditory databases as well as custom designed modeling and data analysis software tools. A fully functional online auditory modeling environment is also available, as well as downloadable models in several languages. The models cover many aspects of auditory function and at many different levels of detail ranging from multi-compartment celluar models to high-level abstractions of large portions of the auditory pathway. Currently a few models are available that can be run online and others are available for downloading. EarLab also provides custom cross-platform software for creating your own distributed auditory modeling environment, as well as software for analyzing the results from experimentation. A database of auditory modules is available for online use or download for the distributed auditory modeling environment, as well as instructions and specifications for creating your own modules. All these databases and custom software tools can be used in a wide variety of hearing research applications. This unique resource provides a wealth of information on auditory processing in humans and other animals. Mathematical models are also provided.

BREAKDANCER
type: Resource
type: NamedIndividual
has db xref: biotools:breakdancer
has db xref: nlx_154253
has db xref: OMICS_00307
abbrev: BreakDancer
IAO_0000115: A Perl/C++ software package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. (entry from Genetic Analysis Software)

CAROL
type: Resource
type: NamedIndividual
has db xref: nlx_154254
has db xref: OMICS_00143
synonym: Combined Annotation scoRing toOL
IAO_0000115: Software application that is a combined functional annotation score of non-synonymous coding variants. A major challenge in interpreting whole-exome data is predicting which of the discovered variants are deleterious or neutral. To address this question in silico, they have developed a score called Combined Annotation scoRing toOL (CAROL), which combines information from two bioinformatics tools: PolyPhen-2 and SIFT, in order to improve the prediction of the effect of non-synonymous coding variants. The combination of annotation tools can help improve automated prediction of whole-genome/exome non-synonymous variant functional consequences. (entry from Genetic Analysis Software) The software should run on any UNIX or GNU/Linux system.

COMPASS
type: Resource
type: NamedIndividual
has db xref: OMICS_05640
synonym: Combinatorial Polyfunctionality Analysis of Single Cells
synonym: COMPASS - Combinatorial Polyfunctionality Analysis of Single Cells
synonym: COMPASS: Combinatorial Polyfunctionality Analysis of Single Cells
IAO_0000115: Software for combinatorial polyfunctionality analysis of single cells. It is a statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. It uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject's immune response to external stimuli such as infection or vaccination.

CASAVA
type: Resource
type: NamedIndividual
has db xref: nlx_154257
has db xref: OMICS_01123
synonym: Consensus Assessment of Sequence And VAriation
IAO_0000115: Software package that creates genomic builds, calls SNPs, detects indels, and counts reads from data generated from one or more sequencing runs. In addition, CASAVA automatically generates a range of statistics, such as mean depth and percentage chromosome coverage, to enable comparison with previous builds or other samples. CASAVA analyzes sequencing reads in three stages: * FASTQ file generation and demultiplexing * Alignment to a reference genome * Variant detection and counting

National Society of Genetic Counselors
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100010237
has db xref: grid.429579.4
has db xref: ISNI: 0000 0001 2179 5189
has db xref: nif-0000-10367
synonym: National Society of Genetic Counselors (NSGC)
abbrev: NSGC
IAO_0000115: Professional society of genetic counselors that promotes networking, continuing education opportunities, advocacy, and discussion of relevant issues in the field of genetics.

National Institutes of Health Stroke Scale
type: Resource
type: NamedIndividual
has db xref: nif-0000-10368
synonym: NIHSS
IAO_0000115: The National Institutes of Health Stroke Scale (NIHSS) is a systematic assessment tool that provides a quantitative measure of stroke-related neurological deficit. The NIHSS was originally designed as a research tool to measure baseline data on patients in acute stroke clinical trials. Now, the scale is also widely used as a clinical assessment tool to evaluate acuity of stroke patients, determine appropriate treatment, and predict patient outcome. The NIHSS can be used as a clinical stroke assessment tool to evaluate and document neurological status in acute stroke patients. The stroke scale is valid for predicting lesion size and can serve as a measure of stroke severity. The NIHSS has been shown to be a predictor of both short and long term outcome of stroke patients. Additionally, the stroke scale serves as a data collection tool for planning patient care and provides a common language for information exchanges among healthcare providers. Performing the scale takes between 5-8 minutes. Emergency physicians and nurses, neurologists, neuroscience nurses and other stroke team members are typical examples of who should be certified to perform the NIHSS. The NINDS/NIH training and testing DVD can be obtained from the National Institute of Neurological Disorders and Stroke. Sponsors: NIHSS is supported by the National Institute of Neurological Disorders and Stroke (NINDS).

Neural Engineering with Louisiana North Excellence Consoritium
type: Resource
type: NamedIndividual
has db xref: nif-0000-10371
synonym: The NewLANE Consortium
IAO_0000115: This Consortiums objectives are to 1)synergistically enhance neuroscience research and neural engineering development activities in North Louisiana, 2) design and create via a multi-disciplinary team approach, better and more versatile techniques for studying and activating the nervous system, 3) refine these techniques in a collaborative and iterative manner; 4) use these techniques to advance our understanding of the nervous system in its normal, hypoxic and ischemic states; and 5) design neuroprostheses. By bringing engineers, life scientists, and clinicians together, the Consortium pursues a multimodal approach to neuroscience that enables a deeper understanding of normal and pathological neural conditions and opens new doors in the study and treatment of neurological impairment. It attacks a discrete set of problems that have been outside of the reach of neuroscience research, and propose solutions through the judicious application of neural engineering. And it is developing innovative techniques for minimally-invasive, fast-response, precisely localizable, wide-aperture, chronic measurement and stimulation of neural activity. These New Lanes are the novel methods and microdevices for monitoring and under-standing neural function, and providing potential functional replacements. By employing micro- and nano-system techniques, the NewLANE Consortium provides NewLANEs novel methods for monitoring various aspects of neuronal activity that are more sensitive, reliable, and versatile than currently available and novel met-hods for providing potential functional replacements all of which have direct applicability to the US veteran population. Sponsors: Funding comes from various sources including a VA Sr. Rehab. Research Career Scientist award.

Neural Ensemble - NeuroTools
type: Resource
type: NamedIndividual
has db xref: nif-0000-10372
synonym: Neuro Tools
synonym: NeuroTools
IAO_0000115: Collection of tools to support all tasks associated with a neural simulation project, which are not handled by the simulation engine. NeuroTools is written in Python and works best with PyNN and other simulation engines with a Python front-end such as NEURON, NEST, PCSIM, BrainScaleS Neuromorphic VLSI, Brian, MOOSE/GENESIS, and Neurospaces/GENESIS. NeuroTools provides modules to facilitate simulation setup, parameterization, data management, analysis and visualization. The data-related tools are equally suited to analysis of experimental data.

flowClust
type: Resource
type: NamedIndividual
has db xref: OMICS_05595
synonym: flowClust - Clustering for Flow Cytometry
IAO_0000115: A Bioconductor software package for automated gating of flow cytometry data that implements a robust model-based clustering approach based on multivariate t mixture models with the Box-Cox transformation.

Atlas3D
type: Resource
type: NamedIndividual
has db xref: nif-0000-10373
synonym: NeSys Atlas3D
synonym: Neural Systems and Graphics Computing Laboratory: Atlas3D Software
IAO_0000115: A multi-platform visualization tool which allows import and visualization of 3-D atlas structures in combination with tomographic and histological image data. The tool allows visualization and analysis of the reconstructed atlas framework, surface modeling and rotation of selected structures, user-defined slicing at any chosen angle, and import of data produced by the user for merging with the atlas framework. Tomographic image data in NIfTI (Neuroimaging Informatics Technology Initiative) file format, VRML and PNG files can be imported and visualized within the atlas framework. XYZ coordinate lists are also supported. Atlases that are available with the tool include mouse brain structures (3-D reconstructed from The Mouse Brain in Stereotaxic Coordinates by Paxinos and Franklin (2001)) and rat brain structures (3-D reconstructed from The Rat Brain in Stereotaxic Coordinates by Paxinos and Watson (2005)). Experimental data can be imported in Atlas3D and warped to atlas space, using manual linear registration, with the possibility to scale, rotate, and position the imported data. This facilitates assignment of location and comparative analysis of signal location in tomographic images.

HSA
type: Resource
type: NamedIndividual
has db xref: OMICS_01944
IAO_0000115: A splice alignment software tool of RNA-Seq reads mapping.

SPADE
type: Resource
type: NamedIndividual
has db xref: OMICS_05639
synonym: SPADE - An analysis and visualization tool for Flow Cytometry
synonym: Spanning tree Progression of Density normalized Events
IAO_0000115: An analysis and visualization software tool for high dimensional flow cytometry data that organizes cells into hierarchies of related phenotypes.

Neural Systems and Graphics Computing Laboratory: Micro3D Software
type: Resource
type: NamedIndividual
has db xref: nif-0000-10375
synonym: NeSys Micro3D
IAO_0000115: The Micro3D 2004 is a software for 3-D reconstruction, visualization, and analysis of neuronal populations and brain regions. Micro3D generates geometric models from line and point coded data sets, representing labeled objects such as cell bodies or axonal plexuses, and boundaries of brain regions in serial sections. Data are typically imported from image-combining computerized microscopy systems, such as Neurolucida (MicroBrightField, Colchester, VT). The models may be rotated and zoomed in real-time. Surfaces are re-synthesized on the basis of stacks of contour lines. Clipping is used for defining section-independent subdivisions of the model. Flattening of sheets of points in curved layers (e.g., neurons in a cortical lamina) facilitates inspection of complicated distribution patterns. Micro3D computes color-coded density maps, and allows production of mpeg videos. Micro3D 2004 runs on LINUX PCs equipped with Open Inventor. It performs operations similar to the Silicon Graphics based version that has been used in more than 25 investigations and in various species, ranging from insects to monkeys, at the LM- and EM-level. Sponsors:Micro 3D was developed with support from The Research Council of Norway and The Oslo Research Park / FORNY.

Brain Machine Interface Platform
type: Resource
type: NamedIndividual
has db xref: nif-0000-10378
synonym: BMI (Brain Machine Interface) Platform
synonym: BMI platform
synonym: BMI-platform
synonym: Brain Machine Interface Platform (BMI PF)
abbrev: BMI PF
abbrev: BMI-PF
IAO_0000115: Databases of accumulating BMI (Brain Machine Interfaces)-related experimental data, mathematical models, and tools generated in neuroscience, computational theory, and robotics. Databases include: # Database of BMI (Brain Machine Interfaces)-related papers: More than 3500 BMI-related papers are registered. Each paper has original tags, for example, recording method and subject, for easy searching. # Database of original contents: BMI-related materials (Movie, Picture, Data, Program) provided by scientists. # Database of BMI-related research sites: 185 BMI-related research sites in the world (university, institute and company) are registered. The research site can be searched either by the location using clickable map or by the field of interest. # Database of BMI-related materials: Links to BMI-related materials (Movie, Picture, Document, Data, Program) are listed. You can easily find materials of your interest since each material is classified into research field. # BMI-related column: The columns are written by researchers specialized in BMI. Original contents include: * Neuronal activity during performance of a memory-guided movement * Reconstructed visual images from human fMRI activity * fMRI data and program for visual image reconstruction * Brain sections of monkeys, stained for several gene markers * Cortical Box Method: The Cortical box method is an analytical method that standardizes the serial coronal sections of rodent cortex for quantitative analysis. * Multineuron activity in monkey prefrontal cortex * Monkey Atlas: **Brain sections of monkeys, stained for AChE, ER81 mRNA and Sema3E mRNA - These pictures are low-resolution photos of serial brain sections of monkeys, stained for AChE as well as for ER81 and Sema3E mRNAs. The compressed file contains JPEG photos and html files for web browser navigation. Other materials are available at our website BraInSitu dedicated for in situ hybridization resources for brains. BraInSitu http://www.nibb.ac.jp/brish/i…

Kindai University; Osaka; Japan
type: Organization
type: NamedIndividual
has db xref: grid.258622.9
has db xref: ISNI:0000 0004 1936 9967
has db xref: nlx_149308
has db xref: Wikidata:Q912329
synonym: Kinki University
IAO_0000115: Private non-sectarian and coeducational university based in Higashiosaka, Osaka, Japan.

AStalavista
type: Resource
type: NamedIndividual
has db xref: OMICS_01943
synonym: Alternative Splicing transcriptional landscape visualization tool
IAO_0000115: Tool that extracts and displays alternative splicing (AS) events from a given genomic annotation of exon-intron gene coordinates. By comparing all given transcripts, it detects the variations in their splicing structure and identifies all AS events (like exon skipping, alternate donor, etc) by assigning to each of them an AS code. It provides a visual summary of the AS landscape in the analyzed dataset, the possibility to browse the results on the UCSC website or to download them in GTF or ASTA format. You can use AStalavista for any genome by providing your own annotation set, the identifier of your gene(s) of interest, or analyze the AS landscape of reference annotation datasets like Gencode, RefSeq, Ensembl, FlyBase, etc.

CLUSTAG
type: Resource
type: NamedIndividual
has db xref: nlx_154273
synonym: CLUSTAG: Hierarchical Clustering and Graph Methods for Selecting Tag SNPs
IAO_0000115: Software application that uses hierarchical clustering and graph methods for selecting tag SNPs (single nucleotide polymorphisms). Cluster and set-cover algorithms are developed to obtain a set of tag SNPs that can represent all the known SNPs in a chromosomal region, subject to the constraint that all SNPs must have a squared correlation R2 > C with at least one tag SNP, where C is specified by the user. The program is implemented with Java, and it can run in Windows platform as well as the Unix environment.

Neuronland: NLMorphologyConverter
type: Resource
type: NamedIndividual
has db xref: nif-0000-10381
synonym: NLMorphologyConverter
IAO_0000115: NLMorphologyConverter is a simple command-line program for converting between the various neuron morphology data formats which are used to describe the three-dimensional physical branching structure of biological neurons. The aim is to provide coverage of all formats, old and new, in which data is available online, and/or which are supported by free and commercial software packages (e.g. software for neuron reconstruction, generation, simulation, visualization, and analysis of neuron morphology). Permission is granted for this software to be freely copied. Main Features Currently 21 different morphology file formats fully or partially supported. Automatic detection of input file format. Faithful reproduction of output file formatting. Many command line options for manipulating the imported data Intensively tested using over 10000 publicly available morphology data files. Sponsors. This software is supported by NeuronLand.

NeuroExplorer
type: Commercial Organization
type: NamedIndividual
has db xref: nif-0000-10382
has db xref: nlx_158483
synonym: NeuroExplorer: Neurophysiological Data Analysis Package
IAO_0000115: Data analysis software for neurophysiology with a multitude of features, including: * Import of native data files created by many popular data acquisition systems * All standard histogram and raster analyses * Shift predictors in crosscorrelograms and color markers in perievent rasters * Joint PSTH, burst analysis and many more analyses of timestamped data * Spectral analysis of spike and continuous data * 3D data view and animation * Fully customizable WYSIWYG graphics * Custom analysis and batch mode processing with internal scripting language * Direct data link to Matlab and Excel * Statistical tests via direct link to R-project

Neuroscience Postdoctoral Researcher Jobs
type: Resource
type: NamedIndividual
has db xref: nif-0000-10384
synonym: PhDs.org
abbrev: PhD's Jobs
IAO_0000115: Interactive web site that brings together tools that graduate students can use to find jobs and that potential students can use to select graduate programs. The site also includes links to excellent resources on networking, writing a curriculum vita, interviewing and writing grants.

Visual Molecular Dynamics
type: Resource
type: NamedIndividual
has db xref: OMICS_03804
abbrev: VMD
IAO_0000115: A molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.

EXTREME
type: Resource
type: NamedIndividual
has db xref: OMICS_03428
IAO_0000115: A motif discovery algorithm designed to find DNA-binding motifs in ChIP-Seq and DNase-Seq data.

Office of Research on Womens Health: Reseach
type: Resource
type: NamedIndividual
has db xref: nif-0000-10387
synonym: ORWH Research
IAO_0000115: The mission of the Office of Research on Women's Health (ORWH) is to stimulate and encourage meritorious research on women's health, including the role of sex and gender in health and disease. The priorities signify approaches and areas for which there is a need to stimulate and encourage research on women's health, or sex/gender factors, and the advancement of women in biomedical research careers. These research priorities are not an exclusive list of research areas important to women's health; therefore other innovative or significant research areas should also be considered. The following four overarching themes are important for addressing research on women's health: Lifespan, Sex/Gender Determinants, Health Disparities/Differences and Diversity, ad Interdisciplinary Research. Special Areas of Emphasis - Prevention/Treatment: from basic biological factors, including identifying and validating biomarkers, to risk and its applications to disease prevention, early detection, and treatment. - Sex and Genetics/Pharmacogenomics: genetic, molecular, and cellular basis for action of pharmacologic agents known to have different effects in females than in males. Research on effects of sex as a modifier of gene function and response is under-investigated. Sponsors: This research is funded by the NAtional Institutes of Health.

CYRILLIC
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_154279
has db xref: OMICS_00208
synonym: CyrillicSoftware
abbrev: Cyrillic
IAO_0000115: Software application for pedigree drawing with fully integrated risk analysis and support for industry standard databases (MS Access and Corel Paradox). It is designed for genetic counselors and others who work with patients. Cyrillic 2 draws pedigrees, works with genetic marker data, lets you do haplotyping and allows exports to a range of linkage analysis packages.

wikiCancer
type: Resource
type: NamedIndividual
has db xref: nlx_15428
IAO_0000115: A place where people connected to cancer can share real-life experiences -- fears, insights, stories, and advice. Adding perspectives is easy, and every contribution builds the site into a more valuable and unique community resource. Content, resources, and support on wikiCancer: * Just been diagnosed with cancer? * Living with cancer * For cancer survivors * How to support someone with cancer * Connect with other cancer patients, survivors, family and caregivers

Online Encyclopedia for Genetic Epidemiology studies
type: Resource
type: NamedIndividual
has db xref: nif-0000-10388
synonym: OEGE - Online Encyclopedia for Genetic Epidemiology studies
abbrev: OEGE
IAO_0000115: Portal for researchers to locate information relevant to interpretation and follow-up of human genetic epidemiological discoveries, including: a range of population and case and family genetic epidemiological studies, relevant gene and sequence databases, genetic variation databases, trait measurement, resource labs, journals, software, general information, disease genes and genetic diversity.

Online Papers on Consciousness
type: Resource
type: NamedIndividual
has db xref: nif-0000-10389
synonym: Consciousness Papers
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. This is a directory of 5311 free online papers on consciousness in philosophy and in science, and of related topics in the philosophy of mind. The papers in this directory are drawn from PhilPapers, a database of both online and offline works in philosophy. Sponsors: Sponsored by the Joint Information Systems Committee as part of the Information Environment Programme.

DINDEL
type: Resource
type: NamedIndividual
has db xref: biotools:dindel
has db xref: nlx_154283
has db xref: OMICS_00096
synonym: Dindel: Accurate indel calls from short-read data
abbrev: Dindel
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Software program for calling small indels from short-read sequence data ("next generation sequence data"). It is currently designed to handle only Illumina data. Dindel takes BAM files with mapped Illumina read data and enables researchers to detect small indels and produce a VCF file of all the variant calls. It has been written in C++ and can be used on Linux-based and Mac computers (it has not been tested on Windows operating systems).

Royal Institute of Technology: PDC
type: Resource
type: NamedIndividual
has db xref: nif-0000-10408
synonym: KTH PDC
IAO_0000115: PDC operates leading-edge, high-performance computers on a national level. PDC offers easily accessible computational resources that primarily cater to the needs of Swedish academic research and education. PDC also takes part in major international projects to develop high-performance computing for the future and stay a leading national resource in parallel computing.

Open Provenance Model
type: Resource
type: NamedIndividual
has db xref: nif-0000-10392
synonym: OPM Provenance Model
synonym: The OPM Provenance Model
synonym: The OPM Provenance Model (OPM)
abbrev: OPM
IAO_0000115: A model of provenance that is designed to meet the following requirements: (1) To allow provenance information to be exchanged between systems, by means of a compatibility layer based on a shared provenance model. (2) To allow developers to build and share tools that operate on such a provenance model. (3) To define provenance in a precise, technology-agnostic manner. (4) To support a digital representation of provenance for any "thing", whether produced by computer systems or not. (5) To allow multiple levels of description to coexist. (6) To define a core set of rules that identify the valid inferences that can be made on provenance representation.

FMRISTAT - A general statistical analysis for fMRI data
type: Resource
type: NamedIndividual
has db xref: nif-0000-00303
abbrev: FMRISTAT
IAO_0000115: A Matlab toolbox for the statistical analysis of fMRI data. The fMRI data was first converted to percentage of whole volume. The statistical analysis of the percentages was based on a linear model with correlated errors. The design matrix of the linear model was first convolved with a hemodynamic response function modelled as a difference of two gamma functions timed to coincide with the acquisition of each slice. Temporal drift was removed by adding a cubic spline in the frame times to the design matrix (one covariate per 2 minutes of scan time), and spatial drift was removed by adding a covariate in the whole volume average. The correlation structure was modelled as an autoregressive process of degree 1. At each voxel, the autocorrelation parameter was estimated from the least squares residuals using the Yule-Walker equations, after a bias correction for correlations induced by the linear model. The autocorrelation parameter was first regularized by spatial smoothing, then used to "whiten" the data and the design matrix. The linear model was then re-estimated using least squares on the whitened data to produce estimates of effects and their standard errors. In a second step, runs, sessions and subjects were combined using a mixed effects linear model for the effects (as data) with fixed effects standard deviations taken from the previous analysis. This was fitted using ReML implemented by the EM algorithm. A random effects analysis was performed by first estimating the the ratio of the random effects variance to the fixed effects variance, then regularizing this ratio by spatial smoothing with a Gaussian filter. The variance of the effect was then estimated by the smoothed ratio multiplied by the fixed effects variance. The amount of smoothing was chosen to achieve 100 effective degrees of freedom. The resulting T statistic images were thresholded using the minimum given by a Bonferroni correction and random field theory, taking into account the non-isotropic spat…

PANDORA Matlab Toolbox
type: Resource
type: NamedIndividual
has db xref: nif-0000-10396
synonym: Pandora
synonym: PANDORA Matlab Toolbox and Other Utilities
IAO_0000115: Matlab toolbox for analyzing neuronal electrophysiology data and constructing databases.

Parkinson's Disease Foundation
type: Resource
type: NamedIndividual
has db xref: nif-0000-10397
has db xref: nif-0000-11759
has db xref: SCR_002025
abbrev: PDF
IAO_0000115: A U.S. organization which funds Parkinson's disease research and provides materials and services to patients. PDF funds research through: research centers at major universities; early-career investigators that devote their talents to the study of Parkinsons; funding independent investigators through the International Research Grants Program; and collaboration with other organizations on innovative projects.

ASprofile
type: Resource
type: NamedIndividual
has db xref: OMICS_01942
IAO_0000115: A suite of programs for extracting, quantifying and comparing alternative splicing (AS) events from RNA-seq data.

OrderedList
type: Resource
type: NamedIndividual
has db xref: OMICS_03525
synonym: OrderedList - Similarities of Ordered Gene Lists
IAO_0000115: An R / bioconductor package for detecting similarity in ordered gene lists. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively.

PathCase Pathways Database System
type: Resource
type: NamedIndividual
has db xref: nif-0000-10398
has db xref: nif-0000-20885
has db xref: SCR_002104
synonym: PathCase
synonym: PathCase - Metabolic Pathway Database System
IAO_0000115: An integrated software system for storing, managing, analyzing, and querying biological pathways at different levels of genetic, molecular, biochemical and organismal detail. The system contains a pathways database and associated tools to store, compare, query, and visualize metabolic pathways. The aim is to develop an integrated database and the associated tools to support computational analysis and visualization of biochemical pathways. At the computational level, PathCase allows users to visualize pathways in multiple abstraction levels, and to pose predetermined and ad hoc queries using a graphical user interface. Pathways are represented as graphs, and implemented as a relational database. The available functional annotations include the identity of the substrate(s), product(s), cofactors, activators, inhibitors, enzymes or other processing molecules, GO-categories of enzymes (as well as GO hierarchy visualizations two-way-linked to PathCase enzymes), EC number information and the associated links, and synonyms and encoding genes of gene products.

Koc University; Istanbul; Turkey
type: Organization
type: NamedIndividual
has db xref: nlx_151421
synonym: Koc University
synonym: Koç University
synonym: Koç Üniversitesi
abbrev: KU
IAO_0000115: Non-profit private university in Istanbul, Turkey that offers undergraduate and graduate degree programs in sciences, humanities, engineering, social sciences, medicine, and nursing.

PhosphoSitePlus: Protein Modification Site
type: Resource
type: NamedIndividual
has db xref: biotools:phosphositeplus
has db xref: nif-0000-10399
synonym: PhosphoSite
synonym: PhosphoSitePlus
abbrev: PSP
IAO_0000115: A freely accessible on-line systems biology resource devoted to all aspects of protein modification, as well as other post-translational modifications. It provides valuable and unique tools for both cell biologists and mass spectroscopists. PhosphoSite is a human- and mouse-centric database. It includes features such as: viewing the locations of modified residues on molecular models; browsing and searching MS2 records by disease, tissue, and cell line; submitting lists of peptides to identify previously reported genes; searching by sub-cellular localization, treatment, tissues, cell types, cell lines and diseases, and protein types and protein domains; searching for experimentally-verified kinase substrates and viewing preferred substrate motifs; and viewing MS2 spectra for peptides and sites not previously published.

ArkDB - Genomes For The Rest of Us
type: Resource
type: NamedIndividual
has db xref: nif-0000-02568
has db xref: r3d100012788
synonym: ArkDB
IAO_0000115: The ArkDB database system aims to provide a comprehensive public repository for genome mapping data from farmed and other animal Species. The system also aims to provide a route in to genomic and other sequence from the initial viewpoint of linkage mapping, RH mapping, physical mapping or - possibly more importantly - QTL mapping data. Sponsors: ArkDB is funded by Biotechnology and Biological Sciences Research Council (BBSRC), UK. Cat, Chicken, Cow, Deer, Duck, Horse, Pig, Quail, Salmon, Sea Bass, Sheep, Turkey, QLT map, Linkage map, RH map, Farm animal, Genome map, Sequence, Mapping

Psychology Training - VA Fellowships and Internships
type: Resource
type: NamedIndividual
has db xref: nif-0000-10403
synonym: VA Psychology Training
IAO_0000115: VA provides Internships, Postdoctoral Fellowships, and Practicum Training in many sites across the U.S. With about 470 internship positions at 93 locations and 260 postdoctoral fellowship positions at 65 sites funded each year, VA is the largest provider of training in Psychology in the nation. We have continued to expand our training opportunities and added 70 additional positions for the 2011-2012 academic year. These positions included additional internship and postdoctoral positions within existing training programs and the development of new internship programs in Boise ID, Canandaigua NY, Columbia SC, Huntington WV, Indianapolis IN, Madison WI, Philadelphia PA, Tuscaloosa AL, and West Palm Beach FL. In the meantime, the four internships started in 2008 (Anchorage AK, Asheville NC, Iowa City IA, and Richmond VA) have graduated their second classes and have now begun their third year. The internship program in Richmond is accredited through 2017. The other three programs do not yet have APA accreditation, but all have begun the accreditation process. In the interim, graduates of these programs will be eligible for employment as psychologists within the Department of Veterans Affairs just as are graduates from accredited programs. All existing VA Internship and many Postdoctoral Psychology training programs hold APA accreditation status.

TCAG
type: Resource
type: NamedIndividual
has db xref: nif-0000-12519
synonym: Centre for Applied Genomics
synonym: The Centre for Applied Genomics
IAO_0000115: Service and training support for academic, government, and private sector scientists worldwide in genomics, including laboratory experimentation, statistical analysis, and comprehensive bioinformatics support, including large-scale genome comparisons, algorithm and tools development, and database curation, annotation and hosting. The Centre for Applied Genomics hosts a variety of databases related to ongoing supported projects: *Autism Chromosome Rearrangement Database *Cystic Fibrosis Mutation Database *The Lafora Progressive Myoclonus Epilepsy Mutation and Polymorphism Database *Database of Genomic Variants *The Chromosome 7 Annotation Project *Human Genome Segmental Duplication Database *Non-Human Segmental Duplication Database Healthy control DNA samples from the Ontario Population Genomics Platform are available. The Biobanking and Databasing Facility provides DNA extraction from lymphoblasts, fibroblasts and other cell types, archiving of white cell pellets, preparation and immortalization of cell lines, and comprehensive databasing and tracking of samples and/or cell lines within the facility.

Published Association Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-10405
abbrev: PADB
IAO_0000115: It aims to help researchers to utilize information more efficiently from the published association data. This database is freely accessible only for academic users under the GNU GPL PADB indexes the sentences containing "associat*" or "case-control*" or "cohort*" or "meta-analysis" or "systematic review" or "odds ratio*" or "hazard ratio*" or "risk ratio*" or "relative risk*" from PubMed abstracts and automatically extracts the numeric values of odds ratios, hazard ratios, risk ratios and relative risks data when available. PADB automatically identifies HUGO official symbols of human genes using NCBI Entrez Gene data, and each gene is linked to the UCSC genome browser and International HapMap Project database. Furthermore, molecular pathways listed in BioCarta or KEGG databases can be accessed through the link using CGAP gene annotation data. Also, each record in PADB is linked to GAD or HPLD if it is available from those databases. Currently, (Last Update of Database Contents : Dec. 20, 2006) PADB indexes more than 1,500,000 abstracts including about 190,000 risk values ranging from 0.00001 to 4878.9 and 3,442 human genes related to 461 molecular pathways. Sponsors: This work was supported by the Brain Korea 21 Project for Medical Science, Yonsei University, Seoul, Korea and a faculty research grant of Yonsei University College of Medicine for 2006, Seoul, Korea.

GenABEL
type: Resource
type: NamedIndividual
has db xref: nlx_154328
has db xref: OMICS_00234
synonym: GenABEL package
synonym: R/GENABEL
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. R software library for genome-wide association analysis for quantitative, binary and time-till-event traits.

CCAT
type: Resource
type: NamedIndividual
has db xref: biotools:ccat
has db xref: OMICS_00428
synonym: Control based ChIP-Seq Analysis Tools
IAO_0000115: THIS RESOURCE IS OUT OF SERVICE, documented on April 5, 2017, A software package for the analysis of ChIP-seq data with negative control., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

LinkHub: A Semantic Web System that facilitates cross-database queries and information retrieval in proteomics
type: Resource
type: NamedIndividual
has db xref: nif-0000-10406
synonym: LinkHub
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. LinkHub is a software system using Semantic Web RDF that manages the graph of identifier relationships and allows exploration with a variety of interfaces. It leverages Semantic Web standards-based integrated data to provide novel information retrieval to identifier-related documents through relational graph queries, simplifies and manages connections to major hubs such as UniProt, and provides useful interactive and query interfaces for exploring the integrated data. For efficiency, it is also provided with relational-database access and translation between the relational and RDF versions. LinkHub is practically useful in creating small, local hubs on common topics and then connecting these to major portals in a federated architecture; LinkHub was used to establish such a relationship between UniProt and the North East Structural Genomics Consortium. LinkHub also facilitates queries and access to information and documents related to identifiers spread across multiple databases, acting as connecting glue between different identifier spaces. LinkHub is available at hub.gersteinlab.org and hub.nesg.org with supplement, database models and full-source code. Sponsors: Funding for this work comes from NIH/NIGMS grant P50 GM62413-01, NIH grant K25 HG02378, and NSF grant DBI-0135442.

Rafael Yustes Laboratory
type: Resource
type: NamedIndividual
has db xref: nif-0000-10407
synonym: Cortical Circuits and Dendritic Spines
synonym: Rafael Yuste''s Laboratory
abbrev: Yuste Lab
IAO_0000115: Laboratory that aims to understand the function of the cortical microcircuit by reverse-engineering of the cortical microcircuit using the mouse neocortex in vitro and in vivo as their experimental preparations. The techniques applied are electrophysiology, anatomy, and a variety of optical methods, including infrared-DIC, voltage- and ion-sensitive dye imaging with confocal, two-photon and second harmonic microscopy. They also use laser uncaging, biolistics, electroporation, electron microscopy and numerical simulations, and make extensive use of genetically modified mouse strains. They focus is on two major questions: (1) What is the function of dendritic spines? (2) What are the multicellular patterns of activity under spontaneous or evoked activation of the circuit? Resources include: * Cell Reconstructions: Cell Database, PDF Images, .DAT Files * Circuit Diagrams: Full Circuit Diagram, Inhibitory Circuit Diagram, Excitatory Circuit Diagram, Simplified Circuit Diagram, Layer to Layer Simplified Circuit, Circuit diagram references

Alt Event Finder
type: Resource
type: NamedIndividual
has db xref: OMICS_01941
synonym: Alt Event Finder: A tool for extracting alternative splicing events from RNA-seq data
IAO_0000115: Software tool for deriving data-driven alternative splicing (AS) events from RNA-seq data. It analyses the transcripts built by Cufflinks or Scripture and outputs AS event annotations which is compatible with MISO. It can be used for annotating novel AS events from a well-annotated species such as human. It can also be used for species of which known AS event annotation is not available. The current release (v0.1) supports skipped exon events only.

FreeSurfer
type: Resource
type: NamedIndividual
has db xref: nif-0000-00304
IAO_0000115: Open source software suite for processing and analyzing human brain MRI images. Used for reconstruction of brain cortical surface from structural MRI data, and overlay of functional MRI data onto reconstructed surface. Contains automatic structural imaging stream for processing cross sectional and longitudinal data. Provides anatomical analysis tools, including: representation of cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from rest of brain, skull stripping, B1 bias field correction, nonlinear registration of cortical surface of individual with stereotaxic atlas, labeling of regions of cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures.Operating System: Linux, macOS.

Mining On-Line Expert on MedLine
type: Resource
type: NamedIndividual
has db xref: nif-0000-21258
synonym: MedMOLE
IAO_0000115: MedMOLE improves the comprehension of microarray experimental results by grouping co-regulated genes on the basis of the informational content of MEDLINE documents. The tool relies on two components: a gene name extractor and a mining algorithm. The name extractor is based on existing dictionaries of gene names and aliases. The mining algorithm analyses the co-occurrences of words in the selected documents in order to automatically interpret the context, identify where the gene names appear, and map documents/genes into functional classes. DNA microarray technology is a high throughput method for gaining information on gene function. This large amount of data can be analyzed to identify groups of genes that share common expression characteristics, but the obtained results provide little information regarding the presence of functional biological correlations of genes within clusters. The published literature, on the other hand, provides a potential source of information to assist in interpretation of clustering results. We have developed a tool (MedMOLE) that improves the comprehension of microarray experimental results by grouping co-regulated genes on the basis of the informational content of MEDLINE documents. The tool relies on two components: a gene name extractor and a mining algorithm. The name extractor is based on existing dictionaries of gene names and aliases. The mining algorithm analyses the co-occurrences of words in the selected documents in order to automatically interpret the context, identify where the gene names appear, and map documents/genes into functional classes. Microarray transcriptional profiling is a powerful tool used in the study of transcriptional control mechanisms. An important point in the analysis of microarray data is the identification of hidden correlations between the differentially expressed genes generated upon some kind of cell stimulus. Functional annotation is an important topic for microarray data mining, however this is …

ASAP
type: Resource
type: NamedIndividual
has db xref: nif-0000-02571
has db xref: r3d100010666
synonym: A Systematic Annotation Package for Community Analysis of Genome
synonym: A systematic annotation package for community analysis of genomes
synonym: ASAP: a systematic annotation package for community analysis of genomes
IAO_0000115: Database and web interface developed to store, update and distribute genome sequence data and gene expression data. ASAP was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, and gene expression data from preliminary experiments. Use of some of this preliminary data is conditional, and it is the users responsibility to read the data release policy and to verify that any use of specific data obtained through ASAP is consistent with this policy. There are four main routes to viewing the information in ASAP: # a summary page, # a form to query the genome annotations, # a form to query strain collections, and # a form to query the experimental data. Navigational buttons appear on every page allowing users to jump to any of these four points., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Salk Institute for Biological Studies - Slesinger Lab
type: Resource
type: NamedIndividual
has db xref: nif-0000-10413
synonym: Salk Institute (Slesinger)
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This lab is investigating the molecular details of how potassium ion channels open and close (i.e. gating), the cellular regulation of potassium channels in nerve cells, and more recently, their role in drug addiction and mental disorders. There are currently two related areas of focus in the lab. One main area of research is investigating the G protein regulation of GIRK channels, utilizing structural, biochemical and electrophysiological strategies. The other area extends from the G protein regulation experiments to studies that examine the role of GIRK channels in the neural response to drugs of abuse, utilizing biochemical, electrophysiological and behavioral strategies.

Salk Institute for Medical Research: Laboratory for Cognitive Neuroscience
type: Resource
type: NamedIndividual
has db xref: nif-0000-10415
synonym: Salk Institute LCN
IAO_0000115: The Salk Institute's Laboratory for Cognitive Neuroscience (LCN) is dedicated to the study of the neural and genetic underpinnings of language and cognition. The LCN organizes its resources into two research foci: Linking Gene, Brain, and Cognition, and Language, Modality and the Brain. Linking Gene, Brain, and Cognition: Behavioral Neurogenetics: - This research is designed to increase the understanding of genetically based disorders, to investigate the consequences of genetic alterations on the development of the brain, and to explore the resulting alteration of cognitive capabilities. Language, Modality, and the Brain: - The focus of this research is to obtain a greater understanding of how language and cognition are represented in the brain. Sponsors: This resource is supported by LCN.

Welcome Trust
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100004440
has db xref: grid.52788.30
has db xref: ISNI: 0000 0004 0427 7672
has db xref: nif-0000-16250
has db xref: SCR_011782
has db xref: Wikidata: Q326276
IAO_0000115: The Wellcome Trust is the largest charity in the UK. We fund innovative biomedical research, in the UK and internationally, spending over 600 million each year to support the brightest scientists with the best ideas. The Wellcome Trust is an independent charity funding research to improve human and animal health. Established in 1936 and with an endowment of around 13 billion, it is the UK's largest non-governmental source of funds for biomedical research. What we do We spend over 600 million every year both in the UK and internationally achieving our mission. Funding We support many different kinds of research and activities with the ultimate aim of protecting and improving human and animal health. This support is not restricted to UK researchers - we devote significant funding to international research too. Biomedical science Our biomedical science funding enables the investigation of health and disease in humans and animals. This includes funding for scientists, clinicians and veterinarians at different career stages. Technology transfer Our technology transfer funding supports the development of innovative, early-stage projects with potential medical applications. Medical humanities Our medical humanities funding supports research into biomedical ethics and the history of medicine. Public engagement Our public engagement funding promotes interest, excitement and debate around science and society. Capital funding Our capital funding is for large-scale construction or refurbishment projects in the UK that support science, public engagement, medical history, or the activities of learned societies. Strategic awards Our Strategic Awards provide flexible funding that adds value to excellent research groups. Managing a grant This area contains information and resources to help you manage a grant once it has been awarded, from the grant-start certificate to the end-of-grant report and beyond. Education Resources Teaching and education Resources to help promote contempora…

University of Alberta; Alberta; Canada
type: Organization
type: NamedIndividual
has db xref: nlx_10148
synonym: University of Alberta
IAO_0000115: Public research university in Edmonton, Alberta, Canada that offers degree programs in a variety of fields including business, arts, education, engineering, nursing, and medicine.

San Diego County Medical Society
type: Resource
type: NamedIndividual
has db xref: nif-0000-10416
synonym: SDCMS
IAO_0000115: The San Diego County Medical Society (SDCMS) is a non-profit organization designed to address San Diego healthcare needs for all patients and physicians through innovation, education and service. The SDCMS Foundation is advancing several innovative programs and initiatives: - The Emergency Department Medical Home (EDMH) Project matches uninsured patients in the emergency department with public and private medical coverage and establishes a medical home for them at local community health centers. - Project Access San Diego (PASD) is a program that connects eligible, low-income, uninsured patients with physicians who provide deeply discounted or pro bono care. - The SDCMS Foundation has also established five medical student scholarships at the UCSD School of Medicine.

San Diego Psychiatric Society
type: Resource
type: NamedIndividual
has db xref: nif-0000-10417
synonym: SD Psychiatric Society
abbrev: SD PSYCH
IAO_0000115: The San Diego Psychiatric Society is a local medical specialty society. It is the district branch of the American Psychiatric Association and the California Psychiatric Association. The physician members specialize in the diagnosis and treatment of mental and emotional disorders and substance abuse. The San Diego Psychiatric Society's organizational objectives include the advancement and improvement of care for persons with mental illness through public information, education, and awareness programs and material. The society represents over 400 psychiatrists, who are the primary mental health advocates for quality patient care. The organization works to improve the public's awareness of mental illness and increase legislative and financial support of psychiatric care. Members serve in community mental health organizations, and advise the legislature on mental health issues.

San Diego Supercomputer Center
type: Organization
type: NamedIndividual
has db xref: grid.419957.7
has db xref: nif-0000-10418
has db xref: Wikidata: Q3947008
abbrev: SDSC
IAO_0000115: Founded in 1985, the San Diego Supercomputer Center (SDSC) enables international science and engineering discoveries through advances in computational science and data-intensive, high-performance computing. SDSC is considered a leader in data-intensive computing, providing resources, services and expertise to the national research community including industry and academia. The mission of SDSC is to extend the reach of scientific accomplishments by providing tools such as high-performance hardware technologies, integrative software technologies, and deep interdisciplinary expertise to these communities. From 1997 to 2004, SDSC extended its leadership in computational science and engineering to form the National Partnership for Advanced Computational Infrastructure (NPACI), teaming with approximately 40 university partners around the country. Today, SDSC is an Organized Research Unit of the University of California, San Diego with a staff of talented scientists, software developers, and support personnel. A broad community of scientists, engineers, students, commercial partners, museums, and other facilities work with SDSC to develop cyberinfrastructure-enabled applications to help manage their extreme data needs. Projects run the gamut from creating astrophysics visualization for the American Museum of Natural History, to supporting more than 20,000 users per day to the Protein Data Bank, to performing large-scale, award-winning simulations of the origin of the universe or how a major earthquake would affect densely populated areas such as southern California. Along with these data cyberinfrastructure tools, SDSC also offers users full-time support including code optimization, training, 24-hour help desk services, portal development and a variety of other services. As one of the NSF's first national supercomputer centers, SDSC served as the data-intensive site lead in the agency's TeraGrid program, a multiyear effort to build and deploy the world's first large-scale …

BroadPeak
type: Resource
type: NamedIndividual
has db xref: OMICS_00433
IAO_0000115: Algorithm for identifying broad peaks in diffuse ChIP-seq datasets.

SamSPECTRAL
type: Resource
type: NamedIndividual
has db xref: biotools:samspectral
has db xref: OMICS_05638
synonym: SamSPECTRAL - Identifies cell population in flow cytometry data
IAO_0000115: Software that identifies cell population in flow cytometry data. It demonstrates significant advantages in proper identification of populations with non-elliptical shapes, low density populations close to dense ones, minor subpopulations of a major population and rare populations. It samples large data such that spectral clustering is possible while preserving density information in edge weights. More specifically, given a matrix of coordinates as input, SamSPECTRAL first builds the communities to sample the data points. Then, it builds a graph and after weighting the edges by conductance computation, the graph is passed to a classic spectral clustering algorithm to find the spectral clusters. The last stage of SamSPECTRAL is to combine the spectral clusters. The resulting connected components estimate biological cell populations in the data sample.

SeattleSNPs - Variation Discovery Resource
type: Resource
type: NamedIndividual
has db xref: nif-0000-10423
synonym: SeattleSNPs
IAO_0000115: The SeattleSNPs PGA is focused on identifying, genotyping, and modeling the associations between single nucleotide polymorphisms (SNPs) in candidate genes and pathways that underlie inflammatory responses in humans. SeattleSNPs is focused on variation analysis in genes related to the inflammatory response. These gene targets are found in specific pathways and from interacting molecules contributing to this response. Available Resources: - Baseline assembled and complete genomic sequence and chromosomal location for candidate gene targets - Mapping of exon and repeat structure for candidate genes - Amplification primers and conditions - SNPs mapped by location in gene structure - SNPs with immediate surrounding sequence for genotype assay design - Genotypes and relative allele frequencies of the SNPs - Special features of SNPs - location (5', coding, etc.), amino acid substitutions, recurrent variation - Manuals on all protocols, data analysis procedures, and use of software tools - Workshop on genetic variation analysis and a gene submission program for variation analysis Sponsors: SeattleSNPs is funded as part of the National Heart Lung and Blood Institute's (NHLBI) Programs for Genomic Applications (PGA).

THetA
type: Resource
type: NamedIndividual
has db xref: OMICS_03562
synonym: THetA: Tumor Heterogeneity Analysis
synonym: Tumor Heterogeneity Analysis
synonym: Tumor Heterogeneity Analysis (THetA)
IAO_0000115: An algorithm that estimates the tumor purity and clonal / subclonal copy number aberrations directly from high-throughput DNA sequencing data.

Signal Transduction Knowledge Environment - Database of Cell Signaling
type: Resource
type: NamedIndividual
has db xref: nif-0000-10426
synonym: STKE DB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. This database provides information on the components of cellular signaling pathways and their relations to one another, which are organized into pathways called Connections Maps, which serve as the graphical interface into the database. Access to the database is free. Scientists with expertise in a given field, designated as Pathway Authorities, provide the information. With canonical or general data about cell signaling, as well as specific data about particular signaling processes in specific organisms and cells, there is information for both novices to cell signaling and experts. The Connections Maps are dynamically generated graphical interface to a database of information on the components of cellular signaling pathways and their relations to one another. Information is provided by pathway authorities with expertise in a given field. These Maps provide information on Canonical Pathways -- idealized or generalized pathways that represent common properties of a particular signaling module or pathway. Sponsors: This database is supported by AAAS.

Simons Foundation Autism Research Initiative: Grant Resource
type: Resource
type: NamedIndividual
has db xref: nif-0000-10428
synonym: SFARI Grants
IAO_0000115: The mission of SFARI is to improve the diagnosis, treatment, and prevention of autism and related developmental disorders. SFARI explores neuroscience from multiple directions, including molecular, cellular, systems, immunological, cognitive, behavioral, genetic, theoretical and computational perspectives. Funding for innovative scientific research is available through a peer-reviewed proposal process at regular intervals. Research projects are reviewed by a scientific advisory board and managed by the scientific director and a highly qualified staff. Proposals in multiple research areas are sought, to reflect the complex nature of autism. The Foundation supports innovative scientific projects where our involvement will play an essential role. In the course of this support, The Foundation is interested in partnering with other entities, or providing matching support where appropriate. The Simons Foundation has historically accepted only solicited grant proposals. These grant decisions are made by the Trustees of The Simons Foundation, who review applications on an ongoing basis. In the area of autism research, requests for proposals are issued on an annual basis. The Simons Foundation does not give grants to individuals, except through their institutions.

Social Anxiety Disorder: Learn How to Cope with Anxiety
type: Resource
type: NamedIndividual
has db xref: nif-0000-10429
synonym: Social Anxiety Disorder
IAO_0000115: This site is about Social Anxiety Disorder, how to diagnose social anxiety, how to live and cope with social anxiety, and how to treat social anxiety. Additionally, this website also intends to educate, inform, promote self-help, and provide a way to facilitate dialog between those who suffer from social phobia.

Konrad Lorenz Institute for Evolution and Cognition Research; Altenberg; Austria
type: Organization
type: NamedIndividual
has db xref: nlx_84569
has db xref: nlx_143669
synonym: Konrad Lorenz Institute
abbrev: KLI
IAO_0000115: Institute for the study of theoretical biology with a focus on evolutionary developmental biology and cultural complexity.

Dendritica: Software Tools for Studying Dendritic Signaling
type: Resource
type: NamedIndividual
has db xref: nif-0000-10431
synonym: Dendritica
IAO_0000115: Dendritica is a program package for relating dendritic geometry and signal propagation. The programs are based on those used for the simulations described in the following paper: Vetter, P., Roth, A. & Husser, M. (2001). Action potential propagation in dendrites depends on dendritic morphology. Journal of Neurophysiology, 85: 926-937. Dendritica can functionally be divided into three main parts: - Interactive morphological analysis and electrophysiological simulation of single cells - Automated batch simulations across a set of morphologies using the same simulation parameters - Automated analysis of batch simulation runs Dendritica requires NEURON 4.1.1 with some modifications described in Appendix 1. It was tested for NEURON 4.1.1 on Linux and SGI IRIX. Some modifications to the Dendritica code may be necessary in order to run it on older or newer versions of NEURON. Sponsors: This work was supported by the Wellcome Trust, the European Community, the Max-Planck-Gesellschaft, the Wellcome Trust 4-year PhD Programme in Neuroscience.

Stony Brook University Medical Center: Neuropathology Primer
type: Resource
type: NamedIndividual
has db xref: nif-0000-10438
synonym: Neuropathology Primer
IAO_0000115: This is a primer of basic neuropathology- The Central Nervous System and Skeletal Muscle. It is organized in chapters by category of disease with a separate chapter for skeletal muscle. Many of the diseases could be included in more than one chapter because of overlapping pathophysiology; in each case the disorder is included in a single section in the interest of convenience. In order to recognize pathology one must have a basic foundation in normal structure, so the first chapter is an overview of basic regional central nervous system structure and anatomy. It includes an introduction to neurohistology. Other chapters address the pathophysiology of different categories of disease and provide examples of gross and microscopic pathology when they are available.

South African National Bioinformatics Institute: Resources
type: Resource
type: NamedIndividual
has db xref: nif-0000-10432
synonym: SANBI
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. The South African National Bioinformatics Institute delivers biomedical discovery appropriate to both international and African context. Researchers at SANBI perform the highest level of research and provide excellence in education. Research at SANBI has set well recognized milestones in the field of computational biology. The tools and techniques used have not only been developed but also implemented across heterogeneous domains of advanced research. Local and international efforts have driven our discoveries. Until recently, the core of SANBIs research has focused upon gene expression biology. Methods developed and applied at SANBI revolve around a greater understanding of the underlying causes of diseases. SANBI approaches the problem by comparison of genes, genomes and transcriptomes. It uses computational gene expression biology to create novel biological insights and to provide biomarkers for experimental validation. It also performs analysis of human genome variation, transcriptional diversity on both the expression and splicing level and the unravelling of transcriptional regulatory networks. Resources - Hinv, STACKdb, Malaria resources and Trypanosome databases are available for on-line seaching. - SANBI offers WCD, STACKdb, stackPACK and eVOC and the eVOKE viewer as tools that can be downloaded. Sponsors: SANBI receives funding and support from a range of organisations in South Africa and Internationally. Organisations currently supporting SANBI include: South Africa * South African Medical Research Council * South African AIDS Vaccine Initiative * National Bioinformatics Network * National Research Foundation * Claude Leon Foundation * International Business Machines Inc. Europe * European Unions 6th Framework Programme * World Health Organization USA * US National Institutes of Health * Fogarty International Centre * Ludwig Institute for Cancer Research

Spike Train Analysis Software by Attila Szucs: Orbital Spike 4
type: Resource
type: NamedIndividual
has db xref: nif-0000-10433
synonym: Orbital Spike 4
IAO_0000115: Orbital Spike is a tool for time series analysis. It contains a wide range of methods to analyze data from point processes such as spike arrival times, heart beats or other behavioral episodes. It is optimized this program for spike trains but it works with other types of data, too. The program can analyze up to 8 channels recorded simultaneously each containing a maximum of 132,000 events (spikes). Assuming an average firing rate of 10 Hz for a neuron, you can then analyze a time series of approximately 3 and half hours long. There are up to 8 panels shown in the Orbital Spike desktop. The panels will contain the kind of data of interest. The graphs are associated with a bunch of parameters like window width, bin size, resolution, delay etc. All these parameters are listed in the parameter box, which appears on the right side of the desktop. It is pretty easy to change the parameters and what is nice, the corresponding graph(s) will be recalculated immediately. You can also use a dialog box to change parameters. There are a lot of functions, statistics, graphs and diagrams available. A few of them are: * Interspike interval sequences * ISI Poincar * maps or return maps Instantaneous firing rate * ISI histograms and probability densities * Joint ISI and MSI probability densitograms * Autocorrelation, crosscorrelation * Spike density functions using kernel estimators * Fourier-amplitude spectrum and spectogram * Symbolic maps, recurrence plots * Phase plots of spike density functions Sponsors: Support for this work came from the U.S. Department of Energy, Office of Basic Energy Sciences, Division of Engineering and Geosciences, under Grants DE-FG03-90ER14138 and DE-FG03-96ER14592; from the Office of Naval Research under Grant N00014-00-1-0181; from the National Science Foundation under Grant PHY0097134; from the National Institutes of Health under Grants R01 NS-40110-01A2 and 1RO1 NS-40110; and from the Army Research Office under Contract DAAD19-01-1-0026. R. D. Pint…

SPRUSTON / KATH LAB: Neuraling Modeling Database NEURAL MODELING DATABASE
type: Resource
type: NamedIndividual
has db xref: nif-0000-10434
synonym: SPRUSTON / KATH LAB
IAO_0000115: This database contains morphologies of hippocampal pyramidal cells and interneurons (in Neurolucida, NEURON, and pdf formats) as well as data recorded from those cells. Sponsors:This work was supported by grants from the NIH (T32-GM-08061 to T.J.M., F32-NS-10532 to N.L.G., and R01-NS35180 and R01-NS 46064 to N.S. and W.L.K.) and NSF (IGERT fellowship to Y.K.). NS46064 is part of the NSF/NIH Collaborative Research in Computational Neuroscience Program

Sparse Learning with Efficient Projections
type: Resource
type: NamedIndividual
has db xref: SciRes_000170
synonym: SLEP: Sparse Learning with Efficient Projections
synonym: Sparse Learning with Efficient Projections (SLEP)
abbrev: SLEP
IAO_0000115: Software package that provides functions for solving a family of sparse learning algorithms. The functions implemented enjoy the convergence rate of O(1/k^2), although the objective function is non-smooth. Main features: * First-Order Method. At each iteration, they only need to evaluate the function value and the gradient; and thus the algorithms can handle large-scale sparse data. * Optimal Convergence Rate. The convergence rate O(1/k^2) is optimal for smooth convex optimization via the first-order black-box methods. * Efficient Projection. The projection problem (proximal operator) can be solved efficiently. * Pathwise Solutions. The SLEP package provides functions that efficiently compute the pathwise solutions corresponding to a series of regularization parameters by the warm-start technique.

Korean Ministry of Education Science and Technology
type: Resource
type: NamedIndividual
has db xref: nlx_144423
synonym: Ministry of Education Science and Technology of Korea
abbrev: MEST
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented April 11, 2017. Division within the South Korean government that handled affairs of education and science. It has since been split into Ministry of Science, ICT and Future Planning and Ministry of Education.

AutDB
type: Resource
type: NamedIndividual
has db xref: nif-0000-02587
synonym: AutDB - An Interface to Autism Research
synonym: AutDB: a Genetic Database for Autism Spectrum Disorders
synonym: SFARI Gene
synonym: SFARI Gene: AutDB
synonym: Simons Foundation Autism Research Initiative Gene: Autism Database
IAO_0000115: Curated public database for autism research built on information extracted from the studies on molecular genetics and biology of Autism Spectrum Disorders (ASD). The genetic information includes data from linkage and association studies, cytogenetic abnormalities, and specific mutations associated with ASD. New gene submissions are welcome. Modules: * Human Gene: thoroughly annotated list of genes that have been studied in the context of autism, with information on the genes themselves, relevant references from the literature, and the nature of the evidence. Uniquely, SFARI Gene incorporates information on both common and rare variants. * Animal Model: information about lines of genetically modified mice that represent potential models of autism. This information includes the nature of the targeting construct, the background strain and, most importantly, a thorough summary of the phenotypic features of the mice that are most relevant to autism. * Protein Interaction (PIN): compilation of all known direct protein interactions for those gene products implicated in autism. It presents both graphical and tabular views of interactomes, highlighting connections between autism candidate genes. Each protein interaction is manually verified by consultation with the primary reference. * Copy Number Variant (CNV): a parallel resource providing genetic information about all known copy number variants linked to autism. * Gene Scoring: includes a "score" for each autism candidate gene, based on an assessment of the strength of human genetic evidence.

Stable Isotope Labeling with Amino Acids in Cell Culture
type: Resource
type: NamedIndividual
has db xref: nif-0000-10435
synonym: SILAC
IAO_0000115: Stable isotope labeling with amino acids in cell culture (SILAC) is a simple and straightforward approach for in vivo incorporation of a label into proteins for mass spectrometry (MS)-based quantitative proteomics. SILAC relies on metabolic incorporation of a given "light" or "heavy" form of the amino acid into the proteins. The method relies on the incorporation of amino acids with substituted stable isotopic nuclei (e.g. deuterium, 13C, 15N). In an experiment, two cell populations are grown in culture media that are identical except that one of them contains a "light" and the other a "heavy" form of a particular amino acid (e.g. 12C and 13C labeled L-lysine, respectively). When the labeled analog of an amino acid is supplied to cells in culture instead of the natural amino acid, it is incorporated into all newly synthesized proteins. After a number of cell divisions, each instance of this particular amino acid will be replaced by its isotope labeled analog. Since there is hardly any chemical difference between the labeled amino acid and the natural amino acid isotopes, the cells behave exactly like the control cell population grown in the presence of normal amino acid. It is efficient and reproducible as the incorporation of the isotope label is 100%. SILAC Applications: - Differential expression of proteins and identification of disease biomarkers - Cell signaling dynamics - Analysis of yeast pheromone signaling pathway - Identification of methylation sites - Identification of protease substrates - Study of protein complexes/protein interactions - Analysis of signaling pathways and effect of pharmacological inhibitors - Subcellular proteomics Sponsors: Supported in part by an NIH Roadmap grant Technology Center for Networks & Pathways of Lysine Modification.

Stanford Genomic Resourses
type: Resource
type: NamedIndividual
has db xref: nif-0000-10436
synonym: Genomic Databases
IAO_0000115: This resource hyperlinks to systematic analysis projects, resources, laboratories, and departments at Stanford University.

TCW
type: Resource
type: NamedIndividual
has db xref: biotools:tCW
has db xref: OMICS_01940
synonym: TCW: Transcriptome Computational Workbench
synonym: Transcriptome Computational Workbench
IAO_0000115: Software package for assembling, annotating, querying, and comparing transcript and expression level data that consists of two parts: * singleTCW (sTCW): Single transcript sets or assemblies; annotation; differential expression (EdgeR, DEGSeq, DESeq, GoSeq) * multiTCW (mTCW): Comparison of multiple transcript sets; ortholog grouping (e.g., OrthoMCL) It has been tested on Linux and uses Java, mySQL and optionally R.

GATK
type: Resource
type: NamedIndividual
has db xref: biotools:gatk
has db xref: nlx_154324
has db xref: OMICS_00286
synonym: Genome Analysis ToolKit
IAO_0000115: A software package to analyze next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. This software library makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner. (entry from Genetic Analysis Software)

Flybrain at Stanford
type: Resource
type: NamedIndividual
has db xref: nif-0000-10437
synonym: Flybrain (at) Stanford
synonym: Flybrain (at) Stanford - A warped brain is a good thing
abbrev: Flybrain(at)Stanford
abbrev: FlybrainatStanford
IAO_0000115: Project content including raw image data, neuronal tracings, image registration tools and analysis scripts covering three manuscripts: Comprehensive Maps of DrosophilaHigher Olfactory Centres : Spatially Segregated Fruit and Pheromone Representation which uses single cell labeling and image registration to describe the organization of the higher olfactory centers of Drosophila; Diversity and wiring variability of olfactory local interneurons in the Drosophila antennal lobe which uses single cell labeling to describe the organization of the antennal lobe local interneurons; and Sexual Dimorphism in the Fly Brain which uses clonal analysis and image registration to identify a large number of sex differences in the brain and VNC of Drosophila. Data * Raw Data of Reference Brain (pic, amira) (both seed and average) * Label field of LH and MB calyx and surfaces for these structures * Label field of neuropil of Reference Brain * Traces (before and after registration). Neurolucida, SWC and AmiraMesh lineset. * MB and LH Density Data for different classes of neuron. In R format and as separate amira files. * Registration files for all brains used in the study * MBLH confocal images for all brains actually used in the study (Biorad pic format) * Sample confocal images for antennal lobe of every PN class * Confocal stacks of GABA stained ventral PNs Programs * ImageJ plugins (Biorad reader /writer/Amira reader/writer/IGS raw Reader) * Binary of registration, warp and gregxform (macosx only, others on request) * Simple GUI for registration tools (macosx only at present) * R analysis/visualization functions * Amira Script to show examples of neuronal classes The website is a collaboration between the labs of Greg Jefferis and Liqun Luo and has been built by Chris Potter and Greg Jefferis. The core Image Registration tools were created by Torsten Rohlfing and Calvin Maurer.

Degust
type: Resource
type: NamedIndividual
has db xref: OMICS_01934
synonym: Degust - Take the time to digest and appreciate your Differential Gene Expression data
synonym: DGE-Vis
IAO_0000115: An interactive web tool for visualizing differential gene expression data.

flowUtils
type: Resource
type: NamedIndividual
has db xref: OMICS_05614
synonym: flowUtils - Utilities for flow cytometry
IAO_0000115: Software that provides utilities for flow cytometry data.

Aspergillus Genomes
type: Resource
type: NamedIndividual
has db xref: nif-0000-02577
has db xref: r3d100011253
IAO_0000115: A resource for viewing annotated genes arising from various Aspergillus sequencing and annotation projects, resulting from the merging of Central Aspergillus Data REpository (CADRE) and The Aspergillus Website, which took place in June 2008. The principal role of CADRE is to aid the Aspergillus research community by managing Aspergillus genome data and by providing visualization tools, ranging from relatively simple annotation displays to more complex data integration displays. In contrast, The Aspergillus Website provides a range of information to the medical community (i.e., clinicians, patients and scientists) regarding the genus Aspergillus and the diseases, such as Aspergillosis, that it can cause. CADRE has been implemented using the Ensembl v22 suite. This suite comprises: * a database schema, which has been devised for storing annotated eukaryotic genomes. The schema is implemented with the MySQL relational database management system. * several specialized programming modules for building interfaces (i.e., BioPerl and Ensembl API modules). * a series of programs (i.e., Perl CGI scripts using the API modules) for viewing genomic data within a web browser., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

DAVID
type: Resource
type: NamedIndividual
has db xref: nif-0000-10451
has db xref: nif-0000-30408
has db xref: OMICS_02220
has db xref: SCR_003033
synonym: Database for Annotation Visualization and Integrated Discovery
synonym: DAVID Bioinformatics Resources
synonym: The Database for Annotation
synonym: The Database for Annotation Visualization and Integrated Discovery Bioinformatics Resources
synonym: Visualization and Integrated Discovery Bioinformatics Resources
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. Bioinformatics resource system including web server and web service for functional annotation and enrichment analyses of gene lists. Consists of comprehensive knowledgebase and set of functional analysis tools. Includes gene centered database integrating heterogeneous gene annotation resources to facilitate high throughput gene functional analysis.

EPMBA.ORG: Electronic Prenatal Mouse Brain Atlas
type: Resource
type: NamedIndividual
has db xref: nif-0000-10452
synonym: Electronic Prenatal Mouse Brain Atlas
synonym: EPMBA.org
abbrev: EPMBA
IAO_0000115: The Electronic Prenatal Mouse Brain Atlas, EPMBA, at present consists of two sets of annotated images of coronal sections from Gestational Day (GD) 12 heads and GD 16 brains of C57BL/6J mice. Ten micron thick sections were stained with hematoxylin and eosin. Images were prepared at various resolutions for annotations and for high resolution presentation. A subset of sections were annotated and linked to anatomical terms. Additionally, horizontal sections of a GD 12 head were aligned and re-assembled into a 3D volume for digital sectioning in arbitrarily oblique planes. These images were captured using a Nikon E800 stereomicroscope with a 10X objective. The resolution is 1.35 pixels/micrometer. The PC program used to grab the images, Microbrightfield's Neurolucida (version 6), stitched together a mosaic of between 10 and 50 high-res images for each tissue slice, while the user focused the scope for each mosaic tile. Since the nature of optic lenses is to focus on one central point, it was difficult to obtain a uniformly-focused field of vision; as such, small areas of these images are blurred. Images were then transferred to a Macintosh and processed in Adobe Photoshop (version 7). Color levels were adjusted for maximum clarity of the tissue, and areas surrounding the tissue were cleared of artifacts. Each image is approximately 3350 pixels wide by 2650 pixels high. A scale bar with a length of 1350 pixels/mm is visible in the lower right-hand corner of each image. The annotations have been completed for the Atlas of Developing Mouse Brain Gestational (Embryonic) Day 12 (7/5/07) as well as the Atlas of Developing Mouse Brain Embryonic Day 16 (4/26/07). The 3D EPMBA data set has been mounted on a NeuroTerrain Atlas Server (NtAS). (6/27/07).

The Alternatve Splicing Database
type: Resource
type: NamedIndividual
has db xref: biotools:astd
has db xref: nif-0000-02579
synonym: ASTD
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Alternative Splicing and Transcript Diversity (ASTD) database project is creating a database of alternative splice events and transcripts of genes from human, mouse and rat. Full length transcripts are generated with the aim of understanding the mechanism of alternative splicing on a genome-wide scale. The current release of the human genome consists of: 16715 genes, 14101 have more than one splice isoform, with an average of 5.6 splice patterns per gene. 10831 transcripts are annotated as full length with a transcription start site and a poly(A). The current release of the mouse genome consists of: 16491 genes, 13028 have more than one splice isoform, with an average of 4 splice patterns per gene. 6011 transcripts are annotated as full length with a transcription start site and a poly(A). The current release of the rat genome consists of: 10424 genes, 6344 have more than one splice isoform, with an average of 2.6 splice patterns per gene. 1250 transcripts are annotated as full length with a transcription start site and a poly(A). Sponsors: The ASTD project at EBI is supported by a grant from the EC: Eurasnet Network of Excellence (LSHG-CT-2005-518238). It was also supported by the ASD grant from the EC (QLRT-CT-2001-02062) until November 2005 and the ATD grant from the EC (LSHG-CT-2003-503329) until May 2007.

New England Regional Office HDSA
type: Resource
type: NamedIndividual
has db xref: nif-0000-10472
synonym: HDSA New England Region
synonym: HDSA New England Regional Office
synonym: HDSA-New England
synonym: Huntington's Disease Society of America - New England Region
synonym: New England Region of The Huntington's Disease Society of America
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented April 12, 2016. The New England HDSA office provides education, advocacy, support, and care to people with Huntington's Disease and their families throughout New England. It funds research efforts and has an extensive education outreach program.

NIH VideoCasting
type: Resource
type: NamedIndividual
has db xref: nif-0000-10454
synonym: NIH VideoCast
synonym: NIH VideoCasting and Podcasting
synonym: NIH VideoCasting Podcasting
synonym: NIH VideoCasts
synonym: NIH Videos
abbrev: VideoCast
IAO_0000115: VideoCasting of special NIH events, seminars, conferences, meetings and lectures available to viewers on the NIH network and the Internet from the VideoCast web site. VideoCasting is the method of electronically streaming digitally encoded video and audio data from a server to a client. VideoCast is often referred to as streaming video. Streaming files are not downloaded, but rather are broadcast in a manner similar to television broadcasts. The videos are processed by a compression program into a streaming format and delivered in a staggered fashion to minimize impact upon the network and maximize the experience of the content for the viewer. When users request a streaming file they will receive an initial burst of data after a short delay (file latency). While content is being viewed, the streaming server machine and software continues to stream data in such a manner that the viewer experiences no break in the content. CIT can broadcast your seminar, conference or meeting live to a world-wide audience over the Internet as a real-time streaming video. The event can be recorded and made available for viewers to watch at their convenience as an on-demand video or a downloadable podcast. CIT can also broadcast NIH-only or HHS-only content.

ASTRAL Compendium for Sequence and Structure Analysis
type: Resource
type: NamedIndividual
has db xref: nif-0000-02580
synonym: The ASTRAL Compendium for Sequence and Structure Analysis
abbrev: ASTRAL
IAO_0000115: It provides databases and tools useful for analyzing protein structures and their sequences. It is partially derived from, and augments the SCOP: Structural Classification of Proteins database, a database created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. Most of the resources provided here depend upon the coordinate files maintained and distributed by the Protein Data Bank. Sponsors: This work is supported by grants from the NIH (1-P50-GM62412, 1-K22-HG00056) and the Searle Scholars Program (01-L-116), and by the US Department of Energy under contract DE-AC03-76SF00098.

Harvey Project: Open Course Collaboratories
type: Resource
type: NamedIndividual
has db xref: nif-0000-10457
synonym: The Harvey Project
abbrev: Harvey Project
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. It is an international collaboration of educators, researchers, physicians, students, programmers, instructional designers and graphic artists working together to build interactive, dynamic human physiology course materials on the Web. Sponsors: This work has received funding from the US National Science Foundation.

RchyOptimyx
type: Resource
type: NamedIndividual
has db xref: OMICS_05637
synonym: RchyOptimyx - Optimyzed Cellular Hierarchies for Flow Cytometry
synonym: RchyOptimyx: Optimyzed Cellular Hierarchies for Flow Cytometry
IAO_0000115: Software that constructs a hierarchy of cells using flow cytometry for maximization of an external variable (e.g., a clinical outcome or a cytokine response).

Axel Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02590
abbrev: Axeldb
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 21, 2011. Database focusing on gene expression in the frog Xenopus laevis, it is the web companion to the research papers describing a large-scale in situ hybridization screening in Xenopus embryos. The goals of this large-scale in situ screen project are to identify genes by the characterization of their expression pattern, to partially sequence the corresponding cDNAs and to maintain a database collecting the results.

Johns Hopkins NIMH Research Center Novel Therapeutics of HIV-associated Cognitive Disorders
type: Resource
type: NamedIndividual
has db xref: nif-0000-10462
synonym: JHU NIMH Center for Novel Therapeutics of HIV-associated Cognitive Disorders
synonym: Johns Hopkins National Institute of Mental Health (NIMH) Center for Novel Therapeutics of HIV-associated Cognitive Disorders
synonym: Johns Hopkins National Institute of Mental Health Center for Novel Therapeutics of HIV-associated Cognitive Disorders
IAO_0000115: The Johns Hopkins NIMH Center is comprised of an interdisciplinary research team who has pooled their talents to study the nature of HIV-associated neurocognitive disorders (HAND). Their aim is to translate discoveries of the pathophysiological mechanisms into novel therapeutics for HAND. Objectives * To integrate aspects of ongoing research in HAND and SIV encephalitis * Develop high-throughput and screening assays for identifying novel therapeutic compounds * Use proteomics and lipidomics approaches to indentifying surrogate markers of disease activity * Disseminate information and education about HAND through existing and new educational systems, including the JHU AIDS Education Training Center and the JHU Center for Global Clinical Education * Facilitate the entry of new investigators into Neuro-AIDS research, and to catalyze new areas of research, particularly where relevant for drug discovery or the development of validated surrogate markers

StatAlign
type: Resource
type: NamedIndividual
has db xref: biotools:StatAlign
has db xref: OMICS_03743
synonym: StatAlign 2.0
IAO_0000115: Software package for Bayesian analysis of protein, DNA and RNA sequences. It utilizes multiple alignments, phylogenetic trees and evolutionary parameters to quantify uncertainty in these analyses. It is written in Java.

Vascular Modeling Toolkit
type: Resource
type: NamedIndividual
has db xref: nlx_155869
has db xref: OMICS_13947
synonym: vmtk - the Vascular Modeling Toolkit
abbrev: vmtk
IAO_0000115: Software collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels.

Alignable Tight Genomic Cluster
type: Resource
type: NamedIndividual
has db xref: nif-0000-02581
abbrev: ATGC
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. ATGC stands for Alignable Tight Genomic Cluster, which is cluster of closely related prokaryotic genomes. ATGC is the principal notion of this web resource. The purpose of this web resource is to prepare ATGC-derived data sets for a variety of research projects in functional and evolutionary genomics. Unique features of ATGC include: * Reliable identification of orthologs (high degree of similarity between the genomes in the set allow an extensive use of synteny in ortholog identification); * Fine granularity of protein classification (in comparisons of more distant genomes, proteins belonging to families of paralogs are often lumped into a singlegroup; under the ATGC approach, comparison of genomic sequences from highly similar genomes allows one to track each set of orthologs separately); * Relative rarity of changes of any kind (in sequence, genome organization and gene content) allows the use of parsimony-related methods of analysis.

Longhorn Array Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-10465
abbrev: LAD
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Longhorn Array Database (LAD) is a MIAME compliant microarray database that operates on PostgreSQL and Linux. It is a fully open source version of the Stanford Microarray Database (SMD), one of the largest microarray databases. LAD provides a simple, free, open, reliable and proven solution for storage and analysis of two-color microarray data. It stores raw and normalized data from microarray experiments, as well as their corresponding image files. In addition, LAD provides interfaces for data retrieval, analysis, and visualization.

Arabidopsis thaliana Protein Interactome Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02585
has db xref: OMICS_01898
synonym: AtPID Database
abbrev: AtPID
IAO_0000115: Centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome. The Protein-protein interaction pairs are predicted by integrating several methods with the Naive Baysian Classifier. All other related information curated is manually extracted from published literature and other resources from some expert biologists. You are welcomed to upload your PPI or subcellular localization information or report data errors. Arabidopsis proteins is annotated with information (e.g. functional annotation, subcellular localization, tissue-specific expression, phosphorylation information, SNP phenotype and mutant phenotype, etc.) and interaction qualifications (e.g. transcriptional regulation, complex assembly, functional collaboration, etc.) via further literature text mining and integration of other resources. Meanwhile, the related information is vividly displayed to users through a comprehensive and newly developed display and analytical tools. The system allows the construction of tissue-specific interaction networks with display of canonical pathways.

FGED
type: Resource
type: NamedIndividual
has db xref: nif-0000-10466
has db xref: OMICS_01778
synonym: Functional Genomics Data Society
synonym: MGED
synonym: MGED Society
synonym: The Functional Genomics Data Society
synonym: The Microarray Gene Expression Data Society
IAO_0000115: Society that develop standards for biological research data quality, annotation and exchange. They facilitate the creation and use of software tools that build on these standards and allow researchers to annotate and share their data easily. They promote scientific discovery that is driven by genome wide and other biological research data integration and meta-analysis. Historically, FGED began with a focus on microarrays and gene expression data. However, the scope of FGED now includes data generated using any technology when applied to genome-scale studies of gene expression, binding, modification and other related applications.

MPIDB
type: Resource
type: NamedIndividual
has db xref: nif-0000-10467
has db xref: r3d100010673
synonym: Microbial Protein Interaction Database
synonym: The Microbial Protein Interaction Database
IAO_0000115: Database that collects and provides all known physical microbial interactions. Currently, 24,295 experimentally determined interactions among proteins of 250 bacterial species/strains can be browsed and downloaded. These microbial interactions have been manually curated from the literature or imported from other databases (IntAct, DIP, BIND, MINT) and are linked to 26,578 experimental evidences (PubMed ID, PSI-MI methods). In contrast to these databases, interactions in MPIDB are further supported by 68,346 additional evidences based on interaction conservation, co-purification, and 3D domain contacts (iPfam, 3did). (spoke/matrix) binary interactions inferred from pull-down experiments are not included.

MLRN
type: Resource
type: NamedIndividual
has db xref: nif-0000-10468
synonym: The Mind and Life Research Network
IAO_0000115: A project of the Mind and Life Institute, fosters multidisciplinary communication about scientific research on meditation and other contemplative practices. It is dedicated to fostering dialog and research at the highest possible level between modern science and the great living contemplative traditions, especially Buddhism. It builds on a deep commitment to the power and value of both of these ways of advancing knowledge and their potential to alleviate suffering. Membership is free, and this loose affiliation of scientists, meditators, and people interested in research promotes opportunities for researchers and meditators to communicate together. All perspectives, scientific fields, and styles of meditation are welcome. The MLRN includes cognitive neuroscientists who skillfully use scientific methods in the study of meditation, meditation scholars interested in scientific interfaces, and people who can help support meditation research. MLRN members are likely to be recruited to serve as advisors, referees, participants, and collaborators in upcoming studies on meditation. The MLRN encompasses a variety of meditation practices, and incorporates both contemplative and scientific approaches. The MLRN includes a low-volume, moderated electronic announcement list. This list maintains a high signal-to-noise ratio by distributing infrequent but important messages to large numbers of recipients. Members of this announcement list receive bibliographic updates on recent publications, announcements of upcoming conferences, calls for papers for special-issue journals and conference symposia, synopses of recent meetings, announcements of relevant email lists, websites, and other resources, and other announcements appropriate for widespread distribution. Sponsors: The Hershey Family Foundation has been patron since 1990. This Institute has received generous financial support from the Fetzer Institute, The Nathan Cummings Foundation, Branco Weiss, Adam Engle, Michael Sautman, Mr…

University of California at San Diego, Department of Psychiatry Postdoctoral Positions
type: Organization
type: NamedIndividual
has db xref: nif-0000-10506
synonym: UCSD Psychiatry PostDoc Positions
IAO_0000115: Postdoctoral positions within the UCSD Department of Psychiatry available for qualified candidates. The following are the available postdoctoral opportunities: - Post-Doctoral Position in Co-Occurring Disorders - Postdoctoral Positions in Behavioral Neuroscience in the areas of nicotine dependence, depression and schizophrenia - Postdoctoral Position in Neuroimaging and Twin Research - Postdoctoral Fellowship in Behavioral Neuroscience in the area of methamphetamine dependence and HIV

Arabidopsis thaliana Genome Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02582
synonym: Arabidopsis thaliana Genome DB
abbrev: AtGDB
IAO_0000115: Database providing a sequence-centered genome view for Arabidopsis thaliana, with a narrow focus on gene structure annotation. The current genome assembly displayed at AtGDB is version TAIR9. Annotated gene models are TAIR10. They have mapped the complete set of 176,915 publicly available Arabidopsis EST sequences onto the Arabidopsis genome using GeneSeqer, a spliced alignment program incorporating sequence similarity and splice site scoring. About 96% of the available ESTs could be properly aligned with a genomic locus, with the remaining ESTs deriving from organelle genomes and non-Arabidopsis sources or displaying insufficient sequence quality for alignment. The mapping provides verified sets of EST clusters for evaluation of EST clustering programs. Analysis of the spliced alignments suggests corrections to current gene structure annotation and provides examples of alternative and non-canonical pre-mRNA splicing.

Korea Advanced Institute of Science and Technology; Daejeon; South Korea
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100007107
has db xref: grid.37172.30
has db xref: ISNI: 0000 0001 2292 0500
has db xref: nlx_155859
has db xref: Wikidata: Q39949
synonym: Korea Advanced Institute of Science and Technology
abbrev: KAIST
IAO_0000115: Institute dedicated to research in science and technology in South Korea modeled after a research university.

OBART
type: Resource
type: NamedIndividual
has db xref: nif-0000-10473
synonym: Online Brain Atlas Reconciliation Tool
synonym: The Online Brain Atlas Reconciliation Tool
IAO_0000115: Tool that provides an interactive method to examine quantitative relationships between brain regions defined by different digital atlases or parcellation methods. Its current focus is for human brain imaging, though the techniques generalize to other domains. The method offers a quantitative answer to the nomenclature problem in neuroscience by comparing brain parts on the basis of their geometrical definitions rather than on the basis of name alone. Thus far these tools have been used to quantitatively compare eight distinct parcellations of the International Consortium for Brain Mapping (ICBM) single-subject template brain, each created using existing atlasing methods. This resources provides measures of global and regional similarity, and offers visualization techniques that allow users to quickly identify the correspondences (or lack of correspondences) between regions defined by different atlases.

ExpressionPlot
type: Resource
type: NamedIndividual
has db xref: OMICS_01939
abbrev: expressionplot
IAO_0000115: Software package consisting of a default back end, which prepares raw sequencing or Affymetrix microarray data, and a web-based front end, which offers a biologically centered interface to browse, visualize, and compare different data sets.

R Project for Statistical Computing
type: Resource
type: NamedIndividual
has db xref: biotools:r
has db xref: nif-0000-10474
has db xref: OMICS_01147
has db xref: SCR_021974
synonym: R Package
synonym: R Project
synonym: R project
synonym: R software
synonym: R version 3.5.1
synonym: R version 3.6.1
synonym: R-3
synonym: The R Project for Statistical Computing
IAO_0000115: Software environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS.

Rosetta Bit
type: Resource
type: NamedIndividual
has db xref: nlx_155947
IAO_0000115: Public datasets that have been transcoded into multiple formats. This library of valid file format conversions (DICOM->NIFTI, DICOM->PAR/REC, etc.) will provide a reference for tool developers seeking to support multiple sources of data.

Scripps Research Institute
type: Organization
type: NamedIndividual
has db xref: grid.214007.0
has db xref: ISNI: 122199231
has db xref: nif-0000-10475
has db xref: Wikidata: Q793867
synonym: Scripps Research
synonym: The Scripps Research Institute
abbrev: TSRI
IAO_0000115: Nonprofit American medical research facility that focuses on research and education in the biomedical sciences. Headquartered in San Diego, California with a sister facility in Jupiter, Florida, the institute has laboratories employing scientists, technicians, graduate students, and administrative and other staff, making it the largest private, non-profit biomedical research organization in the United States and among the largest in the world.

S-MART
type: Resource
type: NamedIndividual
has db xref: biotools:mapperanalyzer
has db xref: biotools:s-mart
has db xref: OMICS_01937
IAO_0000115: Software toolbox that manages your RNA-Seq and ChIP-Seq data and also produces many different plots to visualize your data. It performs several tasks that are usually required during the analysis of mapped RNA-Seq and ChIP-Seq reads, including data selection and data visualization. It includes the selection (or the exclusion) of the data that overlaps with a reference set, clustering and comparative analysis. It also provides many ways to visualize data: size of the reads, density on the genome, distance with respect to a reference set, and the correlation of two data sets (with cloud plots). A computer science background is not required to run it through a graphical interface and it can be run on any personal computer, yielding results within an hour for most queries.

Pecan
type: Resource
type: NamedIndividual
has db xref: biotools:pecan
has db xref: OMICS_03739
IAO_0000115: A Java consistency based multiple sequence alignment software program.

University of Utah Genetic Science Learning Center - Learn Genetics
type: Resource
type: NamedIndividual
has db xref: nif-0000-10482
synonym: Genetic Science Learning Center
synonym: Genetic Science Learning Center - Learn Genetics
synonym: Genetic Science Learning Center - Learn.Genetics
synonym: University of Utah Genetic Science Learning Center
abbrev: Learn Genetics
abbrev: Learn.Genetics
IAO_0000115: Educational resources that provide accurate and unbiased information about topics in genetics, bioscience and health for global and local audiences. They are jargon-free, target multiple learning styles, and often convey concepts through animation and interactivity. The Genetic Science Learning Center is a science and health education program located in the midst of the bioscience research being carried out at the University of Utah. Our mission is making science easy for everyone to understand. * Two websites, available free of charge to Internet users worldwide: ** Learn.Genetics delivers educational materials on genetics, bioscience and health topics. They are designed to be used by students, teachers and members of the public. The materials meet selected US education standards for science and health. ** Teach.Genetics provides resources for K-12 teachers, higher education faculty, and public educators. These include PDF-based Print-and-Go™ activities, unit plans and other supporting resources. The materials are designed to support and extend the materials on Learn.Genetics. *Professional development programs that update K-16 teachers' expertise in bioscience and health topics as well as prepare them to implement the materials on our websites. * Community programs that engage with diverse communities in discussions about genetics and health, and in developing culturally and linguistically-appropriate educational materials. Some topics in genetics and bioscience research are controversial. The Center does not take sides in political or ethical controversies. Rather, our goal is to provide comprehensive information that promotes a lively discussion of these topics, so that individuals can arrive at their own informed decisions.

Korean Ministry of Science ICT and Future Planning
type: Resource
type: NamedIndividual
has db xref: nlx_144422
synonym: Ministry of Science ICT and Future Planning
synonym: Ministry of Science ICT and Future Planning (MISP)
abbrev: MISP
IAO_0000115: Division of the South Korea government responsible for formulating national science and technology policies and plans.

BioChemWeb.org - The Virtual Library of Biochemistry Molecular Biology and Cell Biology
type: Resource
type: NamedIndividual
has db xref: nif-0000-10483
synonym: BioChemWeb
synonym: BioChemWeb.org - The Virtual Library of Biochemistry Molecular Biology Cell Biology
abbrev: BioChemWeb.org
IAO_0000115: This site is provided as a service to scientists, educators, students and others simply interested in the Biological subjects. While many of the resources listed on these pages are designed for scientific professionals, those that require little or no background are labeled as Beginner's Level. Topics include: Angiogenesis, Apoptosis, Carbohydrates, Cell Adhesion & ECM, Cell Cycle, Cell Senescence, Chemical Biology, Cytoskeleton & Motility, Development, Enzymes, Genes, Lipids & Membranes, Metabolism, Microscopy, Organelles, Proteins, Signaling, Structural Biology, Systems Biology Other available categories include: General Resources & Tutorials, Scientific Research Groups, Databases & Tools, Methods, Software, Vendors, Books, Journals, Literature Search, Career & Funding, Organizations & Meetings

SeqMonk
type: Resource
type: NamedIndividual
has db xref: OMICS_01936
IAO_0000115: Software tool to visualize and analyse high throughput mapped sequence data.

Yerkes National Primate Research Center
type: Resource
type: NamedIndividual
has db xref: nif-0000-10485
synonym: Yerkes Primate Research Center
synonym: Yerkes Research Center
IAO_0000115: Center for advancing scientific understanding and improving the health and well-being of humans and nonhuman primates. The Center conducts research in microbiology and immunology, neurologic diseases, neuropharmacology, behavioral, cognitive and developmental neuroscience, and psychiatric disorders.

Ray
type: Resource
type: NamedIndividual
has db xref: biotools:ray
has db xref: OMICS_00027
synonym: Ray - a de novo assembler using MPI 2.2
synonym: Ray - Parallel genome assemblies for parallel DNA sequencing
IAO_0000115: Software that assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2.

Tropical Diseases Research to Foster Innovation & Knowledge Application
type: Resource
type: NamedIndividual
has db xref: nif-0000-10487
synonym: Tropical Diesease
IAO_0000115: TropIKA.net (Tropical Disease Research to foster Innovation and Knowledge Application) was created as a global knowledge management electronic portal to share essential information and to facilitate identification of priority needs and major research gaps in the field of infectious diseases of poverty. This website also provides funding opportunities for researchers of tropical diseases. TropIKA.net is a web-based platform for the acquisition, review and sharing of current information and knowledge on: - Public health research needs and scientific opportunities - Research-based evidence in support of control and policy - High profile research activities and control projects - International research funding and support opportunities - Potential innovations for interventions and control of infectious diseases of poverty. The Primary goals of TropIKA.net are to - Present up-to-date content in a context that makes sense for health researchers and policy makers - Improve access to scientific information on infectious diseases of poverty - Facilitate broad-based participation of disease-endemic countries in discussions and the formulation of current and emerging research priorities and agenda setting - Provide health researchers and decision makers with a comprehensive resource about best practices and authoritative summaries of research findings that have implications for their efforts to meet the challenges of infectious disease control. - Be used as an interactive knowledge platform for infectious diseases of poverty at health forums Sponsors: This website is supported by The Special Programme for Research and Training in Tropical Diseases (TDR).

tbrowse
type: Resource
type: NamedIndividual
has db xref: OMICS_01935
synonym: tbrowse - HTML5 Transcriptome Browser
IAO_0000115: Software providing a HTML5/javascript based browser for visualizing RNA-seq results in the familiar track layout of common genome browser. But given the quantitative nature of RNA-seq data, in addition to visualizing sequence coverage, the browser quantitates transcript abundance across regions of interest. The HTML5 functionality is made of use to render all the tracks using the canvas drawing element. This greatly reduces the load on servers and allows for rich interactive graphics without the need for third-party plugins. Furthermore, this framework completely segregates data from visualization, making development much easier. The browser is designed to run on all modern browsers: Firefox, Safari, Chrome, Opera and Internet Explorer (though not recommended).

United Kingdom National Health Service: National Genetics Education and Development Centre
type: Resource
type: NamedIndividual
has db xref: nif-0000-10488
synonym: UK NHS Genetics Education
IAO_0000115: The NHS National Genetics Education and Development Centre is working with a range of groups throughout the UK to facilitate the integration of genetics education into all levels of education and training for all NHS health professionals. The key aims of this center: 1. Providing leadership in genetics education 2. Helping to raise awareness 3. Involving patients and their families in informing all aspects of our work 4. Identifying the genetics knowledge, skills and attitudes which are useful for clinical role 5. Developing a framework for competences in genetics 6. Facilitating the integration of genetics into curricula and courses 7. Identifying and developing resources appropriate to the needs of health professionals (and their trainers) 8. Supporting and disseminating learning from service development initiatives in genetics Sponsors: The Centre is funded by the Department of Health as one of the major initiatives of the 2003 Genetics White Paper, Our Inheritance, Our Future - Realising the potential of genetics in the NHS which set out the Governments strategy for ensuring that the potential benefits of genetics are realised by the NHS.

University of California at Berkeley: The Neural Prediction Challenge
type: Resource
type: NamedIndividual
has db xref: nif-0000-10490
synonym: UCB Neural Challenge
IAO_0000115: The aim of the Neural Prediction Challenge is to accelerate the development of predictive models and to provide computational neuroscientists an opportunity to test their models objectively. The challenge is really quite simple: you will be given some (visual and/or auditory) stimuli and corresponding neural responses, and you must try to predict responses to other stimuli. Each data set will be divided in to two subsets: a fit set (90% of the data) that includes both the stimuli and the corresponding neuronal responses; and a validation set (10% of the data) that includes only stimuli (no responses). Your job is to use the fit set to fit your model and then to generate predicted responses based on the stimuli provided in the validation set. Once you have the predictions you should return them to us. We will compare your predicted responses to the responses actually observed in the validation set. Current data consist of recordings from visual and auditory neurons during naturalistic stimulation. Data are provided in simple ascii files that are easily readable in Matlab (or by any other modern programming language). Details on data formatting are provided with each data set. Predictions will be evaluated continuously as they are received and results will be posted in aggregate form. Individuals' names, prediction scores and models will not be posted without prior permission (though we may contact participants directly, see official rules). Please note that this is an academic research project, it is not a traditional contest. There is no real ending date, and there is nothing to win. Sponsors: This project is supported by the NIH Human Brain Project.

University of California at Los Angeles - Department of Energy Institute for Genomics and Proteomics
type: Resource
type: NamedIndividual
has db xref: nif-0000-10491
synonym: UCLA-DOE
IAO_0000115: The UCLA-DOE Institute for Genomics and Proteomics carries out research in bioenergy, structural biology, genomics and proteomics, consistent with the research mission of the United States Department of Energy. Major interests of the 12 Principal Investigators and 9 Associate Members include systems approaches to organisms, structural biology, bioinformatics, and bioenergetic systems. The Institute sponsors 5 Core Technology Centers, for X-ray and NMR structural determination, bioinformatics and computation, protein expression and purification, and biochemical instrumentation. Services offered by this Institute: - Databases: * DIP (The Database of Interacting Proteins): The DIPTM database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. * ProLinks Database of Functional Linkages: The Prolinks database is a collection of inference methods used to predict functional linkages between proteins. These methods include the Phylogenetic Profile method which uses the presence and absence of proteins across multiple genomes to detect functional linkages; the Gene Cluster method, which uses genome proximity to predict functional linkage; Rosetta Stone, which uses a gene fusion event in a second organism to infer functional relatedness; and the Gene Neighbor method, which uses both gene proximity and phylogenetic distribution to infer linkage. - Data-to-Structure Servers: * SAVEs Structure Verification Server * Merohedral Twinning Test Server * SER Surface Entropy Reduction Server * VERIFY3D Structure Verification Server * ERRAT Structure Verification Server - Structure-to-Function Servers: * ProKnow Protein Functionator * Hot Patch Functional Site Locator

Laboratory of Neuro Imaging
type: Resource
type: NamedIndividual
has db xref: nif-0000-10494
synonym: Laboratory of Neuroimaging
synonym: UCLA Laboratory of Neuro Imaging
synonym: UCLA LONI
synonym: USC Laboratory of Neuro Imaging
abbrev: LONI
IAO_0000115: Biomedical technology resource center specializing in novel approaches and tools for neuroimaging. It develops novel strategies to investigate brain structure and function in their full multidimensional complexity. There is a rapidly growing need for brain models comprehensive enough to represent brain structure and function as they change across time in large populations, in different disease states, across imaging modalities, across age and sex, and even across species. International networks of collaborators are provided with a diverse array of tools to create, analyze, visualize, and interact with models of the brain. A major focus of these collaborations is to develop four-dimensional brain models that track and analyze complex patterns of dynamically changing brain structure in development and disease, expanding investigations of brain structure-function relations to four dimensions.

AutoPSI database of predicted SCOP classifications
type: Resource
type: NamedIndividual
has db xref: nif-0000-02588
synonym: Automated Protein Structure Identification (AutoPSI) database
synonym: Automated Protein Structure Identification database
synonym: AutoPSI
synonym: AutoPSI Database
IAO_0000115: Searchable database for predicted protein sequences and structures. It has the ability to search through PDB ID, UniProt ID, and descriptive classifiers.

University of California at Los Angeles, School of Medicine: Neuro Imaging Lab of Thompson
type: Resource
type: NamedIndividual
has db xref: nif-0000-10496
synonym: Thompson Lab
synonym: UCLA
IAO_0000115: The UCLA laboratory of neuroimaging is working in several areas to enhance knowledge of anatomy, including brain mapping in large human populations, HIV, Schizophrenia, methamphetamine, tumor growth and 4d brain mapping, genetics and detection of abnormalities.

University of California at Riverside Neuroscience Graduate Program
type: Resource
type: NamedIndividual
has db xref: nif-0000-10498
synonym: UCR Neuroscience
IAO_0000115: Neuroscience is a multidisciplinary approach to understanding nervous systems at levels ranging from the molecular and cellular to the whole organism. The goal of this Program is to prepare students for careers in research, teaching and/or scientific administration. Students are expected to learn the fundamentals of neuroscience, starting with a required core sequence, become knowledgeable concerning a range of research methods as taught in a required neuroscience laboratory course, and demonstrate capability in original research. Graduate student training ultimately reflects the research competence and specialties of the faculty, that is, the specific research training received by a graduate student is the responsibility of the major professor/mentor under whose guidance and in whose laboratory the student carries out the research projects leading to the degree. Students will benefit from an interdisciplinary training approach, tailored by the major advisor but enriched by the readily available expertise and laboratory facilities of program faculty with backgrounds ranging from chemistry to psychology. In addition to this training, it is our intention, through outside speakers and planned forums, to make students aware of alternate careers open to neuroscientists whose interests and talents might lead to areas such as biotechnology, science administration and the like. The Interdepartmental Ph.D Program in Neuroscience at UC Riverside is aimed at providing high quality graduate training for students who come from a variety of undergraduate backgrounds but share a commitment and an intense interest in nervous system research. We currently have nineteen faculty with expertise in various aspects of neuroscience and whose principal appointments are in the Departments of Biology, Cell Biology & Neuroscience, Chemistry, Entomology, and Psychology, and the Division of Biomedical Sciences. A major part of training in neuroscience is in supervised laboratory research, the s…

UCSD Cognitive Science: The Future of Cognitive Science
type: Resource
type: NamedIndividual
has db xref: nif-0000-10499
synonym: UCSD Cognitive Science
IAO_0000115: This UCSD department, the first Cognitive Science Department in the world, provides a focus for the continued evolution of the discipline of cognitive science. Cognitive science is a diverse field unifying three broad categories: the brain, behavior and computation. It's the study of how people, animals and computers think, act and learn. In order to understand the mind/brain, cognitive science brings together the methods and discoveries from neuroscience, psychology, linguistics, anthropology, philosophy and computer science. The interdisciplinary aspects of cognitive science continue to flourish, and the participation of the broader cognitive science community on campus continues to be fundamental to cognitive science as practiced at UCSD. The interdisciplinary Ph.D. program continues to be offered as a degree option (in addition to the departmental Ph.D.), with participation by members of the Departments of Anthropology, Biology, Cognitive Science, Communication, Computer Science and Engineering, Linguistics, Music, Neuroscience, Philosophy, Psychiatry, Psychology, and Sociology. Cognitive Science is a relatively young field that focuses on conducting new research into the field or applying existing knowledge into new applications. This Department contains several research labs each specializing in different areas and the Department's faculty has also been published many times in various publications. Sponsors: This department is supported by the University of California at San Diego.

autoSNPdb
type: Resource
type: NamedIndividual
has db xref: nif-0000-02589
IAO_0000115: We have developed an integrated SNP discovery pipeline, which identifies SNPs from assembled EST sequences. The results are maintained in a custom relational database along with EST source and annotation information. The current database hosts data for the important crops rice, barley and Brassica. Users may rapidly identify polymorphic sequences of interest through BLAST sequence comparison, keyword searches of annotations derived from UniRef90 and GenBank comparisons, GO annotations or in genes corresponding to syntenic regions of reference genomes. In addition, SNPs between specific varieties may be identified for targeted mapping and association studies. SNPs are viewed using a user-friendly graphical interface. The implementation of autoSNPdb allows researchers to query the results of SNP analysis to characterize SNPs between specific groups of individuals or within genes with predicted function. The system is flexible and researchers may add additional levels of annotation, and perform novel queries specific to their area of interest. If you have sequence data you'd like to include please contact Dave Edwards.

Shiley-Marcos Alzheimer's Disease Research Center
type: Resource
type: NamedIndividual
has db xref: nif-0000-10501
synonym: University of California at San Diego Shiley-Marcos Alzheimer's Disease Research Center
abbrev: UCSD ADRC
IAO_0000115: The UCSD ADRC conducts a wide variety of research studies dedicated to understanding the causes, clinical features, and treatments for Alzheimer's disease and related memory disorders. The goal of the center is to discover ways to prevent and eradicate the disease. The Center aims to maintain research subjects, clinical resources, and clinical data to support ongoing and proposed research and to assist in the development of new clinical and interdisciplinary research. An Alzheimer's brain bank with well characterized cases, including Mild Cognitive Impairment and Lewy Body disease, is maintained at the Center.

University of California at San Diego, Center for Medicinal Cannabis Research
type: Resource
type: NamedIndividual
has db xref: nif-0000-10503
synonym: UCSD CMCR
IAO_0000115: The Center for Medicinal Cannabis Research (CMCR) will conduct high quality scientific studies intended to ascertain the general medical safety and efficacy of cannabis products and examine alternative forms of cannabis administration. The Center will be seen as a model resource for health policy planning by virtue of its close collaboration with federal, state, and academic entities. The objectives of this center are: 1. To conduct and support focused controlled clinical trials on the efficacy of cannabis in patients diagnosed with HIV/AIDS, cancer, seizures or muscle spasms associated with a chronic debilitating condition, or any other serious condition providing sufficient theoretical justification. 2. To use prospective clinical trials to determine optimal dosage, timing, and modes of administration for cannabis in various medical disorders. 3. To conduct randomized trials to compare the efficacy and safety of various methods of cannabis administration. 4. To conduct observational studies and randomized trials to assess the safety and toxicity of cannabis in the medically ill. Such studies will evaluate the impact of treatment on daily functioning and on life quality. 5. To conduct limited pre-clinical studies with direct relevance to understanding cannabis as a therapeutic agent. 6. To facilitate the implementation of research by assisting investigators in securing relevant regulatory review and approval by state and federal agencies. 7. To establish a process of rigorous peer review of scientific proposals. 8. To secure external sources of funding to maximize the scope and size of cannabis studies. Sponsors: This resource is supported by the University of California at San Diego.

University of California at San Diego Computational Neuroscience
type: Organization
type: NamedIndividual
has db xref: nif-0000-10504
synonym: UCSD CN
IAO_0000115: The Computational Neuroscience specialization is a new facet of the broader Neuroscience graduate program at UCSD. The goal of the specialization is to train the next generation of neuroscientists with the broad range of computational and analytical skills that are essential to understand the organization and function of complex neural systems. The specialization is intended for students with backgrounds in neuroscience, physics, chemistry, biology, psychology, computer science, engineering, and mathematics. This specialization allows Neuroscience students to concentrate on a focused program of rigorous course work in both the theoretical and experimental aspects of computational neuroscience. Students are encouraged to pursue thesis research that includes both an experimental and a computational component, often arranged by the student as a collaboration between two research groups. The program is focused on these major themes relevant for computational neuroscience research: - Neurobiology of Neural Systems - the anatomy, physiology, and behavior of systems of neurons, with emphasis on basic phenomenology. - Advanced Measurement Tools in Neuroscience - Advanced imaging and recording techniques reflecting the impact of experimental physics on neuroscience. - Algorithms for the Analysis of Neural Data - New algorithms and techniques for analyzing data obtained from physiological recording - Theoretical Basis for Collective Neural Dynamics - A synthesis of approaches from mathematics and physical sciences as well as biology will be used to explore the collective properties and nonlinear dynamics of neuronal systems. Sponsors: This program is supported by the University of California at San Diego.

University of California at San Diego Department of Psychiatry
type: Organization
type: NamedIndividual
has db xref: nif-0000-10505
synonym: UCSD Department of Psychiatry
abbrev: UCSD Psychiatry
IAO_0000115: The Department of Psychiatry at the University of California, San Diego is one of the most innovative and productive academic departments of psychiatry in the country. The guiding principle in this development has been that the educational and research programs of a psychiatry department must be at the cutting edge and encompass and integrate the most current innovations in the field with those approaches from the past which have proven to be valid and effective. The department has a strong commitment to the dynamic understanding of an individual's current social context and feelings, and past behaviors and experiences. We believe we have created one of the best available integrations of the biopsychosocial approaches to understanding normal and abnormal human behavior. By design, a rich diversity of scientific and clinical strategies are represented within the department, but the core organizing ethic of our educational and training programs is a profound commitment to our patients well being. It is the department's conviction that clinical psychiatry can only be learned in the context of meaningful interaction and contact with patients. The Residency Training Program is developmental in nature, appropriately challenging the residents at each level as they move from intensively supervised beginners to autonomous, confident, skilled clinicians and colleagues at graduation. The training occurs within the department's ambiance of collegiality, enthusiasm, openness of communication, intellectual and scientific rigor, and spirit of inquiry, which characterize our highly productive and energetic faculty. The UCSD faculty represent a virtual who's who of world-class basic and clinical scientists and clinicians, all of whom are available and participate in our residents training and experiences. The tradition at UCSD, both on the general campus and within the School of Medicine, is that of academic excellence. The department shares in this tradition and expects it from its…

Immune Technology
type: Organization
type: NamedIndividual
has db xref: nlx_152384
synonym: Immune Technology Corp
IAO_0000115: Commercial antibody supplier that specializes in the development and manufacture of viral antigens and anti-viral antibodies for diagnosis, monitoring, and treatment of significant viral infectious diseases.

Swartz Center for Computational Neuroscience
type: Resource
type: NamedIndividual
has db xref: nif-0000-10509
abbrev: SCCN
IAO_0000115: Computational neuroscience center that observes and models how functional activities in multiple brain areas interact dynamically to support human cognition, creativity and social interaction. Center research involves development computational methods and software, experimental methods and equipment, collection and analysis of human cognitive experiments, and collaborations to analyze data collected by other groups in such experiments. The Center has a 72-channel EEG recording system customized for use in the fMRI environment, and a very-high density Biosemi Active Two active-electrode EEG system, rapidly configurable either as a 256-channel system for a single subject or as two 136-channel systems for recording from two subjects simultaneously. In addition, UCSD now has a 306-channel MEG plus 128-channel EEG system (Neuromag/Elektra). Projects in the Center include studies of human cognitive processes including attention and memory, role of the anterior/posterior cingulate, time perception and emotional expression. Data acquisition includes high-density EEG, concurrent EEG and fMRI recording and analysis, and face video processing. Current analysis approaches include independent component and time-frequency analysis.

Bacteriome.org
type: Resource
type: NamedIndividual
has db xref: nif-0000-02592
has db xref: OMICS_01899
has db xref: r3d100012726
synonym: Bacteriome.org - Bacterial Protein Interaction Database
IAO_0000115: Database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase. Presently the resource offers access to two types of network: * A network of functional interactions derived through exploiting available functional genomic datasets within a Bayesian framework * Two networks of experimentally derived protein-protein interactions - a "core" network consisting of interactions deemed to be of "high quality"; and an "extended" network which extends the "core" network by including interactions for which experimental evidence is less strong.

National Center for Microscopy and Imaging Research: ImageJ Mosaic Plug-ins
type: Resource
type: NamedIndividual
has db xref: nif-0000-10512
synonym: ImageJ Mosaic Plug-Ins
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. 02111-1307, USA. Sponsors: ImageJ Mosaic Plug-Ins software presented here was produced at the National Center for Microscopy and Imaging Research at San Diego, which is supported by the National Institutes of Health (NIH) through a National Center for Research Resources program grant P41 RR04050.

Apollo
type: Resource
type: NamedIndividual
has db xref: biotools:apollo
has db xref: OMICS_01933
has db xref: OMICS_11761
IAO_0000115: A standalone Java application with a GUI (graphical user interface) for editing genome annotations. Like GBrowse, it allows users to scroll and zoom in on areas of interest in a sequence; authorized users can edit annotations and write the changes back to the underlying database. Apollo can run off GFF3 or a Chado database, and it can also integrate with remote services, such as BLAST and Primer BLAST analyses.

RAVEN
type: Resource
type: NamedIndividual
has db xref: OMICS_01932
synonym: RAVEN - Regulatory analysis of Variation in ENhancers
synonym: Regulatory analysis of Variation in Enhancers
IAO_0000115: Tool to search for putative regulatory genetic variation in your favorite gene. Single nucleotide polymorphisms (SNPs) (from dbSNP and user defined) are analyzed for overlap with potential transcription factor binding sites (TFBS) and phylogenetic footprinting using UCSC phastCons scores from multiple alignments of 8 vertebrate genomes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

PEDIGRAPH
type: Resource
type: NamedIndividual
has db xref: biotools:pedigraph
has db xref: nlx_154519
has db xref: OMICS_00212
abbrev: Pedigraph
IAO_0000115: A pedigree visualization program specifically designed to draw large, complex pedigrees. (entry from Genetic Analysis Software) Options include: * Full pedigree * Summarization * Extraction of individual pedigrees * Inbreeding calculation * Coancestry coefficient calculation * Color control * Drawing size * Page size and margins * Drawing styles

National Center for Microscopy and Imaging Research: Jinx
type: Resource
type: NamedIndividual
has db xref: nif-0000-10513
synonym: Jinx
IAO_0000115: Jinx was developed to aid in the 3D reconstruction of tomographic datasets acquired with one of the various electron microscopes available at the resource. Tomographic datasets consist of a series of 2D images from which objects of interest are segmented out for the 3D reconstruction. Jinx offers the user a graphical interface to step through each image of the series and facilities to manually trace out objects of interest. It relies on JadeDisplay to support the display of large images with graphical overlays and the JAI libraries for histogram functionality and other types of image manipulations. Jinx is currently under active development and future releases will offer semi-automated segmentation algorithms based on fuzzy logic, level set, and watershed algorithm. This software is free; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or any later version. See the GNU General Public License for more details. For a copy of the GNU General Public License, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307, USA. Sponsors: Jinx presented here was produced at the National Center for Microscopy and Imaging Research at San Diego, which is supported by the National Institutes of Health (NIH) through a National Center for Research Resources program grant P41 RR04050. open source license, GNU general public license

BAliBASE
type: Resource
type: NamedIndividual
has db xref: nif-0000-02594
has db xref: OMICS_00971
synonym: Benchmark Alignment dataBASE
IAO_0000115: A collection of high quality multiple sequence alignments for objective, comparative studies of alignment algorithms. The alignments are constructed based on 3D structure superposition and manually refined to ensure alignment of important functional residues. A number of subsets are defined covering many of the most important problems encountered when aligning real sets of proteins. It is specifically designed to serve as an evaluation resource to address all the problems encountered when aligning complete sequences. The first release provided sets of reference alignments dealing with the problems of high variability, unequal repartition and large N/C-terminal extensions and internal insertions. Version 2.0 of the database incorporates three new reference sets of alignments containing structural repeats, trans-membrane sequences and circular permutations to evaluate the accuracy of detection/prediction and alignment of these complex sequences. Within the resource, users can look at a list of all the alignments, download the whole database by ftp, get the "c" program to compare a test alignment with the BAliBASE reference (The source code for the program is freely available), or look at the results of a comparison study of several multiple alignment programs, using BAliBASE reference sets.

University of California at San Diego, Neurosciences Graduate Program
type: Resource
type: NamedIndividual
has db xref: nif-0000-10518
synonym: UCSD Neurosciences (Grad)
IAO_0000115: The Graduate Program in Neurosciences at the University of California, San Diego offers an outstanding opportunity for graduate training in one of the most highly interactive scientific environments available in the United States. Recently, our graduate program was named by the National Research Council of the National Academy of Sciences as the top-ranking neuroscience graduate program in the country. The faculty who participate in the Graduate Program in Neurosciences have been brought together from many campus departments, the School of Medicine and from a number of affiliated institutes, including the Salk Institute, the Scripps Research Institute, the Scripps Institute of Oceanography, the UCSD Medical Center, and the Veterans Administration Medical Center. Because there is an enormous breadth of neuroscience research interests represented among the faculty, students are able to pursue study in a wide range of neuroscience areas and they often carry out their dissertation research in collaboration with more than one laboratory. Sponsors: FUnding for this program comes from the University of California at San Diego.

University of California at San Diego, School of Medicine: Graduate Opportunities & Dual Degree Programs
type: Resource
type: NamedIndividual
has db xref: nif-0000-10519
synonym: UCSD Graduate Programs
IAO_0000115: The UCSD School of Medicine are dedicated to producing future leaders in all areas of medicine. As such, the School promotes the pursuit of dual degrees, either in the Medical School's own graduate degree programs or programs offered in other disciplines in the institution. In addition to the study of medicine, the School of Medicine actively encourages its student body to explore broadly in various scholarly areas related to the biomedical sciences. The goal of this additional training is to produce graduates who will bring fresh, innovative ideas to the research laboratory, the public health sector, the humanities and the social sciences, and the business environment. Students may elect to obtain advanced degrees in the following areas: * Biomedical Sciences * Masters in Bioengineering * Masters in Public Health * Masters in Leadership of Health Care Organizations * Masters of Advanced Studies in Clinical Research * Ph.D. Program in the Humanities and Social Sciences * Independent Ph.D. programs Opportunities for enrollment in research or degree programs outside of UCSD are also available, and students are encouraged to investigate these, if interested. Sponsors: This program is supported by the University of California at San Diego.

TEQC
type: Resource
type: NamedIndividual
has db xref: OMICS_03602
synonym: TEQC - Quality control for target capture experiments
IAO_0000115: An R/Bioconductor package for quality assessment of target enrichment experiments. This package provides functionalities for assessing and visualizing the quality of the target enrichment process, like specificity and sensitivity of the capture, per-target read coverage and so on.

Biospecimen Research Database
type: Resource
type: NamedIndividual
has db xref: SciRes_000169
synonym: Biospecimen Research Database (BRD)
synonym: NCI Biospecimen Research Database
abbrev: BRD
IAO_0000115: Free and publicly accessible literature database for peer-reviewed primary and review articles in the field of human Biospecimen Science. Each entry has been created by a Ph.D. level scientist to capture relevant parameters, pre-analytical factors, and original summaries of relevant results.

rSNPs MAPPER
type: Resource
type: NamedIndividual
has db xref: OMICS_01931
IAO_0000115: Data analysis service to identify single nucleotide polymorphisms (SNPs) that may have an effect on the presence of one or more transcription factor binding sites (TFBSs). The input to regulatory SNPs (rSNPs) can consist of one or more genes, a genomic region, or a user-provided sequence. SNPs may be downloaded from dbSNP, entered manually by the user, or obtained by comparing two sequences. The result is a list of TFBSs whose score changes significantly as a consequence of the allele substitution caused by the SNP.

BarleyBase
type: Resource
type: NamedIndividual
has db xref: nif-0000-02596
IAO_0000115: A MIAME/Plant-compliant and plant ontology enhanced expression database for Barley microarray data. It contains data from two Affymetrix genome arrays, Barley1 and Arabidopsis ATH1. Users can search based on experiment type, experimental factors, array design, or experimenter. They can also choose to browse lists of available data.

rSNPBase
type: Resource
type: NamedIndividual
has db xref: OMICS_01929
synonym: rSNPBase - A database for curated regulatory SNPs
IAO_0000115: Database for curated regulatory single nucleotide polymorphisms (SNPs) to assist researchers in selecting candidate SNPs for further genetic studies (especially for QTL studies), identifying causal variants of certain phenotypes, and exploring in-depth molecular mechanisms. It is characterized by several unique features: (i) To improve reliability, all SNPs in rSNPBase are annotated with reference to experimentally supported regulatory elements. (ii) rSNPBase focuses on rSNPs involved in a wide range of regulation types, including proximal and distal transcriptional regulation and post-transcriptional regulation, and identifies their potentially regulated genes. (iii) Linkage disequilibrium (LD) correlations between SNPs were analysed so that the regulatory feature is annotated to SNP-set rather than a single SNP. (iv) rSNPBase provides the spatio-temporal labels and experimental eQTL labels for SNPs.

Center for Bio-Image Informatics
type: Resource
type: NamedIndividual
has db xref: nif-0000-10523
synonym: UCSB BioImage
IAO_0000115: The Center for Bio-Image Informatics is an interdisciplinary research effort between Biology, Computer Science, Statistics, Multimedia and Engineering. The overarching goal of the center is the advancement of human knowledge of the complex biological processes which occur at both cellular and sub-cellular levels. the center employs and develops cutting edge techniques in the fields of imaging, pattern recognition and data mining. Research also focuses on development of new information processing techniques which can afford us a better understanding of biological processes depicted in microscopy images of cells and tissues, specifically on the distributions of biological molecules within these samples. This is achieved by borrowing methods for information processing at the sensor level to enable high speed and super-resolution imaging. By applying pattern recognition and data mining methods to bio-molecular images, full automation of both the extraction of information and the construction of statistically-sound models of the processes depicted in those images was possible. At the heart of the center's reseach is the BISQUE system, an online repository for multidimensional bio-images, and testbed for new research techniques and methods. BISQUE: Online Semantic Query User Environment is an online database for managing up to 5 dimensional scientific images with associated metadata and a flexible, collaborative tagging system. Currently the system has more than 85,000 user-provided tags and 128006 2-D planes from over 6,000 biological images. BISQUE is much more than just a repository for scientific images- the system provides resources for complex scientific analysis over images, result visualization, user-extensible modules, customized organization of images, advanced search features, graphical annotations, textual annotations and compatible client-side applications. Sponsors: This work is supported in part by an NSF infrastructure award No. EIA-0080134 and IIS-0808772…

Patchers Power Tools
type: Resource
type: NamedIndividual
has db xref: SciRes_000167
synonym: Patcher''s Power Tools
synonym: PPT XOP
abbrev: PPT
IAO_0000115: An Igor Pro XOP software tool collection for reading Heka Pulse/PM files and other tools for electrophysiologists.

Keypoint
type: Commercial Organization
type: NamedIndividual
has db xref: SciRes_000159
synonym: Medtronic KeyPoint Portable software
synonym: Medtronic Keypoint XP Edition
synonym: NDX KeypointXP
IAO_0000115: Software for the analysis of neurophysiological patterns and measurements.

Biomedical Simulations Resource
type: Resource
type: NamedIndividual
has db xref: nif-0000-10530
synonym: Biomedical Simulations Resource (BMSR)
abbrev: BMSR
IAO_0000115: Biomedical technology resource center dedicated to the advancement of the state-of-the-art in biomedical modeling and simulation through Core and Collaborative Research projects, as well as the dissemination of this knowledge and related software through Service, Training and Dissemination activities aimed at the biomedical community at large. The BMSR includes four core research projects: * Pharmacokinetic/Pharmacodynamic Systems Analysis * Nonlinear Modeling of Complex Biomedical Systems * Modeling of Autonomic, Metabolic and Vascular Control Interactions * Nonlinear Modeling of the Hippocampus Fifteen Collaborative Research Projects serve as challenging test grounds for the Resource's methodologies and expertise.

Group ICA of fMRI Toolbox
type: Resource
type: NamedIndividual
has db xref: nif-0000-00309
has db xref: SCR_024416
synonym: Group ICA Of fMRI Toolbox (GIFT)
abbrev: GIFT
IAO_0000115: Software MATLAB toolbox which implements multiple algorithms for independent component analysis and blind source separation of group (and single subject) functional magnetic resonance imaging data. GIFT works on MATLAB 6.5 and higher. Many ICA algorithms were generously contributed by Dr. Andrzej Cichocki.

SNP Function Portal
type: Resource
type: NamedIndividual
has db xref: OMICS_01928
IAO_0000115: Database for exploring the function implication of single nucleotide polymorphism (SNP) alleles. It is designed to be a clearing house for all public domain SNP functional annotation data, as well as in-house functional annotations derived from different data sources. It currently contains SNP functional annotations in six major categories including genomic elements, transcription regulation, protein function, pathway, disease and population genetics. Besides extensive SNP functional annotations, it includes a search engine that accepts different types of genetic markers as input and identifies all genetically related SNPs based on the HapMap Phase II data as well as the relationship of different markers to known genes. As a result, the system allows users to identify the potential biological impact of genetic markers and complex relationships among genetic markers and genes, and it greatly facilitates knowledge discovery in genome-wide SNP scanning experiments.

BeetleBase
type: Resource
type: NamedIndividual
has db xref: biotools:beetlebase
has db xref: nif-0000-02599
has db xref: r3d100010921
abbrev: BEETLEBASE
IAO_0000115: A centralized sequence database and community resource for Tribolium genetics, genomics and developmental biology containing genomic sequence scaffolds mapped to 10 linkage groups, genetic linkage maps, the official gene set, Reference Sequences from NCBI (RefSeq), predicted gene models, ESTs and whole-genome tiling array data representing several developmental stages. The current version of Beetlebase is built on the Tribolium castaneum 3.0 Assembly (Tcas 3.0) released by the Human Genome Sequencing Center at the Baylor College of Medicine. The database is constructed using the upgraded Generic Model Organism Database (GMOD) modules. The genomic data is stored in a PostgreSQL relational database using the Chado schema and visualized as tracks in GBrowse. The genetic map is visualized using the comparative genetic map viewer CMAP. To enhance search capabilities, the BLAST search tool has been integrated with the GMOD tools. Tribolium castaneum is a very sophisticated genetic model organism among higher eukaryotes. As the member of a primitive order of holometabolous insects, Coleoptera, Tribolium is in a key phylogenetic position to understand the genetic innovations that accompanied the evolution of higher forms with more complex development. Coleoptera is also the largest and most species diverse of all eukaryotic orders and Tribolium offers the only genetic model for the profusion of medically and economically important species therein. The genome sequences may be downloaded.

University of Leeds - Computational Biology Group
type: Resource
type: NamedIndividual
has db xref: nif-0000-10528
synonym: Leeds CBiol
IAO_0000115: The University of Leeds Computational Biology Group is an interdisciplinary research group based in the Faculty of Biological Sciences, and is part of the Centre for Nonlinear Studies. Research interests are at the interfaces of nonlinear dynamics, computational science and general physiology of excitable tissue (nervous system, cardiac and uterine muscle). A central theme is the reconstruction of tissue and organ physiology and pathologies from networks of intracellular, membrane and cellular models. Sponsors:

flowType
type: Resource
type: NamedIndividual
has db xref: OMICS_05613
synonym: flowType - Phenotyping Flow Cytometry Assays
IAO_0000115: Software for phenotyping Flow Cytometry assays using multidimentional expansion of single dimentional partitions.

Virtual Genetics Education Centre
type: Resource
type: NamedIndividual
has db xref: nif-0000-10529
synonym: GENIE VGEC
synonym: Virtual Genetics Education Center
abbrev: VGEC
IAO_0000115: Hub of evaluated genetics-related teaching resources for teachers and learners in schools and higher education, health professionals and the general public. Suggest or submit a learning resource to the VGEC. Resources include: * simple experiments suitable for all ages * tutorial material * videos on useful techniques * current and relevant links to other evaluated resources The Virtual Genetics Education Centre (VGEC) * Provides information and genetics education resources for higher education, colleges, schools, health professionals and the general public. * Encourages collaboration in the development, evaluation and sharing of genetics education resources * provides links to, and evaluates, sources of information and educational material about genetics. * Explores innovative approaches to teaching and learning in genetics, such as the SWIFT project for example where Second Life is being used to teach some aspects of genetics in a virtual laboratory.

Korea National Institute of Health
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100003653
has db xref: grid.415482.e
has db xref: ISNI: 0000 0004 0647 4899
has db xref: nlx_156100
synonym: Korea NIH
abbrev: KNIH
IAO_0000115: Institute dedicated to medical research to improve biomedical innovation and public health in South Korea.

Hierarchical Attribute Matching Mechanism for Elastic Registration
type: Resource
type: NamedIndividual
has db xref: nif-0000-00310
synonym: HAMMER: Deformable Registration
abbrev: HAMMER
IAO_0000115: Software package that performs high-dimensional warping of brain images. Standard voxel-based analysis can be applied to these tissue density maps, in order to examine regional volumetrics, effects of disease, or correlations with clinical measurements. In order to make HAMMER as robust as possible to different acquisition protocols and conditions, they provide a distribution that assumes that images have been skull-stripped and segmented into gray matter, white matter, and ventricular CSF. We have other software tools that can perform these steps, including skull stripping, reorientation and reslicing, and segmentation tools. Importantly, they use 250 for WM, 150 for GM, 50 for Ventricles and 10 for CSF in the tissue-segmented brain images. Current modules used for group analysis: Labeling subject brain using a manually-labeled brain Model; Generating RAVENS map for each tissue (WM, GM, VN); Normalizing subject brain images

Center for Integrative Biomedical Computing
type: Resource
type: NamedIndividual
has db xref: nif-0000-10535
synonym: NIH/NIGMS Center for Integrative Biomedical Computing
abbrev: CIBC
IAO_0000115: Biomedical technology research center that produces open-source software tools for biomedical image-based modeling, biomedical simulation and estimation, and the visualization of biomedical data. The Center works closely with software users and collaborators in a range of scientific domains to produce user-optimized tools and provides advice, technical support, workshops, and education to enhance user success. Biological projects and collaborations drive their development efforts, all with a single unifying vision: to develop the role of image-based modeling and analysis in biomedical science and clinical practice. The CIBC has a strong, ongoing emphasis on software simulation of bioelectric fields, with clinically oriented collaborations in cardiac defibrillation and the diagnosis/treatment of epilepsy. In addition, the CIBC has expanded in recent years to include applications of statistical shape analysis and three-dimensional visualization to mouse genetics and neuroimaging and applications of image and geometry processing to cell biology.

Commentpress
type: Resource
type: NamedIndividual
has db xref: nif-0000-02602
IAO_0000115: Web application for blogging on WordPress that allows users to annotate in the margins of an online text.

SNPper
type: Resource
type: NamedIndividual
has db xref: OMICS_01926
IAO_0000115: Retrieve known single-nucleotide polymorphisms (SNPs) by position or by association with a gene; save, filter, analyze, display or export SNP sets; explore known genes using names or chromosome positions.

ParaVision
type: Resource
type: NamedIndividual
has db xref: SciRes_000158
synonym: Bruker Paravision 4.0 software
synonym: Paravision
synonym: ParaVision 4
synonym: ParaVision 6
IAO_0000115: Image acquisition software used to acquire images during magnetic resonance imaging.

Visible Human Transverse Section Through the Head
type: Resource
type: NamedIndividual
has db xref: nif-0000-10547
IAO_0000115: Portal for learning resources about the brain. It includes information and interactive images of transverse brain sections.

National Center for PTSD
type: Organization
type: NamedIndividual
has db xref: grid.497281.1
has db xref: ISNI: 0000 0004 0374 606X
has db xref: nif-0000-10538
synonym: National Center for Posttraumatic Stress Disorder
synonym: VA National Center for PTSD
abbrev: NCPTSD
IAO_0000115: We are the center of excellence for research and education on the prevention, understanding, and treatment of PTSD. Our Center has seven divisions across the country. Although we provide no direct clinical care, our purpose is to improve the well-being and understanding of American Veterans. We conduct cutting edge research and apply resultant findings to: Advance the Science and Promote Understanding of Traumatic Stress. The National Center has emerged as the world's leading research and educational center of excellence on PTSD. Its vision is to be the foremost leader in information on PTSD and trauma; information generated internally through its extensive research program, and information synthesized from published scientific research and collective clinical experience that is efficiently disseminated to the field. The Center is organized to facilitate rapid translation of science into practice, assuring that the latest research findings inform clinical care; and translation of practice into science, assuring that questions raised by clinical challenges are addressed using rigorous experimental protocols. By drawing on the specific expertise vested at each separate division (e.g., behavioral, neuroscientific, etc.), the National Center provides a unique infrastructure within which to implement multidisciplinary initiatives regarding the etiology, pathophysiology, diagnosis and treatment of PTSD.

Center for Imaging of Neurodegenerative Diseases
type: Resource
type: NamedIndividual
has db xref: nif-0000-10539
synonym: UCSF Center for Imaging of Neurodegenerative Diseases
abbrev: CIND
IAO_0000115: Biomedical technology research center that develops and validates new imaging methods for detecting brain abnormalities in neurodegenerative diseases, including Alzheimer's disease, vascular dementia, frontotemporal dementia, Parkinson's disease, as well as epilepsy, depression, and other conditions associated with nerve loss in the brain. As people around the globe live longer, the impact of neurodegenerative diseases is expected to increase further with dire social and economical consequences for societies if no effective treatments are developed soon. The development at CIND is aimed to improve magnetic resonance imaging (MRI). The ultimate goal of the scientific program is to identify imaging markers that improve accuracy in diagnosing neurodegenerative diseases at early stages, achieve more reliable prognoses of disease progression, and facilitate the discovery of effective treatment interventions. In addition to addressing the general needs for studying neurodegenerative diseases, another focus of CIND concerns brain diseases associated with military service and war combat, such as post traumatic stress disorder (PTSD), brain trauma, gulf war illness and the long-term effects of these conditions on the mental health of veterans. The symbiosis between CIND and the Veterans Administration Medical Center in San Francisco makes this program uniquely suited to serve military veterans.

XANAT
type: Resource
type: NamedIndividual
has db xref: nif-0000-10559
synonym: XANAT 2.0
IAO_0000115: Neuroscience software that stores the results of numerous tracer studies in a standardized format and provides various tools for performing summaries and comparisons of these studies.

VISN 4 MIRECC
type: Resource
type: NamedIndividual
has db xref: nif-0000-10541
synonym: Education and Clinical Center
synonym: The Stars and Stripes Healthcare Network (VISN 4) Mental Illness Research
IAO_0000115: The mission of the VISN 4 MIRECC is the treatment and prevention of comorbid medical, mental health, and/or substance use disorders, with the aim of improving the health, quality of life, and outcomes of healthcare services for veterans with mental illness. This is accomplished through the integration of basic, clinical, and services research and educational and clinical programs. The objectives of this MIRECC are: * Develop new empirical knowledge that can be directly applied to improve the clinical care of veterans * Provide education to providers and trainees to enhance the delivery of high quality healthcare to veterans * Impact public health in terms of veterans' mental health and quality of life * Serve as a national resource in education, research, and treatment of patients with comorbidity, and as a replicable model of excellence in clinical and educational programs Examine causal factors in the development of comorbid conditions. Assess impact of comorbidity on: * the identification and classification of disorders * the development and implementation of treatments * access to treatment and the impact of treatments on outcomes Sponsors: This work is supported by the US Department of Veterans Affairs

Prediction of Activity Spectra for Substances
type: Resource
type: NamedIndividual
has db xref: nif-0000-10543
synonym: PASS
IAO_0000115: PASS is a computer program which predicts the biological activity spectrum for a compound on the basis of its structural formula. The result of prediction is displayed for free. PASS Inet predicts 3678 pharmacological effects, mechanisms of action, mutagenicity, carcinogenicity, teratogenicity and embryotoxicity. PASS gives you hits in the following: - Finding most probable new leads with required activity spectra among the compounds from in-house and commercial data bases. - Revealing new effects and mechanisms of action for the old substances in corporate and private data bases. - Providing the basis for selection of the most prospective compounds for high throughput screening from the set of available samples. - Determining the assays that are more relevant for a particular compound. Sponsors: This work is supported by the Russian Foundation for Basic Research (Grant # 03-07-90282).

VideoLectures.NET
type: Resource
type: NamedIndividual
has db xref: nif-0000-10544
synonym: Video Lectures: Exchange Ideas and Share Thoughts
synonym: VideoLectures
synonym: VideoLectures.Net: Exchange Ideas & Share Thoughts
IAO_0000115: Award-winning free and open access educational video lectures repository. The lectures are given by distinguished scholars and scientists at the most important and prominent events like conferences, summer schools, workshops and science promotional events from many fields of Science. The portal is aimed at promoting science, exchanging ideas and fostering knowledge sharing by providing high quality didactic contents not only to the scientific community but also to the general public. All lectures, accompanying documents, information and links are systematically selected and classified through the editorial process taking into account also users' comments.

Wellcome Trust Case Control Consortium
type: Resource
type: NamedIndividual
has db xref: nif-0000-10551
synonym: Wellcome Trust Case-Control Consortium (WTCCC)
abbrev: WTCCC
IAO_0000115: Consortium of 50 research groups across the UK to harness the power of newly-available genotyping technologies to improve our understanding of the aetiological basis of several major causes of global disease. The consortium has gathered genotype data for up to 500,000 sites of genome sequence variation (single nucleotide polymorphisms or SNPs) in samples ascertained for the disease phenotypes. Analysis of the genome-wide association data generated has lead to the identification of many SNPs and genes showing evidence of association with disease susceptibility, some of which will be followed up in future studies. In addition, the Consortium has gained important insights into the technical, analytical, methodological and biological aspects of genome-wide association analysis. The core of the study comprised an analysis of 2,000 samples from each of seven diseases (type 1 diabetes, type 2 diabetes, coronary heart disease, hypertension, bipolar disorder, rheumatoid arthritis and Crohn's disease). For each disease, the case samples have been ascertained from sites widely distributed across Great Britain, allowing us to obtain considerable efficiencies by comparing each of these case populations to a common set of 3,000 nationally-ascertained controls also from England, Scotland and Wales. These controls come from two sources: 1,500 are representative samples from the 1958 British Birth Cohort and 1,500 are blood donors recruited by the three national UK Blood Services. One of the questions that the WTCCC study has addressed relates to the relative merits of these alternative strategies for the generation of representative population cohorts. Genotyping for this main Case Control study was conducted by Affymetrix using the (commercial) Affymetrix 500K chip. As part of this study a total of 17,000 samples were typed for 500,000 SNPs. There are two additional components to the study. First, the WTCCC award is part-funding a study of host resistance to infectious diseases in…

World Federation for Culture Collections
type: Resource
type: NamedIndividual
has db xref: nif-0000-10555
abbrev: WFCC
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Collects, authenticates, maintains and distributes cultures of microorganisms and cultured cells. Its aim is to promote and support the establishment of culture collections and related services, to provide liaison and set up an information network between the collections and their users, to organize workshops and conferences, publications and newsletters and work to ensure the long term perpetuation of important collections. The WFCC (through the activities of Professor Skerman, University of Queensland, Australia, and his colleagues in the 1960's) pioneered the development of an international database on culture resources worldwide. The result is the WFCC World Data Center for Microorganisms (WDCM). This data resource is now maintained at National Institute of Genetics (NIG), Japan and has records of nearly 476 culture collections from 62 countries. The records contain data on the organization, management, services and scientific interests of the collections. Each of these records is linked to a second record containing the list of species held. The WDCM database forms an important information resource for all microbiological activity and also acts as a focus for data activities among WFCC members.

Center for Computational Medicine and Biology
type: Resource
type: NamedIndividual
has db xref: nif-0000-10580
synonym: CCMB
IAO_0000115: The CCMB was created to facilitate interdisciplinary research in computational medicine and biology and to forge collaborative relationships with faculty across campus and the US. Computational medicine and bioinformatics, is an emerging field that pursues biological questions using advanced computational technology such as complex merged datasets and powerful computing clusters. The Center currently has three components: The Bioinformatics Graduate Program (BGP), The Collaborative Computing & Data Unit, and The Interdisciplinary Research Program. Faculty from all areas of campus are affiliated with the center. The Bioinformatics Graduate Program (BGP) trains masters and Ph.D-level scholars, and oversees the research computing for four faculty members with partial appointments in the program. The Bioinformatics Graduate Program currently has 24 doctoral and 11 master-level students. The Collaborative Computing & Data Unit provides expert support for large cluster computing -- a necessary component for doing research in computational medicine and biology. This core also works with the UM Medical School and Office of the Vice President for Research (OVPR) to address long-term deficits in computing needs across campus. Finally, The Interdisciplinary Research Program oversees several NIH and state-funded projects, the largest being the National Center for Integrative Biomedical Informatics, whose goal is developing tools to facilitate biomedical research. The IDR also provides support to faculty applying for interdisciplinary grants in all areas of bioinformatics research.

Biositemaps
type: Resource
type: NamedIndividual
has db xref: nif-0000-10583
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 27,2023. Biositemaps represent a mechanism for computational biologists and bio-informaticians to openly broadcast and retrieve meta-data about biomedical data, tools and services (i.e., biomedical resources) over the Internet. All Institutions with an interest in biomedical research can publish a biositemap.rdf file on their Internet site. The technology, developed by the Biositemaps Working Group of the NIH Roadmap National Centers of Biomedical Computing (NCBC), addresses (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. Each site which intends to contribute to the inventory instantiates a file on its Internet site biositemap.rdf which conforms to a defined RDF schema and uses concepts from the Biomedical Resource Ontology to describe the resources. Each biositemap.rdf file is simply a list of controlled metadata about resources (software tools, databases, material resources) that your organization uses or believes are important to biomedical research. The key enabling technologies are the Information Model (IM) which is the list of metadata fields about each resource (resource_name, description, contact_person, resource_type,...) and the Biomedical Resource Ontology (BRO) which is a controlled terminology for the resource_typeand which is used to improve the sensitivity and specificity of web searches. Biositemaps blend the features of Sitemaps (enabling efficient web-content exploration) and RSS Feeds (a mechanism for wide and effective news dissemination). As a hybrid between Sitemaps and RSS feeds, the Biositemap infrastructure facilitates a decentralized, portable, extensible and computationally tractable generation and consumption of meta-data about existent, revised and new resources for biomedical computation. Web browsers, crawlers and robots can discover, accumulate, process, integrate and deliver Biositemaps content to (human or machine) users in a…

Immundiagnostik
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_152383
synonym: Immundiagnostik AG
IAO_0000115: Commercial company that develops and provides laboratory diagnostics and other medical research products.

Organization for Human Brain Mapping
type: Resource
type: NamedIndividual
has db xref: nif-0000-10633
synonym: OHBM
IAO_0000115: International society dedicated to advancing understanding of anatomical and functional organization of human brain using neuroimaging. Primary function of society is to provide educational forums for exchange of up-to-the-minute and groundbreaking research across neuroimaging methods and applications. OHBM achieves this through its member led committees and Annual Meeting that is held in different locations throughout the world.

MADELINE
type: Resource
type: NamedIndividual
has db xref: nlx_154446
has db xref: OMICS_00210
synonym: Madeline
IAO_0000115: Software tool designed for preparing, visualizing, and exploring human pedigree data used in genetic linkage studies. It converts pedigree and marker data into formats required by popular linkage analysis packages, provides powerful ways to query pedigree data sets, and produces Postscript pedigree drawings that are useful for rapid data review.

CanSNPer
type: Resource
type: NamedIndividual
has db xref: biotools:cansnper
has db xref: OMICS_03706
IAO_0000115: Software that is a hierarchical genotype classifier of clonal pathogens.

ADaCGH2
type: Resource
type: NamedIndividual
has db xref: biotools:adacgh2
has db xref: OMICS_03697
synonym: ADaCGH2 - Analysis of big data from aCGH experiments using parallel computing and ff objects
IAO_0000115: Software for analysis and plotting of array comparative genomic hybridization (CGH) data. It allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.

SGA
type: Resource
type: NamedIndividual
has db xref: biotools:sga
has db xref: OMICS_00028
synonym: String Graph Assembler
synonym: String Graph Assembler (SGA)
IAO_0000115: Software package that functions as a de novo genome assembler based on the concept of string graphs. It is designed as a modular set of programs used to assemble large genomes from high coverage short read data.

Hunter Genomic Facility
type: Resource
type: NamedIndividual
has db xref: nlx_156341
IAO_0000115: Facility which provides instruments and instrument resources for analyzing DNA, RNA, protein, and radio-labeled substances.

American Society of Radiologic Technologists
type: Resource
type: NamedIndividual
has db xref: nif-0000-10661
abbrev: ASRT
IAO_0000115: Society of Radiologic Technologists to advance the medical imaging and radiation therapy profession and to enhance the quality of patient care, leading and serving its members, the profession, other health care providers and the public on all issues that affect the radiologic sciences. The mission of the ASRT is to foster the professional growth of radiologic technologists by expanding knowledge through education, research and analysis; promoting exceptional leadership and service; and developing the radiologic technology community through shared ethics and values. This portal offers information on Continuing Education opportunities, and has a variety of other resources including a marketplace, news, publications, events and conferences, career center, studies and surveys, professional resources, and much more. Scholarly Journals Members can earn CE credit through the Directed Readings program in the ASRT journals, Radiologic Technology and Radiation Therapist. By maintaining continuous membership, members can earn at least 12 Category A CE credits. Answer sheets for Directed Reading Quizzes can be completed on our Web site or mailed to the ASRT for grading. You will receive pass or fail notification immediately on the Web site or ASRT will notify you within 30 days if your completed quiz is mailed. A passing grade of 75 percent or better is required to receive the assigned Category A credit.

California Institute of Technology - Computation and Neural Systems
type: Resource
type: NamedIndividual
has db xref: nif-0000-10665
synonym: CNS
IAO_0000115: Portal offers information on people, research, seminars, academics, admissions, positions, and news, associated with interdisciplinary program to study problems arising at interface between neurobiology, electrical engineering, computer science, and physics. Applicants for Graduate Admissions should have undergraduate major in electrical engineering, biology, physics, mathematics, or computer science, and general background that will permit enrolling in advanced courses in other relevant disciplines. Admitted students will become affiliated with one of three participating divisions as appropriate to their background and interests. Post-doc positions are also available.

IMGENEX
type: Organization
type: NamedIndividual
has db xref: nlx_152382
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2025. Commercial antibody supplier. Imgenex has merged with Novus Biologicals.

www.brainmapping.org
type: Resource
type: NamedIndividual
has db xref: nif-0000-10669
synonym: brainmapping.org
IAO_0000115: This is a topical portal dedicated to the communication of news, science, and information of interest to the brain mapping community, and to sharing and promoting the science of brain mapping. The purpose and goal of brain mapping is to advance the understanding of the relationship between structure and function in the human brain. Scientists in this field seek to gain knowledge of the physical processes that underly human sensation, attention, awareness and cognition. These results are immediately applicable to surgical intervention, to the design of medical interventions and to the treatment of psychological and psychiatric disorders.

International Society for Magnetic Resonance in Medicine
type: Organization
type: NamedIndividual
has db xref: grid.420361.2
has db xref: ISNI: 0000 0001 2107 6555
has db xref: nif-0000-10673
synonym: ISMRM
IAO_0000115: The International Society for Magnetic Resonance in Medicine is an international, nonprofit, scientific association whose purpose is to promote communication, research, development, and applications in the field of magnetic resonance in medicine and biology and other related topics and to develop and provide channels and facilities for continuing education in the field. In addition to its large scientific meetings, the Society holds workshops and publishes two journals, Magnetic Resonance in Medicine and the Journal of Magnetic Resonance Imaging, and a newsletter, MR Pulse. It also sponsors study groups on specific areas of scientific interest and chapters based on geographical location. Its multidisciplinary membership of over 6,000 consists of clinicians, physicists, engineers, biochemists, and technologists. The ISMRMs inception, on January 1, 1994, resulted from a merger of the Society of Magnetic Resonance in Medicine and the Society of Magnetic Resonance Imaging forming the Society of Magnetic Resonance (now named the International Society for Magnetic Resonance in Medicine). The purposes of the Society are: (A) (i) To promote communication, research, development, applications, and the availability of information on magnetic resonance in medicine and biology and other related topics internationally; (ii) To develop and provide channels and facilities for continuing education and communication in the field, to publish and assist in the publishing of journals and other publications in the field; and (iii) To provide information and advice on those aspects of public policy which are concerned with magnetic resonance in medicine and biology and other related topics, and otherwise perform charitable, scientific and educational functions with respect to magnetic resonance applications in medicine and biology and other related topics. (B) To work with or for, and to co-operate with local, regional and national governments and governmental and private agencies, organi…

ISCBFM - International Society for Cerebral Blood Flow and Metabolism
type: Resource
type: NamedIndividual
has db xref: nif-0000-10674
synonym: International Society for Cerebral Blood Flow and Metabolism
synonym: International Society for Cerebral Blood Flow Metabolism
synonym: ISCBFM - International Society for Cerebral Blood Flow Metabolism
abbrev: ISCBFM
IAO_0000115: The International Society for Cerebral Blood Flow & Metabolism is a corporation operated exclusively for the purpose of promoting the advancement of education in the science of cerebral blood flow and metabolism throughout the world. The ISCBFM produces a quarterly newsletter, an official journal (Journal of Cerebral Blood Flow & Metabolism), have a yearly meeting, opportunities to host summer schools and a job board. ISCBFM members organize summer schools which are courses that have the aim to bring together young and experienced scientists for educational purposes. The biennial Brain Meetings also have a substantial part of the time allocated for educational purposes for young scientists interested in the field of cerebral blood flow and metabolism. Preference will be given to suggestions that are seen as a complement to scheduled courses in connection with the Brain Meetings and to courses that are given in between Brain Meetings.

Cognitive Neuroscience Society
type: Resource
type: NamedIndividual
has db xref: nif-0000-10675
synonym: CNS
IAO_0000115: The Cognitive Neuroscience Society (CNS) is committed to the development of mind and brain research aimed at investigating the psychological, computational, and neuroscientific bases of cognition. Since its founding in 1994, the Society has been dedicated to bringing its 2000 worldwide members the latest research and dialogues in order to facilitate public, professional and scientific discourse. The term cognitive neuroscience has now been with us for almost three decades, and identifies an interdisciplinary approach to understanding the nature of thought. Our members, who are engaged in research focused on elucidating the biological underpinnings of mental processes, form a network of scientists and scholars working at the interface of mind, brain and behavior research. The findings of this research are presented at our member-supported annual scientific conference. The three-day program of plenary speakers, symposia, posters and special events covers all aspects of cognitive neuroscience research. The Society also disseminates information regarding employment opportunities, training fellowships, research grants, and information on related scientific conferences in its monthly newsletter. Our members can receive the Journal of Cognitive Neuroscience at a substantial discount.

Helen Wills Neuroscience Institute
type: Organization
type: NamedIndividual
has db xref: nif-0000-10720
IAO_0000115: Portal for UC Berkeley's neuroscience research center. The group focuses on interdisciplinary collaboration between neuroscientists and members of UC Berkeley programs in engineering, chemistry, statistics, and computation. It also runs the neuroscience PhD program.

Brain and Behavior Research Foundation
type: Resource
type: NamedIndividual
has db xref: nif-0000-12459
synonym: Brain & Behavior Research Foundation
synonym: Brain Behavior Research Foundation
synonym: NARSAD: The Brain and Behavior Research Fund
synonym: NARSAD: The Worlds Leading Charity Dedicated to Mental Health Research
synonym: National Alliance for Research on Schizophrenia Depression
synonym: National Alliance on Research in Schizophrenia and Depression
IAO_0000115: The Brain and Behavior Research Foundation (formerly NARSAD, the National Alliance for Research on Schizophrenia and Depression) is committed to alleviating the suffering of mental illness by awarding grants that will lead to advances and breakthroughs in scientific research. Additionally, learn about brain and behavior disorders and upcoming events. 100% of all donor contributions for research are invested in NARSAD Grants leading to discoveries in understanding causes and improving treatments of disorders in children and adults, such as depression, bipolar disorder, schizophrenia, autism, attention deficit hyperactivity disorder, and anxiety disorders like obsessive-compulsive and post-traumatic stress disorders. Over a quarter of a century, we have awarded nearly $300 million worldwide to more than 3,000 scientists carefully selected by our prestigious Scientific Council. We receive no government funding. All of our work relies on contributions from families, foundations and other caring donors.

BioModels
type: Resource
type: NamedIndividual
has db xref: nif-0000-02609
has db xref: r3d100010789
synonym: BioModels Database
synonym: BioModels Database - A Database of Annotated Published Models
abbrev: BIOMD
IAO_0000115: Repository of mathematical models of biological and biomedical systems. Hosts selection of existing literature based physiologically and pharmaceutically relevant mechanistic models in standard formats. Features programmatic access via Web Services. Each model is curated to verify that it corresponds to reference publication and gives proper numerical results. Curators also annotate components of models with terms from controlled vocabularies and links to other relevant data resources allowing users to search accurately for models they need. Models can be retrieved in SBML format and import/export facilities are being developed to extend spectrum of formats supported by resource.

Internet Brain Segmentation Repository
type: Resource
type: NamedIndividual
has db xref: nif-0000-00032
abbrev: IBSR
IAO_0000115: Data set of manually-guided expert segmentation results along with magnetic resonance brain image data. Its purpose is to encourage the development and evaluation of segmentation methods by providing raw test and image data, human expert segmentation results, and methods for comparing segmentation results. Please see the MediaWiki for more information. This repository is meant to contain standard test image data sets which will permit a standardized mechanism for evaluation of the sensitivity of a given analysis method to signal to noise ratio, contrast to noise ratio, shape complexity, degree of partial volume effect, etc. This capability is felt to be essential to further development in the field since many published algorithms tend to only operate successfully under a narrow range of conditions which may not extend to those experienced under the typical clinical imaging setting. This repository is also meant to describe and discuss methods for the comparison of results.

NormaCurve
type: Resource
type: NamedIndividual
has db xref: OMICS_00814
IAO_0000115: Analysis methodology that allows simultaneous quantification and normalization of reverse phase protein array (RPPA) data.

XPP-Aut: X-Windows Phase Plane plus Auto
type: Resource
type: NamedIndividual
has db xref: nif-0000-10767
synonym: XPP as well as XPPAUT
IAO_0000115: XPPAUT is a tool for solving differential equations, difference equations, delay equations, functional equations, boundary value problems, and stochastic equations. It evolved from a chapter written by John Rinzel and me on the qualitative theory of nerve membranes and eventually became a commercial product for MSDOS computers called PHASEPLANE. It is now available as a program running under X11 and Windows. The code brings together a number of useful algorithms and is extremely portable. All the graphics and interface are written completely in Xlib which explains the somewhat idiosyncratic and primitive widgets interface. XPP contains the code for the popular bifurcation program, AUTO . Thus, you can switch back and forth between XPP and AUTO, using the values of one program in the other and vice-versa. I have put a ``friendly'' face on AUTO as well. You do not need to know much about it to play around with it. XPP has the capabilities for handling up to 590 differential equations. There are over a dozen solvers including several for stiff systems, a solver for integral equations and a symplectic solver. Up to 10 graphics windows can be visible at once and a variety of color combinations is supported. PostScript output is supported as well as GIF and animator GIF movies Post processing is easy and includes the ability to make histograms, FFTs and applying functions to columns of your data. Equilibria and linear stability as well as one-dimensional invariant sets can be computed. Nullclines and flow fields aid in the qualitative understanding of two-dimensional models. Poincare maps and equations on cylinders and tori are also supported. Some useful averaging theory tricks and various methods for dealing with coupled oscillators are included primarily because that is what I do for a living. Equations with Dirac delta functions are allowable. I have added an animation package that allows you to create animated versions of your simulations, such as a little pendulum m…

Dataverse Network Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-00316
has db xref: r3d100010051
synonym: Dataverse
synonym: Dataverse Network
synonym: Dataverse Project
synonym: Harvard Dataverse
synonym: The Dataverse Project
IAO_0000115: Project portal for publishing, citing, sharing and discovering research data. Software, protocols, and community connections for creating research data repositories that automate professional archival practices, guarantee long term preservation, and enable researchers to share, retain control of, and receive web visibility and formal academic citations for their data contributions. Researchers, data authors, publishers, data distributors, and affiliated institutions all receive appropriate credit. Hosts multiple dataverses. Each dataverse contains studies or collections of studies, and each study contains cataloging information that describes the data plus the actual data files and complementary files. Data related to social sciences, health, medicine, humanities or other sciences with an emphasis in human behavior are uploaded to the IQSS Dataverse Network (Harvard). You can create your own dataverse for free and start adding studies for your data files and complementary material (documents, software, etc). You may install your own Dataverse Network for your University or organization.

NIPS - Neural Information Processing Systems Conference
type: Resource
type: NamedIndividual
has db xref: nif-0000-10786
synonym: NIPS
IAO_0000115: The Neural Information Processing Systems (NIPS) Foundation is a non-profit corporation whose purpose is to foster the exchange of research on neural information processing systems in their biological, technological, mathematical, and theoretical aspects. Neural information processing is a field which benefits from a combined view of biological, physical, mathematical, and computational sciences. The primary focus of the NIPS Foundation is the presentation of a continuing series of professional meetings known as the Neural Information Processing Systems Conference, held over the years at various locations in the United States and Canada.

GapMis
type: Resource
type: NamedIndividual
has db xref: OMICS_03692
IAO_0000115: A software tool for pairwise sequence alignment with a single gap.

Italian Rett Syndrome database
type: Resource
type: NamedIndividual
has db xref: nif-0000-12492
abbrev: Rett syndrome bank
IAO_0000115: Data and biospecimen from Rett Syndrome patients shared with the scientific community with the ability to visualize the list of available samples and select those with specific clinical and molecular features. It also contains information on biospecimen samples from x-linked retardation, microdeletion, duplication syndromes, autosomal MR, and retinoblastoma. The bank is active since 1998 and it is located in the Medical Genetics Unit, at the University Hospital of Siena. The bank is divided in three distinct sections: # Rett Syndrome. This section contains samples from patients affected by Rett syndrome, a neurodegenerative disease affecting almost exclusively girls with an estimated frequency of 1:10000-15000 live born. By accessing the section users can see a list of all patients available with their phenotype, the specific MECP2 or CDKL5 mutation if known and the kind of biological samples available for each patient. The availability of this large panel of patients is potentially important for the clarification of the molecular bases of Rett syndrome. In fact, a 20-30 of Rett cases do not have MECP2 or CDKL5 mutations. These patients might bear intronic/promoter MECP2 or CDKL5 mutations or they might have alterations in one or more genes different from MECP2 or CDKL5, as suggested by the identification of various chromosomal rearrangements. To confirm a causative role of these rearrangements, and to identify the relevant gene/s, it is important to collect a great number of patients in which to search for overlapping rearrangements or point mutations in candidate genes. # X-Linked Mental Retardation. This section contains samples collected by the centers belonging to the Italian network on X-linked mental retardation, which includes the laboratory of bank curators (for specific information on the network goals and organization, go to the section page). Mental retardation (MR) is the most frequent cause of serious handicap in humans with an estimated prevalence of …

Neural ElectroMagnetic Ontologies (NEMO) Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-10899
synonym: Neural ElectroMagnetic Ontologies
abbrev: NEMO
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. NIH tombstone webpage lists Project Period : 2009 - 2013. NIH funded project to create EEG and MEG ontologies and ontology based tools. These resources will be used to support representation, classification, and meta-analysis of brain electromagnetic data. Three pillars of NEMO are: DATA, ONTOLOGY, and DATABASE. NEMO data consist of raw EEG, averaged EEG (ERPs), and ERP data analysis results. NEMO ontologies include concepts related to ERP data (including spatial and temporal features of ERP patterns), data provenance, and cognitive and linguistic paradigms that were used to collect data. NEMO database portal is large repository that stores NEMO consortium data, data analysis results, and data provenance. EEG and MEG ontologies and ontology-based tools to support representation, classification, and meta-analysis of brain electromagnetic data. Raw EEG and ERP data may be uploaded to the NEMO FTP site., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

NIDA Data Share
type: Resource
type: NamedIndividual
has db xref: nif-0000-21981
synonym: CTN Data Share
synonym: CTN database
synonym: NIDA Clinical Trials Data Share
synonym: NIDA CTN Data Share
IAO_0000115: Website which allows data from completed clinical trials to be distributed to investigators and public. Researchers can download de-identified data from completed NIDA clinical trial studies to conduct analyses that improve quality of drug abuse treatment. Incorporates data from Division of Therapeutics and Medical Consequences and Center for Clinical Trials Network.

TRAMS
type: Resource
type: NamedIndividual
has db xref: OMICS_01924
synonym: Tool for Rapid Annotation of Microbial SNPs
synonym: Tool for rapid annotation of microbial SNPs (TRAMS): a simple program for rapid annotation of genomic variation in prokaryotes
synonym: Tool for rapid annotation of microbial SNPs: a simple program for rapid annotation of genomic variation in prokaryotes
synonym: TRAMS: a simple program for rapid annotation of genomic variation in prokaryotes
IAO_0000115: A software program for functional annotation of genomic single nucleotide polymorphisms (SNPs) which is available to download as a single file executable for WINDOWS users with limited computational experience and as a Python script for Mac OS and Linux users. It needs only a tab delimited text file containing SNP locations, reference nucleotide and SNPs in different strains along with a reference genome sequence in standard GenBank or EMBL format. It annotates SNPs as synonymous, non-synonymous or nonsense. Non-synonymous SNPs in start and stop codons are separated as non-start and non-stop SNPs, respectively. SNPs in overlapping features are annotated separately for each feature and multiple nucleotide polymorphisms (MNPs) within a codon are combined prior to annotation. A workflow has also been developed for use in Galaxy to map short reads to a reference genome and extract and annotate the SNPs.

NeuronBank
type: Resource
type: NamedIndividual
has db xref: nif-0000-10901
has db xref: SCR_005058
synonym: NeuronBank wiki
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. Platform for Neuroscientists to describe neurons and neural circuitry. Registered users may edit. The ultimate goal is advance the field of Neuromics by creating an encyclopedia of neurons and neural circuitry. NOTE: The database is no longer being maintained due to lack of funding.

SNPMeta
type: Resource
type: NamedIndividual
has db xref: OMICS_01923
IAO_0000115: A Python and BioPython-based tool to generate metadata for single nucleotide polymorphisms (SNPs) for easy filtering, or submission to SNP databases. Information reported includes gene name, whether the SNP is coding or noncoding, and whether the SNP is synonymous or nonsynonymous. SNPMeta outputs in either a dbSNP submission report format, or a tab-delimited format. There is a also Web-based version available that only annotates with default settings, and only annotates a maximum of 20 SNPs at one time. The script may be downloaded for full functionality.

Laboratory for Neural Computation and Cognition
type: Resource
type: NamedIndividual
has db xref: nif-0000-10906
IAO_0000115: Lab that studies multiple levels of computational modeling and experimental work to understand the neural mechanisms underlying reinforcement learning, decision making and cognitive control.

Wavelet-based Image Fusion
type: Resource
type: NamedIndividual
has db xref: nlx_156018
IAO_0000115: Matlab toolbox that implements the wavelet-based image fusion technique for orthogonal images, introduced in (Aganj et al, MRM 2012).

National Hydrocephalus Foundation
type: Resource
type: NamedIndividual
has db xref: nif-0000-11667
abbrev: NHF
IAO_0000115: Online portal with resources for education about hydrocephalus as well as community resources for those directly affected, family, and friends. The portal includes a community membership opportunity for people and families affected by hydrocephalus.

Basal Ganglia Model in Action
type: Resource
type: NamedIndividual
has db xref: nif-0000-10908
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Online portal with educational resources such as videos, images, diagrams, and descriptions of basal ganglia activity. The model also includes interactions with areas of prefrontal cortex to examine BG roles in higher level cognitive functions such as working memory, attentional shifting, and decision making.

ITK-SNAP
type: Resource
type: NamedIndividual
has db xref: nif-0000-00317
IAO_0000115: Open source interactive software application for three dimentional medical images, manual delineation of anatomical regions of interest, and performing automatic image segmentation. Used for delineating anatomical structures and regions in MRI, CT and other 3D biomedical imaging data.WebGL-based viewer for volumetric data. It is capable of displaying arbitrary (non axis-aligned) cross-sectional views of volumetric data, as well as 3-D meshes and line-segment based models (skeletons).

Neurofed
type: Resource
type: NamedIndividual
has db xref: nif-0000-10988
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. The NeuroFed resource is a listing of neuroscience research funding contacts in the Federal government. It is an informal compendium (PDF) of names and contact information for nearly 300 research grant and scientific review administrators in 21 organizational units of the federal government. An electronic (PDF) version of the most recent update of this list is available on the Society for Neuroscience website at: http://www.sfn.org/index.aspx?pagename=professionalDevelopment_training. The list is updated annually by NIH personnel.

SNPAAMapper
type: Resource
type: NamedIndividual
has db xref: biotools:snpaamapper
has db xref: OMICS_01922
synonym: SNPAAMapper - A SNP Amino Acid Mapping tool
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. A downstream variant annotation program that can effectively classify variants by region (e.g. exon, intron, etc), predict amino acid change type (e.g. synonymous, non-synonymous mutation, etc), and prioritize mutation effects (e.g. CDS versus 5?UTR, etc). Major features: * The pipeline accepts the VCF (Variant Call Format) input file in tab-delimited format and processes the vcf input file containing all cases (G5, lowFreq, and novel) * The variant mapping step has the option of letting users select whether they want to report the bp distance between each identified intron variant and its nearby exon * The pipeline can deal with VCF files called by different SAMTools versions (0.1.18 and older ones) and also offers flexibility in dealing with vcf input files generated using SAMTools with two or three samples * The spreadsheet result file contains full protein sequences for both ref and alt alleles, which makes it easier for downstream protein structure/function analysis tools to take

METAL
type: Resource
type: NamedIndividual
has db xref: nlx_154476
has db xref: OMICS_00239
synonym: METa AnaLysis Helper
synonym: Metal - Meta Analysis Helper
IAO_0000115: Software application designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner. (entry from Genetic Analysis Software)

Parkinson Society Canada
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100000263
has db xref: grid.453461.1
has db xref: nif-0000-11672
IAO_0000115: A not-for-profit, volunteer based charity whose purpose is to find a cure for Parkinson's disease through research, advocacy, education and support services. Parkinson Society Canadas leads initiatives that include: raising funds for research through national events; funding research, movement disorder clinics, and outreach programs across Canada; staffing a national Information and Referral Centre; developing educational and information materials; providing up to date detailed information about Parkinson's disease; and providing support for regional partners to better meet the needs of people living with Parkinson's services. Researchers can apply for various funding awards and fellowships by following the funding process outlined by Parkinson Society Canada.

OLORIN
type: Resource
type: NamedIndividual
has db xref: nlx_154503
has db xref: OMICS_01556
IAO_0000115: An interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees. It integrates gene flow output from Merlin and next generation sequencing data. Users can interactively filter and prioritize variants based on haplotype sharing across different sets of selected individuals and allele frequency in reference datasets. (entry from Genetic Analysis Software)

OSA
type: Resource
type: NamedIndividual
has db xref: nlx_154504
synonym: Ordered Subset Analysis
synonym: Ordered Subset Analysis Program
synonym: OSA Program
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Software application that allows the researcher to evaluate evidence for linkage even when heterogeneity is present in a data set. This is not an unusual occurrence when studying diseases of complex origin. Families are ranked by covariate values in order to test evidence for linkage among homogeneous subsets of families. Because families are ranked, a priori covariate cutpoints are not necessary. Covariates may include linkage evidence at other genes, environmental exposures, or biological trait values such as cholesterol, age at onset, and so on.

National Parkinson Foundation
type: Resource
type: NamedIndividual
has db xref: nif-0000-11702
synonym: NPF
IAO_0000115: The mission of the National Parkinson Foundation is to improve the quality of care for people with Parkinson's disease through research, education and outreach. NPF funds research through four main programs: the Centers of Excellence Network, which focuses on clinical studies of new therapeutic approaches; the Parkinson's Outcomes Project, a large clinical study of Parkinson's disease; the Grants/Clinical Research Fund, which provides funding to individual researchers; and fellowship awards, which are used to train neurologists in the movement disorder specialty.

openADAM
type: Resource
type: NamedIndividual
has db xref: OMICS_01921
IAO_0000115: A web-based database management system for the large amount of genotype data generated from the Affymetrix GeneChip Mapping Array and Genome-Wide Human SNP Array platforms.

Pennsylvania State Hershey College of Medicine; Pennsylvania; USA
type: Organization
type: NamedIndividual
has db xref: nlx_82737
synonym: Penn State Hershey College of Medicine
synonym: Penn State Hershey College of Medicine; Pennsylvania; USA
synonym: Pennsylvania State Hershey College of Medicine
IAO_0000115: Public, land-grant research university in Pennsylvania, USA. The College of Medicine offers professional degree programs in medicine.

BioCurrents Research Center
type: Resource
type: NamedIndividual
has db xref: nif-0000-24482
abbrev: BRC
IAO_0000115: The BioCurrents Research Center (BRC) is an integrated technology resource of the NIH:NCRR. The activities of the Center focus on molecular physiology as it relates to the cell function and disease. Our particular interest is how the dynamics of cell responses are reflected in the chemical profiles of microdomains surrounding single living cells. In order to measure complex cellular boundary layers, the BRC has specialized in the development of extremely sensitive signal acquisition and processing methods along with miniaturized electrochemical sensor designs. The technique is non-invasive and termed self-referencing. Since its establishment in 1996, the BRC has directed its technological research and development to the design and application of ultra-microelectrodes (tip diameters of less than 10m) tailored for the detection of specific chemicals. These have been successfully applied to the boundary layer profiles of many different cell types, with thematic strength in diabetes research, reproductive health and development (see collaborative profiles). More recently, it is changing its focus to technical developments, enhancing the integrative approach to cell function. To understand a cell as a dynamic and integrated whole, BRC must be able to examine responses from different domains as near to real time and as synchronously as possible. To this end, it is developing imaging capabilities to work in parallel with electrochemistry and conventional electrophysiological techniques. Imaging includes a spinning disc confocal, as well as a low light/luminescent imager designed and built within the BRC. The technologies developed or under development are in high demand within the biomedical community. Over 40 investigators work with the Center each year in a collaborative or service capacity. Over 80 of our visitor pool is NIH funded, representing approximately 25 NIH divisions and institutes. As part of our training and dissemination program we host occasional workshops …

SeqEM
type: Resource
type: NamedIndividual
has db xref: biotools:seqem
has db xref: OMICS_00074
IAO_0000115: Online tool for utilizing a genotype calling algorithm for next-generation sequence data.

Parkinsons UK
type: Resource
type: NamedIndividual
has db xref: nif-0000-11750
has db xref: nlx_143576
has db xref: SCR_004150
synonym: Parkinson's Disease Society
synonym: Parkinson's Disease Society of the United Kingdom
synonym: Parkinson's UK
synonym: Parkinsons Disease Society of the United Kingdom
IAO_0000115: The Parkinsons Disease Society funds research, offers educational information, advice, and support from medical professionals, and runs campaigns with the goal of offering support, raising money, and finding a cure for Parkinsons disease. In addition to funding research, the Society offers a Helpline to support those suffering from Parkinsons and their caregivers, and also offers a range educational materials. The Society has a network of over 330 branches and support groups located across the UK. Additionally, the Society campaigns for and influences government policy and the development of high-quality services at a local and national level.

MEDx
type: Resource
type: NamedIndividual
has db xref: nif-0000-00325
synonym: Medical Xcalibur
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 06, 2013. Per the associated paper, Aguirre GK (2012) FIASCO, VoxBo, and MEDx: behind the code. Neuroimage 62: 765-7, the MedX software was discontinued. The website itself however, looks like you can still buy it (website last updated 2004). Highly optimized, portable, commercial software for the visualization, processing, and analysis of medical images. The packages include: SPM '99, FSL, DICOM Import/Export, ABLe, Functional Data Simulator. Designed especially for medical imaging researchers and system developers, MEDx brings multi-modality, multi-dimensional image processing functionality to the medical imaging research community. With MEDx, users display images and control menus using the industry-standard XWindow display system and Tcl/Tk interface language. MEDx transforms your computer into a powerful image processing workstation that displays, analyzes, and processes your medical image data in a myriad of innovative ways.

National VA Parkinson's Disease Consortium
type: Resource
type: NamedIndividual
has db xref: nif-0000-11756
synonym: The National VA Parkinson's Disease Consortium
IAO_0000115: A consortium created to support the provision of optimal care and education for veterans diagnosed with Parkinson's disease and related movement disorders through professional education, collaboration and advocacy.

SHARCGS
type: Resource
type: NamedIndividual
has db xref: biotools:sharcgs
has db xref: OMICS_00029
synonym: SHARCGS - SHort read Assembler based on Robust Contig extension for Genome Sequencing
synonym: SHort read Assembler based on Robust Contig extension for Genome Sequencing
synonym: SHort read Assembler based on Robust Contig extension for Genome Sequencing (SHARCGS)
IAO_0000115: Software package for a DNA assembly program designed for de novo assembly of 25-40mer input fragments and deep sequence coverage.

PDtrials- Parkinsons Disease Clinical Trials
type: Resource
type: NamedIndividual
has db xref: nif-0000-11762
synonym: PDtrials
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. A collaborative initiative of Parkinson's organizations dedicated to increasing education and awareness about clinical research. PDtrials provides up-to-date information on Parkinson's disease trials currently enrolling participants in the U.S. and Canada, as well as information about Parkinson's studies for people living with PD, their families and caregivers. Researchers can list their own trials on the PDtrials website. Patients can browse trial listings by type, location, symptom, or keyword.

Bgee: dataBase for Gene Expression Evolution
type: Resource
type: NamedIndividual
has db xref: nif-0000-11819
has db xref: r3d100014596
synonym: Bgee: dataBase Gene Expression Evolution
synonym: dataBase Gene Expression Evolution
abbrev: Bgee
IAO_0000115: Database to retrieve and compare gene expression patterns between animal species. Bgee first maps heterogeneous expression data (currently bulk RNA-Seq, scRNA-Seq, Affymetrix, in situ hybridization, and EST data) to anatomy and development of different species. Bgee is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of gene expression.

TheBrainMatters.org
type: Resource
type: NamedIndividual
has db xref: nif-0000-11829
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 18, 2016. TheBrainMatters.org is a comprehensive resource for the public that provides information on on more than 250 neurologic disorders . This site combines important information from such credible sources as the American Academy of Neurology and the National Institute of Neurological Disorders and Stroke websites into one clean, organized, and user-friendly site designed specifically for users to become better informed about neurologic disorders.

DMET-Analyzer
type: Resource
type: NamedIndividual
has db xref: OMICS_01920
synonym: DMETANALYZER
synonym: DMETANALYZER - A tool for supporting pharmacogenomics data analysis
IAO_0000115: Software tool for the automatic association analysis among the variation of the patient genomes and the clinical conditions of patients, i.e. the different response to drugs. The system allows: (i) to automatize the workflow of analysis of DMET (drug metabolism enzymes and transporters)-SNP (Single Nucleotide Polymorphism) data avoiding the use of multiple tools; (ii) the automatic annotation of DMET-SNP data and the search in existing databases of SNPs (e.g. dbSNP), (iii) the association of SNP with pathway through the search in PharmaKGB, a major knowledge base for pharmacogenomic studies. It has a simple graphical user interface that allows users (doctors/biologists) to upload and analyze DMET files produced by Affymetrix DMET-Console in an interactive way.

PEDHUNTER
type: Resource
type: NamedIndividual
has db xref: biotools:pedhunter
has db xref: nlx_154518
has db xref: OMICS_00211
abbrev: PedHunter
IAO_0000115: Software package that facilitates creation and verification of pedigrees within large genealogies. The pedigrees are produced as files in LINKAGE format ready for linkage analysis and for drawing with a variety of drawing programs, such as PEDDRAW and cranefoot.

AffyPipe
type: Resource
type: NamedIndividual
has db xref: biotools:affypipe
has db xref: OMICS_05203
synonym: AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow
IAO_0000115: An open-source software pipeline for Affymetrix Axiom genotyping workflow.

WebPath - The Internet Pathology Laboratory for Medical Education
type: Resource
type: NamedIndividual
has db xref: nif-0000-11854
synonym: WebPath
IAO_0000115: This popular web resource includes over 1900 images along with text, tutorials, laboratory exercises, and examination items for self-assessment that demonstrate gross and microscopic pathologic findings associated with human disease conditions. Content includes pathology cases (surgical pathology, autopsy, cytopathology, forensic pathology, clinical pathology) at the University of Utah Health Sciences Center and affiliated hospitals and laboratories, and from contributors at other institutions worldwide. The content at this web site will assist a medical student in achievement of an important goal: passing step 1 of the USMLE examination required to become licensed as a physician. This site was conceived from the necessity to create useful multimedia teaching resources for medical students at the University of Utah for use in the pathology courses given in the second year of the curriculum.

World Parkinson Congress
type: Resource
type: NamedIndividual
has db xref: nif-0000-11855
synonym: World Parkinson's Disease Congress
IAO_0000115: A nonprofit organization dedicated to providing an international forum for the latest scientific discoveries, medical practices and caregiver initiatives related to Parkinson's disease. It hosts the annual World Parkinson Congress, an event which focuses on bringing physicians, scientists, allied health professionals, caregivers and people diagnosed with Parkinson's disease together, in order to create a global dialogue that will help expedite treatment practices and the discovery of a cure .

World Parkinson Disease Association
type: Resource
type: NamedIndividual
has db xref: nif-0000-11857
synonym: WPDA
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The World Parkinson's Disease Association is an alliance of members from all over the world who have come together to share information about Parkinson's disease. In order to further Parkinson's research and better the condition of those diagnosed with the disease, the Association: establishes computerized connections; takes part in and/or finances research activities; urges pharmaceutical companies and government institutions of the various countries to support the guidelines recommended by the associations of Parkinson's patients; and coordinates and promotes interchange of information among its members with the aim of solving problems of mutual interest.

Candida Genome Database
type: Resource
type: NamedIndividual
has db xref: biotools:cgd
has db xref: nif-0000-02634
has db xref: r3d100010617
abbrev: CGD
abbrev: CGD LOCUS
abbrev: CGD REF
IAO_0000115: Database of genetic and molecular biological information about Candida albicans. Contains information about genes and proteins, descriptions and classifications of their biological roles, molecular functions, and subcellular localizations, gene, protein, and chromosome sequence information, tools for analysis and comparison of sequences and links to literature information. Each CGD gene or open reading frame has an individual Locus Page. Genetic loci that are not tied to DNA sequence also have Locus Pages. Provides Gene Ontology, GO, to all its users. Three ontologies that comprise GO (Molecular Function, Cellular Component, and Biological Process) are used by multiple databases to annotate gene products, so that this common vocabulary can be used to compare gene products across species. Development of ontologies is ongoing in order to incorporate new information. Data submissions are welcome.

Addgene
type: Resource
type: NamedIndividual
has db xref: biotools:Addgene
has db xref: grid.482682.2
has db xref: ISNI: 0000 0004 5912 0787
has db xref: nif-0000-11872
has db xref: Wikidata: Q4681063
synonym: Addgene Plasmid Database
synonym: Addgene Repository
IAO_0000115: Non-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmids. Facilitates archiving and distributing DNA-based research reagents and associated data to scientists worldwide. Repository contains over 65,000 plasmids, including special collections on CRISPR, fluorescent proteins, and ready-to-use viral preparations. There is no cost for scientists to deposit plasmids, which saves time and money associated with shipping plasmids themselves. All plasmids are fully sequenced for validation and sequencing data is openly available. We handle the appropriate Material Transfer Agreements (MTA) with institutions, facilitating open exchange and offering intellectual property and liability protection for depositing scientists. Furthermore, we curate free educational resources for the scientific community including a blog, eBooks, video protocols, and detailed molecular biology resources.

The Eye Lab Image Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-11980
synonym: The Eye Lab
IAO_0000115: The Image Repository contains a collection of images produced by the research of John Clark's Eye Lab. Experiments include: Irradiated CP49 KO and wildtype, Hypothesis: CP49 KO mice will be more sensitive to X-irradiation than controls Huntington Mice Cataract ID, Hypothesis: Individuals can be identified by the pattern of their cataract. Alpha-Synuclein Mice, Hypothesis: Mice transgenic for the EGFP-tagged, mutant and WT strains of human alpha-synuclein gene, will provide a model for the testing of drugs on aggregation of the protein. alpha B Crystallin/SPARC DKO, Hypothesis: The absence of the chaperone protein, alpha B-Crystallin, causes a greater intensity and earlier onset in the opacifying effects of an absence of the matricellular protein, SPARC. Survey of SPARC KO and WT Survey of SPARC KO and WT Mice The repository is being built through a collaboration between the University of Washington's Department of Biological Structure, led by John Clark, and the Structural Informatics Group, led by Jim Brinkley. As an aim of the Biomedical Information Sciences Technology Initiative (BISTI), members of the Structural Informatics Group have been talking with biomedical researchers to find out their informatics needs. Tools such as this repository are being created in response to those needs. This web tool allows the researchers to add their images to a repository facilitating the organization and management of their data.

WIRM - Web Interfacing Repository Manager
type: Resource
type: NamedIndividual
has db xref: nif-0000-11991
synonym: WIRM
IAO_0000115: WIRM is an innovative software toolkit that allows the creation of web applications that facilitate the acquisition, integration, and dissemination of multimedia biomedical data over the web, thereby reducing the cost of knowledge sharing. WIRM reduces the complexity of building custom biomedical web applications and it's visual modeling tools enable domain experts to describe the structure of their knowledge, from which WIRM automatically generates full-featured, customizable content management systems. WIRM is a Perl-based application server that provides a high-level programming environment for developing web information systems. WIRM consists of an object-relational database and a suite of Perl interfaces for visualizing, integrating and analyzing heterogeneous multimedia data. WIRM provides facilities for creating context-sensitive views over a multimedia database, allowing developers to rapidly build dynamic web sites that adapt their content and presentation to multiple classes of end-users. WIRM was developed by Rex Jakobovits as part of his PhD dissertation at the University of Washington Computer Science department, under the guidance of Dr. James F. Brinkley of the Department of Biological Structure. The system was generalized from work funded by NIH SBIR grant R43-MH61277-01 and Human Brain Project grant DC/LM02310.

Thomson Reuters Biology Browser
type: Resource
type: NamedIndividual
has db xref: nif-0000-12071
synonym: Biology Browser
synonym: BiologyBrowser
synonym: Reuters Biology Browser
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented April 7, 2018. Online portal and searchable database with resources for the greater scientific community such as zoological records, nomenclature guides, and relevant scientific news stories and websites.

ISA Infrastructure for Managing Experimental Metadata
type: Resource
type: NamedIndividual
has db xref: nif-0000-12074
synonym: Investigation / Study / Assay (ISA) infrastructure
synonym: Investigation / Study / Assay infrastructure
synonym: Investigation/Study/Assay (ISA) infrastructure
synonym: Investigation/Study/Assay infrastructure
synonym: ISA infrastructure
synonym: ISA metadata tracking tools
synonym: ISA tools
synonym: isainfrastructure
synonym: ISAtools
IAO_0000115: Desktop software suite targeted to curators and experimentalists that assists in the reporting and local management of experimental metadata, engages with minimum information checklists and ontologies and formats studies for submission to international public repositories. The ISA software suite is the product of an ongoing collaboration between various research and service groups from diverse life science domains. It represents an opportunity for the wider research community to start taking data management into their own hands by supporting graduated adherence to community standards and the efficient curation of experimental metadata at source, shielded from underlying complexities. The software suite is comprised of several platform-independent Java-based software components for local use, including a relational database, built around the ISA-Tab format. The components work both as stand-alone applications and as a unified system.

Minimum Information for Biological and Biomedical Investigations
type: Resource
type: NamedIndividual
has db xref: nif-0000-12075
synonym: MIBBI: Minimum Information for Biological and Biomedical Investigations
abbrev: MIBBI
IAO_0000115: A common portal for minimum information (MI) checklists to act as a one-stop shop for those exploring the range of extant projects, foster collaborative development and ultimately promote gradual integration. Goals include * To increase the visibility of projects developing guidance for the reporting of biological and biomedical science. * To encourage appropriate collaborative development between projects to avoid duplication of effort or competition. * To promote the adoption of consensus guidance on reporting by journals and funders.

Mouse Neuronal Expression Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-12084
synonym: NIH Neuroscience Blueprint Cre Driver Network - Expression DB
synonym: NIH Neuroscience Blueprint Cre Driver Network Expression DB
abbrev: MNED
IAO_0000115: Database of microarray analysis of twelve major classes of fluorescent labeled neurons within the adult mouse forebrain that provide the first comprehensive view of gene expression differences. The publicly available datasets demonstrate a profound molecular heterogeneity among neuronal subtypes, represented disproportionately by gene paralogs, and begin to reveal the genetic programs underlying the fundamental divisions between neuronal classes including that between glutamatergic and GABAergic neurons. Five of the 12 populations were chosen from cingulate cortex and included several subtypes of GABAergic interneurons and pyramidal neurons. The remaining seven were derived from the somatosensory cortex, hippocampus, amygdala and thalamus. Using these expression profiles, they were able to construct a taxonomic tree that reflected the expected major relationships between these populations, such as the distinction between cortical interneurons and projection neurons. The taxonomic tree indicated highly heterogeneous gene expression even within a single region. This dataset should be useful for the classification of unknown neuronal subtypes, the investigation of specifically expressed genes and the genetic manipulation of specific neuronal circuit elements. Datasets: * Full: Here you can query gene expression results for the neuronal populations * Strain: Here you can query the same expression results accessed under the full checkbox, with one additional population (CT6-CG2) included as a control for the effects of mouse strain. This population is identical to CT6-CG (YFPH) except the neurons were derived from wild-type mice of three distinct strains: G42, G30, and GIN. * Arlotta: Here you can query the same expression results accessed under the full checkbox, with nine additional populations from the dataset of Arlotta et al., 2005. These populations were purified by FACS after retrograde labeling with fluorescent microspheres. Populations are designated by the pref…

Rat Resource and Research Center
type: Resource
type: NamedIndividual
has db xref: nif-0000-12085
synonym: National Center for Research Resources
synonym: National Rat Resource Research Center
synonym: NCRR
synonym: Rat Resource & Research Center
synonym: Rat Resource Research Center
abbrev: NCRR RRRC
abbrev: NRRRC
abbrev: RRRC
IAO_0000115: Supplies biomedical investigators with rat models, embryonic stem cells, related reagents, and protocols they require for their research. In addition to repository, cryostorage and distribution functions, RRRC can facilitate acquisition of rat strains from other international repositories as well as provide consultation and technical training to investigators using rat models.

pSTIING
type: Resource
type: NamedIndividual
has db xref: OMICS_01916
synonym: Protein Signalling Transcriptional Interactions & Inflammation Networks Gateway
synonym: Protein Signalling Transcriptional Interactions and Inflammation Networks Gateway
IAO_0000115: A publicly accessible knowledgebase about protein-protein, protein-lipid, protein-small molecules, ligand-receptor interactions, receptor-cell type information, transcriptional regulatory and signal transduction modules relevant to inflammation, cell migration and tumourigenesis. It integrates in-house curated information from the literature, biochemical experiments, functional assays and in vivo studies, with publicly available information from multiple and diverse sources across human, rat, mouse, fly, worm and yeast. The knowledgebase allowing users to search and to dynamically generate visual representations of protein-protein interactions and transcriptional regulatory networks. Signalling and transcriptional modules can also be displayed singly or in combination. This allow users to identify important "cross-talks" between signalling modules via connections with key components or "hubs". The knowledgebase will facilitate a "systems-wide" understanding across many protein, signalling and transcriptional regulatory networks triggered by multiple environmental cues, and also serve as a platform for future efforts to computationally and mathematically model the system behavior of inflammatory processes and tumourigenesis.

PTMcode
type: Resource
type: NamedIndividual
has db xref: OMICS_01915
abbrev: PTMCode
IAO_0000115: Database of known and predicted functional associations between protein posttranslational modifications (PTMs) within proteins. In its first release it contains 13 different PTM types. PTM types are abbreviated in a two letter code as: Ph (phosphorylation), NG (N-linked glycosylation), Ac (acetylation), OG (O-linked glycosylation), Ub (ubiquitination), Me (methylation), SM (SUMOylation), Hy (hydroxylation), Ca (carboxylation), Pa (palmitoylation), Su (sulfation), Ni (nitrosylation) and CG (C-linked glycosylation). These PTMs are present in 25,765 proteins of 8 different eukaryotes. The database is focused on the exploration of the global post-translational regulation of proteins, not only by describing the set of its modifications, but by identifying the functional associations among the PTMs present in the protein. To do that, they combine five different evidence channels based on a literature survey, the modified residue co-evolution, their structural proximity, their competition for the same residue and the location within PTM highly-enriched protein regions (hotspots) and show the functional associations within the context of the protein architecture.

ASPGD
type: Resource
type: NamedIndividual
has db xref: biotools:aspgd
has db xref: nif-0000-12244
synonym: Aspergillus Genome Database
synonym: ASPGD LOCUS
synonym: ASPGD REF
IAO_0000115: Database of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus including information about genes and proteins of Aspergillus nidulans and Aspergillus fumigatus; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Sgenus species. Also available are Gene Ontology (GO) and community resources. Based on the Candida Genome Database, the Aspergillus Genome Database is a resource for genomic sequence data and gene and protein information for Aspergilli. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). Search options allow you to: *Search AspGD database using keywords. *Find chromosomal features that match specific properties or annotations. *Find AspGD web pages using keywords located on the page. *Find information on one gene from many databases. *Search for keywords related to a phenotype (e.g., conidiation), an allele (such as veA1), or an experimental condition (e.g., light). Analysis and Tools allow you to: *Find similarities between a sequence of interest and Aspergillus DNA or protein sequences. *Display and analyze an Aspergillus sequence (or other sequence) in many ways. *Navigate the chromosomes set. View nucleotide and protein sequence. *Find short DNA/protein sequence matches in Aspergillus. *Design sequencing and PCR primers for Aspergillus or other input sequences. *Display the restriction map for a Aspergillus or other input …

SHORTY
type: Resource
type: NamedIndividual
has db xref: biotools:shorty
has db xref: OMICS_00030
IAO_0000115: Software for targeted de novo assembly of microreads with mate pair information and sequencing errors.

National Eye Health Education Program
type: Resource
type: NamedIndividual
has db xref: nif-0000-00576
synonym: NEHEP
IAO_0000115: NEI established NEHEP to increase awareness among healthcare professionals and the public of scientifically based health information that can be applied to preserving sight and preventing blindness. NEHEP works in partnership with a variety of public and private organizations that conduct eye health education programs. Program activities are designed to promote the importance of early detection and timely treatment of eye disease and the use of vision rehabilitation services using strategies that are culturally appropriate, health-literate, and evidence-based. NEHEP ensures that vision is a health priority by translating eye and vision research into public and professional education programs. NEHEP supports collaboration among eye health professionals, healthcare providers, patients, and the public. NEHEP programs provide healthcare professionals with information, materials, and resources to educate patients and the public about eye health and the importance of comprehensive dilated eye examinations. NEHEP is supported by a Planning Committee and a Partnership, which bring a vast array of knowledge about eye health and experience with populations at higher risk for eye disease. NEHEP Programs *Diabetic Eye Disease: The NEHEP Diabetic Eye Disease (DED) Education Program is designed to increase awareness about DED among people with diabetes, particularly those at higher risk. *Glaucoma: The NEHEP Glaucoma Education Program provides information about glaucoma to people at higher risk as well as those living with the disease. *Low Vision: The NEHEP Low Vision Education Program is designed to create awareness among adults, their families and friends, and the general public about vision rehabilitation services. *Ojo con su Vision: Ojo con su visin or Watch out for your vision is the Spanish-language program of NEHEP that targets the Hispanic/Latino community. Healthy Vision Program Healthy People 2010, the health promotion and disease prevention framework for the Nation, …

Stanford Genomics Service Center Core Facility
type: Resource
type: NamedIndividual
has db xref: ABRF_200
has db xref: nif-0000-12246
has db xref: nif-0000-31997
has db xref: SCR_008627
synonym: Stanford Functional Genomics Facility
synonym: Stanford Genomics
synonym: Stanford Genomics Service Center
synonym: Stanford Medicine Stanford Functional Genomics Facility
synonym: Stanford School of Medicine Stanford Functional Genomics Facility
synonym: Stanford University Functional Genomics Core Facility
abbrev: SFGF
IAO_0000115: Stanford Genomics formerly Stanford Functional Genomics Facility provides services for high throughput sequencing, single cell assays, gene expression and genotyping studies utilizing microarray and real time PCR, and related services. High throughput sequencing (Illumina HiSeq 4000, NextSeq 500, MiSeq and MiniSeq), microarray gene expression and genotyping services (Affymetrix, Agilent and Illumina). Provides 24/7 access to instruments, equipment and software utilized within genomics field.

POLYMUTT
type: Resource
type: NamedIndividual
has db xref: nlx_154539
has db xref: OMICS_00088
synonym: POLYmorphism and de novo MUTaTion call in families with sequencing data
abbrev: Polymutt
IAO_0000115: Software program that implemented a likelihood-based framework for calling single nucleotide variants and detecting de novo point mutation events in families for next-generation sequencing data. The program takes as input genotype likelihood format (GLF) files which can be generated following the Creation of GLF files instruction and outputs the result in the (VCF) format. The variant calling and de novo mutation detection are modelled jointly within families and can handle both nuclear and extended pedigrees without consanguinity loops. The input is a set of GLF files for each of family members and the relationships are specified through the .ped file. (entry from Genetic Analysis Software)

TissueNet - The Database of Human Tissue Protein-Protein Interactions
type: Resource
type: NamedIndividual
has db xref: OMICS_01913
abbrev: TissueNet
IAO_0000115: Database of human tissue protein-protein interactions (PPIs) that associates each interaction with human tissues that express both pair mates. This was achieved by integrating current data of experimentally detected PPIs with extensive data of gene and protein expression across 16 main human tissues. Users can query TissueNet using a protein and retrieve its PPI partners per tissue, or using a PPI and retrieve the tissues expressing both pair mates. The graphical representation of the output highlights tissue-specific and tissue-wide PPIs. Thus, TissueNet provides a unique platform for assessing the roles of human proteins and their interactions across tissues.

SAMHSAs National Clearinghouse for Alcohol and Drug Information
type: Resource
type: NamedIndividual
has db xref: nif-0000-12280
synonym: National Clearinghouse for Alcohol and Drug Information
synonym: SAMHSA's National Clearinghouse for Alcohol and Drug Information
synonym: SAMHSA's NCADI
abbrev: NCADI
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on 7/15/13. The Nation's one-stop resource for information about substance abuse prevention and addiction treatment offering more than 500 items to the public, many of which are free of charge. They distribute the latest studies and surveys, guides, videocassettes, and other types of information and materials on substance abuse from various agencies, such as the U.S. Departments of Education and Labor, the Center for Substance Abuse Prevention, the Center for Substance Abuse Treatment, the National Institute on Alcohol Abuse and Alcoholism, and the National Institute on Drug Abuse. They staff both English- and Spanish-speaking information specialists who are skilled at recommending appropriate publications, posters, and videocassettes; conducting customized searches; providing grant and funding information; and referring people to appropriate organizations. They are available 24 hours a day, 7 days a week to take your calls at 1-800-729-6686. NCADI services include: * an information services staff (English, Spanish, TDD capability) equipped to respond to the public's alcohol, tobacco, and drug (ATD) inquiries; * the distribution of free or low-cost ATD materials, including fact sheets, brochures, pamphlets, monographs, posters, and video tapes from an inventory of over 1,000 items; * a repertoire of culturally-diverse prevention, intervention, and treatment resources tailored for use by parents, teachers, youth, communities and prevention/treatment professionals; * customized searches in the form of annotated bibliographies from alcohol and drug data bases; * access to the Prevention Materials database (PMD) including over 8,000 prevention-related materials and the Treatment Resources Database, available to the public in electronic form; * rapid dissemination of Federal grant announcements for ATD prevention, treatment, and research funding opportunities.

Neural Network Resources
type: Resource
type: NamedIndividual
has db xref: nif-0000-12290
IAO_0000115: An alphabetical listing of worldwide neural network research groups and resources.

Medical Image Processing and Visualization
type: Resource
type: NamedIndividual
has db xref: nif-0000-00326
synonym: MeVisLab: Medical Image Processing and Visualization
abbrev: MeVisLab
IAO_0000115: Modular framework for the development of image processing algorithms and visualization and interaction methods, with a special focus on medical imaging. It includes advanced medical imaging modules for segmentation, registration, volumetry, and quantitative morphological and functional analysis. The platform allows fast integration and testing of new algorithms and the development of application prototypes that can be used in clinical environments. In MeVisLab, individual image processing, visualization and interaction modules can be combined to complex image processing networks using a graphical programming approach. The algorithms can easily be integrated using a modular, platform-independent C++ class library. An abstract, hierarchical definition language allows the design of efficient graphical user interfaces, hiding the complexity of the underlying module network to the end user. JavaScript components can be added to implement dynamic functionality on both the network and the user interface level. MeVisLab is based on the Qt application framework, the OpenInventor 3D visualization toolkit and OpenGL. Several clinical prototypes have been realized on the basis of MeVisLab, including software assistants for neuro-imaging, dynamic image analysis, surgery planning, and vessel analysis. Feature Overview: :- Basic image processing algorithms and advanced medical imaging modules :- Full featured, flexible 2D/3D visualization and interaction tools :- High performance for large datasets :- Modular, expandable C++ image processing library :- Graphical programming of complex, hierarchical module networks :- Object-oriented GUI definition and scripting :- Full scripting functionality using Python and JavaScript :- DICOM support and PACS integration :- Intuitive user interface :- Integrated movie and screenshot generation for demonstration purposes :- Generic integration of the Insight Toolkit (ITK) and the Visualization Toolkit (VTK) :- Cross-platform support for Windows,…

HUDSEN Electronic Atlas of the Developing Human Brain
type: Resource
type: NamedIndividual
has db xref: nif-0000-12494
synonym: Electronic Atlas of the Developing Human Brain
abbrev: EADHB
abbrev: HUDSEN EADHB
IAO_0000115: Interactive digital atlas and movies comprising 3-D reconstructions at all stages of human development from Carnegie Stage 12 (CS12; ~26 days post conception (dpc)) to CS23 (~ 56 dpc) and anatomical annotations of the 3-D models linked to an anatomical database. The 3D models are generated using Optical Projection Tomography (OPT; Sharpe et al 2002). The digital atlas is also linked to a gene expression database that has been developed from the Edinburgh Mouse Atlas Project gene expression database (EMAGE). In the future, the HUDSEN EADHB aims to provide the wider scientific and medical communities with a dynamic tool for documenting and analyzing gene expression patterns and morphological changes in the developing human brain.

PUMA
type: Resource
type: NamedIndividual
has db xref: nif-0000-12498
synonym: Propagating Uncertainty in Microarray Analysis
synonym: Propagating Uncertainty in Microarray Analysis (PUMA)
IAO_0000115: Software program for developing probabilistic models for the analysis of microarray data.

TRIP Database
type: Resource
type: NamedIndividual
has db xref: OMICS_01912
synonym: Mammalian TRansient receptor potential channel-Interacting Protein Database
IAO_0000115: A manually curated database of protein-protein interactions (PPIs) for mammalian transient receptor potential (TRP) channels. The detailed summary of PPI data, fits into 4 categories: screening, validation, characterization, and functional consequence. These categorizations give answers for four basic questions about PPIs: how to identify PPIs (screening); how to confirm PPIs (validation); what are biochemical properties of PPIs (characterization); what are biological meaning of PPIs (functional consequence). Users can find in-depth information specified in the literature on relevant analytical methods, gene constructs, and cell/tissue types. The database has a user-friendly interface with several helpful features, including a search engine, an interaction map, and a function for cross-referencing useful external databases.

Washington University Neuromuscular Disease Center
type: Resource
type: NamedIndividual
has db xref: nif-0000-00158
has db xref: nif-0000-12503
synonym: Neuromuscular Disease Center
abbrev: WU Neuromuscular
IAO_0000115: Organization portal for neuromuscular disease community and contains comprehensive listing of biological and clinical aspects of neuromuscular disorders.This knowledge base contains information on the physiology, structure of ion channels, neurotransmitters, neuroreceptors, and associated diseases. Major categories include DISORDERS & SYNDROMES, INDEXES, NEUROMUSCULAR EVALUATION, ANTIBODY TESTING and NEUROMUSCULAR DIVISION.

Internet Brain Volume Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-00033
abbrev: IBVD
IAO_0000115: A database of brain neuroanatomic volumetric observations spanning various species, diagnoses, and structures for both individual and group results. A major thrust effort is to enable electronic access to the results that exist in the published literature. Currently, there is quite limited electronic or searchable methods for the data observations that are contained in publications. This effort will facilitate the dissemination of volumetric observations by making a more complete corpus of volumetric observations findable to the neuroscience researcher. This also enhances the ability to perform comparative and integrative studies, as well as metaanalysis. Extensions that permit pre-published, non-published and other representation are planned, again to facilitate comparative analyses. Design strategy: The principle organizing data structure is the "publication". Publications report on "groups" of subjects. These groups have "demographic" information as well as "volume" information for the group as a whole. Groups are comprised of "individuals", which also have demographic and volume information for each of the individuals. The finest-grained data structure is the "individual volume record" which contains a volume observation, the units for the observation, and a pointer to the demographic record for individual upon which the observation is derived. A collection of individual volumes can be grouped into a "group volume" observation; the group can be demographically characterized by the distribution of individual demographic observations for the members of the group.

SNVer
type: Resource
type: NamedIndividual
has db xref: biotools:snver
has db xref: OMICS_00076
IAO_0000115: Statistical software tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. This software is optimized for analysis of whole-exome sequencing data and whole-genome sequencing data.

Amorphium
type: Commercial Organization
type: NamedIndividual
has db xref: SciRes_000164
synonym: Amorphium 3
synonym: Amorphium 3.0
IAO_0000115: Graphics software for a real-time approach to creating 3D graphics that offers a variety of intuitive, powerful design tools to create your 3D masterpiece. The graphics engine allows for a completely interactive environment, where all operations occur on solid objects in real time. A rendering engine allows you to produce stunning 3D imagery at virtually any resolution for Web, print, digital video, and film. Advanced capabilities include Radiosity rendering for photo-realistic scenes, Raytracing for true-to-life surface reflections and refractions, as well as variable smoke and lighting effects.

Arabidopsis Reactome
type: Resource
type: NamedIndividual
has db xref: nif-0000-20812
synonym: Arabidopsis Reactome - a curated knowledgebase of plant biological pathways
IAO_0000115: Curated database of core pathways and reactions in plant biology that covers biological pathways ranging from the basic processes of metabolism to high-level processes such as cell cycle regulation. While it is targeted at Arabidopsis pathways, it also includes many biological events from other plant species. This makes the database relevant to the large number of researchers who work on other plants. Arabidopsis Reactome currently contains both in-house curated pathways as well as imported pathways from AraCyc and KEGG databases. All the curated information is backed up by its provenance: either a literature citation or an electronic inference based on sequence similarity. Their ontology ensures that the various events are linked in an appropriate spatial and temporal context.

BISC
type: Resource
type: NamedIndividual
has db xref: biotools:bisc
has db xref: OMICS_01902
synonym: BInary SubComplex Database
IAO_0000115: A protein-protein interaction (PPI) database intending to bridge between the two communities most active in their characterization: structural biology and functional genomics researchers. It offers users access to binary subcomplexes, (i.e. physical direct interactions between proteins) that are either structurally characterized or modellable entries in the main functional genomics PPI databases BioGRID, IntAct and HPRD. Selected web services are available to further investigate the validity of postulated PPI by inspection of their hypothetical modelled interfaces., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Primate Orthologous Exon Database
type: Resource
type: NamedIndividual
has db xref: OMICS_01895
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Database of orthologous exon regions in the genomes of human, chimpanzee, and rhesus macaque. It can be used in analysis of multi-species RNA-seq expression data, allowing for comparisons of exon-level expression across primates, as well as comparative examination of alternative splicing and transcript isoforms.

NeuralAct
type: Resource
type: NamedIndividual
has db xref: SciRes_000162
synonym: NeuralAct: A tool to visualize cortical activity on a 3D model of the cortex
IAO_0000115: Software to visualize electrocorticographic (ECoG) and possibly also other kinds of neural activity (EEG / EMG/ DOT) on a 3D model of the cortical surface. The tool has been used to produce cortical activation images and image sequences in several recent studies using ECoG. The tool is written in matlab. The package is thoroughly documented and includes a demo.

InteroPorc
type: Resource
type: NamedIndividual
has db xref: biotools:interoporc
has db xref: nif-0000-20816
synonym: Automatic molecular interaction predictions
synonym: InteroPorc: Automatic molecular interaction predictions
IAO_0000115: Automatic prediction tool to infer protein-protein interaction networks, it is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8. Users can use this page to ask InteroPorc for all species present in Integr8. Some results are already computed and users can run InteroPorc to investigate any other species. Currently, the following databases are processed and merged (with datetime of the last available public release for each database used): IntAct, MINT, DIP, and Integr8.

PurBayes
type: Resource
type: NamedIndividual
has db xref: biotools:purbayes
has db xref: OMICS_03561
synonym: PurBayes: Bayesian Estimation of Tumor Purity and Clonality
IAO_0000115: An MCMC-based algorithm that uses next-generation sequencing data to estimate tumor purity and clonality for paired tumor-normal data.

Cell Signaling and Neuroscience: Pathway Slides and Charts
type: Resource
type: NamedIndividual
has db xref: nif-0000-20824
synonym: Cell Signaling & Neuroscience Pathway Slides & Charts
synonym: Cell Signaling and Neuroscience Pathway Slides and Charts
synonym: Pathway Slides and Charts
synonym: Sigma Pathway Slides & Charts
abbrev: Sigma Pathway Slides and Charts
IAO_0000115: Free, downloadable Cell Signaling and Neuroscience Pathway Slides with an overview of the pathway and its links to Your Favorite Gene. There you can explore dynamic pathways and locate products in the context of your research. Each overview contains helpful links to the biological pathways, interaction networks, gene details and related products. Slide Categories: *Apoptosis and Cell Cycle *Cytokines, Growth Factors and Hormones *Cytoskeleton and Extracellular Matrix *Gene Regulation and Expression *G Proteins and Cyclic Nucleotides *Immune Cell Signaling and Blood *Ion Channels *Lipids in Cell Signaling *Multi-Drug Resistance *Neurobiology *Neurotransmission *Nitric Oxide and Cell Stress *Protein Phosphorylation

Cell Signaling Pathways
type: Resource
type: NamedIndividual
has db xref: nif-0000-20825
synonym: PathFinder
IAO_0000115: Cell signaling pathways can be explored using PathFinder, the interactive, online graphical representation of cell signaling pathways. The user can use PathFinder to explore the relationships between different cell signaling pathway components while being presented with our high quality small molecules, antibodies, enzymes, siRNA for gene knockdown and qPCR components to aid them in their research.

Cell Signaling Technology
type: Organization
type: NamedIndividual
has db xref: grid.420530.0
has db xref: ISNI: 0000 0004 0580 0138
has db xref: nif-0000-20826
has db xref: nlx_152330
has db xref: Wikidata: Q3392342
abbrev: CST
IAO_0000115: Privately held company that develops and produces antibodies, ELISA kits, ChIP kits, proteomic kits, and other related reagents used to study cell signaling pathways that impact human health.

MRIWarp
type: Resource
type: NamedIndividual
has db xref: nif-0000-00336
IAO_0000115: Warping tool for intersubject registration of brain images consisting of C functions for Unix systems plus Matlab visualization utility functions. Apart from warping there are also (command line) functions for ANALYZE header information, mirroring, translation, subsampling. The package cannot only be used as a preprocessing step in function neuroimaging but also as a step in deformation-based morphometry.

PyroHMMvar
type: Resource
type: NamedIndividual
has db xref: OMICS_00069
IAO_0000115: A software program to call short indels and SNPs for Ion Torrent and 454 data.

NeuronJ: An ImageJ Plugin for Neurite Tracing and Quantification
type: Resource
type: NamedIndividual
has db xref: nif-0000-00108
synonym: NeuronJ
IAO_0000115: NeuronJ is an ImageJ plugin to facilitate the tracing and quantification of elongated structures in two-dimensional (2D) images (8-bit gray-scale and indexed color), in particular neurites in fluorescence microscopy images. Sponsors: The development of NeuronJ started while the primary developer ( Dr. Erik Meijering, PhD) was with the Biomedical Imaging Group (collaborating with people from the Laboratory of Cellular Neurobiology) of the Swiss Federal Institute of Technology in Lausanne (EPFL), Switzerland, and was finished while Dr. Meijering was with the Biomedical Imaging Group Rotterdam in the Netherlands.

flowViz
type: Resource
type: NamedIndividual
has db xref: OMICS_05615
synonym: flowViz - Visualization for flow cytometry
IAO_0000115: Software that provides visualization tools for flow cytometry data.

Database of the Human Proteotheque Initiative
type: Resource
type: NamedIndividual
has db xref: nif-0000-20836
synonym: HuPI
IAO_0000115: The Human Proteotheque Initiative is a multidisciplinary project aimed at building a repertoire of comprehensive maps of human protein interaction networks. The information contained in the Proteotheque is made publicly available through an interactive web site that can be consulted to visualize some of the fundamental molecular connections formed in human cells and to determine putative functions of previously uncharacterized proteins based on guilt by association. The process governing the evolution of HuPI towards becoming a repository of accurate and complete protein interaction maps is described.

Conserved Domain Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02647
has db xref: r3d100010653
synonym: Conserved Domains
synonym: Conserved Domains Database
abbrev: CDD
IAO_0000115: Database of annotations of functional units in proteins including multiple sequence alignment models for ancient domains and full-length proteins. This collection of models includes 3D structures that display the sequence/structure/function relationships in proteins. It also includes alignments of the domains to known three-dimensional protein structures in the MMDB database. The source databases are Pfam, Smart, and COG. Users can identify amino acids in protein sequences with the resources available as well as view single sequences embedded within multiple sequence alignments.

Electronic Molecular Interaction Map
type: Resource
type: NamedIndividual
has db xref: nif-0000-20840
synonym: eMIM
IAO_0000115: The GBG's mission is to manage and assess molecular interaction data obtained through multiple platforms, increase the understanding of the effect of those interactions on the chemosensitivity of cancer, and create tools that will facilitate that process. Translation of that information will be directed towards the recognition of diagnostic and therapeutic cancer biomarkers, and directed cancer therapy.

CASY Cell Counter and Analyser System Model TT
type: Resource
type: NamedIndividual
has db xref: SciRes_000160
synonym: CASY Cell Counter + Analyser System Model TT
synonym: CasyTon Cell Counter and Analyser System
abbrev: CASY Model TT
IAO_0000115: Tool for the qualitative and quantitative assessment of cell cultures including standardized cell counting methods, viability checks, aggregation correction, volumetric measurement with high measuring range dynamics. It enables to create optimal settings for measuring certain cell population numbers (based on size and gating strategies).

ChIPSeq Peak Finder
type: Resource
type: NamedIndividual
has db xref: OMICS_00434
synonym: ChIPSeq Toolbox
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 12, 2017. A software tool to find peaks from ChIPSeq data generated from the Solexa/Illumina platform., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

SpliceAid-F
type: Resource
type: NamedIndividual
has db xref: OMICS_01893
synonym: SpliceAid-F: a database of human splicing factors and their binding sites
IAO_0000115: A database of human splicing factors and their RNA - binding sites. For each splicing factor (SF) the database reports its functional domains and its protein and chemical interactors. Furthermore, experimentally validated RNA-SF interactions are collected, including relevant information on the RNA binding sites such as the genes where these sites lie, their genomic coordinates, the splicing effects, experimental procedures, as well as the corresponding bibliographic references. Information from experiments showing no RNA-SF binding is also collected, at least in the assayed conditions. SpliceAid-F contains 4227 interactions, 2622 RNA binding sites and 1170 no-binding sites, including information on binding and no-binding specificity in different cellular contexts. SpliceAid-F can provide significant information to explain an observed splicing pattern as well as the effect of mutations in functional regulatory elements.

Vennt
type: Resource
type: NamedIndividual
has db xref: OMICS_03549
synonym: Vennt - Dynamic Venn diagrams for Differential Gene Expression
IAO_0000115: A web-tool to generate dynamic Venn diagrams for differential gene expression.

Integrating Network Objects with Hierarchies
type: Resource
type: NamedIndividual
has db xref: nif-0000-20859
synonym: INOH
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. INOH (Integrating Network Objects with Hierarchies) is a pathway database of model organisms including human, mouse, rat and others. In INOH, the term pathway refers to higher order functional knowledge such as relationships among multiple bio-molecules that constitute signal transduction pathways or biological events in general. As most part of this knowledge resides in scientific articles, the database focuses on curating and encoding textual knowledge into a machine-processable form. The system provides pathway information as a composite of biological events, since functional knowledge is usually described as a set of fragmented processes. Each event is annotated with entries of a event ontology, which also has links to GO.

Interaction Reference Index
type: Resource
type: NamedIndividual
has db xref: nif-0000-20860
abbrev: iRefIndex
IAO_0000115: An index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index includes multiple interaction types including physical and genetic (mapped to their corresponding protein products) as determined by a multitude of methods. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein. iRefIndex uses the Sequence Global Unique Identifier (SEGUID) to group proteins and interactions into redundant groups. This method allows users to integrate their own data with the iRefIndex in a way that ensures proteins with the exact same sequence will be represented only once. iRefIndex project has three long term objectives: # to facilitate exchange of interaction data between interaction databases. # to consolidate interaction data from multiple sources. # to provide feedback to source interaction databases. iRefIndex is made available in a number of formats: MITAB tab-delimited text files, iRefWeb interface, iRefScape plugin for Cytoscape, PSICQUIC Web services, and an interface for the R programming language environment.

PepBank Peptide Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-20887
synonym: PepBank
IAO_0000115: A database of peptides based on sequence text mining and public peptide data sources. Only peptides that are 20 amino acids or shorter are stored. Only peptides with available sequences are stored. After submitting a query you can further refine the results using the new heat map retrieval tool to quickly find the entries that are most relevant to you. Text classification helps you find candidate peptides that are related to cancer, cardiovascular diseases, diabetes, apoptosis, angiogenesis and molecular imaging or peptides for which binding data exist.

Icosagen AS
type: Organization
type: NamedIndividual
has db xref: nlx_152381
IAO_0000115: An Antibody supplier

CHEBI
type: Resource
type: NamedIndividual
has db xref: biotools:chebi
has db xref: nif-0000-02655
has db xref: r3d100012626
synonym: Chemical Entities of Biological Interest
abbrev: ChEBI
IAO_0000115: Collection of chemical compounds and other small molecular entities that incorporates an ontological classification of chemical compounds of biological relevance, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.

Glomerular Activity Response Archive
type: Resource
type: NamedIndividual
has db xref: nif-0000-00339
synonym: Glomerular Response Archive
abbrev: GARA
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 24, 2017. Database of images depicting the spatial distribution of 2-deoxyglucose uptake evoked in the glomerular layer of the rat olfactory bulb in response to a wide range of defined odorant stimuli. A number of different display and comparison tools are provided allowing patterns to be viewed from different perspectives, and descriptions of the methods and interpretations of these data are provided. Some of the more advanced tools require you to download software.

SA Instruments | Model 1025 MR-compatible Small Animal Monitoring and Gating System
type: Resource
type: NamedIndividual
has db xref: SciRes_000157
synonym: Model 1025 Monitoring and Gating System
synonym: MR-Compatible Model 1025 Monitoring and Gating System
synonym: Small Animal Monitoring and Gating System
abbrev: Model 1025 Monitoring & Gating System
IAO_0000115: Magnetic resonance compatible monitoring and gating system, including software, that enables monitoring rectal temperature, electrocardiogram and respiration rate during magnetic resonance imaging scan time. The PC displays multiple waveforms, measured values, trends and gating pulses. The data Acquisition modules are controlled by menu driven software from the PC. Data acquisition modules are available to measure the following parameters: ECG, respiration (three ways), temperature (two ways), pressure including invasive blood pressure (two ways), oxygen saturation and end-tidal CO2.

NeuroMorph
type: Resource
type: NamedIndividual
has db xref: SciRes_000156
synonym: NeuroMorph Toolkit
IAO_0000115: A toolset for the morphometric analysis and visualization of 3D models derived from electron microscopy image stacks. It is designed to import, analyze, and visualize mesh models. It has been designed specifically for the morphological analysis of 3D objects derived from serial electron microscopy images of brain tissue, although much of its functionality can be applied to any 3D mesh. These models can be generated by software that allows the images to be segmented so that 3D objects can be built. These objects can be generated by any 3D image segmentation software, such as ilastik or Fiji. The NeuroMorph toolset has been developed as a set of add-ons for Blender, a widely used free and open source 3D modeling software package.

Statistical non-Parametric Mapping
type: Resource
type: NamedIndividual
has db xref: nif-0000-00342
synonym: SnPM - Statistical NonParametric Mapping - A toolbox for SPM
synonym: SnPM: Statistical nonParametric Mapping
synonym: Statistical nonParametric Mapping
abbrev: SnPM
IAO_0000115: A toolbox for Statistical Parametric Mapping (SPM) that provides an extensible framework for voxel level non-parametric permutation/randomization tests of functional Neuroimaging experiments with independent observations. SnPM uses the General Linear Model to construct pseudo t-statistic images, which are then assessed for significance using a standard non-parametric multiple comparisons procedure based on randomization/permutation testing. It is most suitable for single subject PET/SPECT analyses, or designs with low degrees of freedom available for variance estimation. In these situations the freedom to use weighted locally pooled variance estimates, or variance smoothing, makes the non-parametric approach considerably more powerful than conventional parametric approaches, as are implemented in SPM. Further, the non-parametric approach is always valid, given only minimal assumptions. The SnPM toolbox provides an alternative to the Statistics section of SPM.

flowTrans
type: Resource
type: NamedIndividual
has db xref: OMICS_05612
synonym: flowTrans - Parameter Optimization for Flow Cytometry Data Transformation
IAO_0000115: Software for profile maximum likelihood estimation of parameters for flow cytometry data transformations.

SIMIBD
type: Resource
type: NamedIndividual
has db xref: nlx_154622
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software)

Cvapp
type: Resource
type: NamedIndividual
has db xref: nif-0000-00109
IAO_0000115: Online platform for visualizing and editing the morphology of neurons. Written in Java.

Protein interaction and molecular information database
type: Resource
type: NamedIndividual
has db xref: nif-0000-20899
synonym: PRIME
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. PRIME is a developed version of Kinase Pathway Database which is an integrated database concerning completed sequenced major eukaryotes, which contains the classification of protein kinases and their functional conservation and orthologous tables among species, protein-protein interaction data, domain information, structural information, and automatic pathway graph image interface. The protein-protein interactions are extracted by natural language processing (NLP) from abstracts using basic word pattern and protein name dictionary GENA: developed by our group. In this system, pathways are easily compared among species using protein interactions data more than 1,510,000 and orthologous tables. Further, using other organisms interaction data, interaction prediction is also possible.

Spliceosome Database
type: Resource
type: NamedIndividual
has db xref: OMICS_01891
synonym: Spliceosome Component Database
synonym: Spliceosome Database - A source of information for the SLPICEOSOME: The large ribonucleoprotein complex responsible for pre-mRNA splicing
IAO_0000115: A database of proteins and RNAs that have been identified in various purified splicing complexes. Various names, orthologs and gene identifiers of spliceosome proteins have been cataloged to navigate the complex nomenclature of spliceosome proteins. Links to gene and protein records are also provided for the spliceosome components in other databases. To navigate spliceosome assembly dynamics, tools were created to compare the association of spliceosome proteins with complexes that form at specific stages of spliceosome assembly based on a compendium of mass spectrometry experiments that identified proteins in purified splicing complexes.

cisRED: cis-regulatory element
type: Resource
type: NamedIndividual
has db xref: biotools:cisred
has db xref: nif-0000-02665
has db xref: OMICS_01857
has db xref: r3d100010619
synonym: cisRED - Databases of genome-wide regulatory module and element predictions
abbrev: cisRED
IAO_0000115: Database for conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations. Sequence inputs include low-coverage genome sequence data and ENCODE data. The database offers information on atomic motifs, motif groups and patterns. In promoter-based cisRED databases, sequence search regions for motif discovery extend from 1.5 Kb upstream to 200b downstream of a transcription start site, net of most types of repeats and of coding exons. Many transcription factor binding sites are located in such regions. For each target gene's search region, a base set of probabilistic ab initio discovery tools is used, in parallel, to find over-represented atomic motifs. Discovery methods use comparative genomics with over 40 vertebrate input genomes. In ChIP-seq-based cisRED databases, sequence search regions for motif discovery correspond to significant peaks that represent genome-wide sites of protein-DNA binding. Because such peaks occur in a wide range of genic and intergenic locations, ChIP-seq and promoter-based databases are complementary. Currently, motif discovery for ChIP-seq data uses scan-based approaches that make more explicit use of sets of sequences known to be functional transcription factor binding sites, and that consider a wide range of levels of conservation. For the human STAT1 ChIP-seq database search regions in the target species (human) was selected +/- 300 bp around the ChIP-seq peak maximum. Repeats and coding regions were masked. Multiple sequence alignment were used to assemble orthologous input sequences from other species.

Surface-Based Atlases
type: Resource
type: NamedIndividual
has db xref: nif-0000-00346
synonym: Surface-Based Atlas
abbrev: Caret:Atlases
IAO_0000115: THIS RESOURCE IS NO LONGER IS SERVICE. Documented on July,29,2022. Surface-based atlases of human, macaque, rat and mouse cerebral and cerebellar cortices derived from structural MRI volumes developed in the Van Essen laboratory can be downloaded by direct links on the SumsDB database and can be viewed using freely available Caret (offline) and WebCaret (online) software. The human and macaque atlases include a large and growing compendium of experimental data pertaining to the structural and functional organization of primate cerebral cortex.

Pathway Analysis Tool for Integration and Knowledge Acquisition
type: Resource
type: NamedIndividual
has db xref: nif-0000-20882
synonym: Pathway Analysis Tool for Integration and Knowledge Acquisition (PATIKA)
synonym: PATIKA - Pathway Analysis Tools for Integration and Knowledge Acquisition
abbrev: PATIKA
IAO_0000115: The human pathway database which contains different biological entities and reactions and software tools for analysis. PATIKA Database integrates data from several sources, including Entrez Gene, UniProt, PubChem, GO, IntAct, HPRD, and Reactome. Users can query and access this data using the PATIKAweb query interface. Users can also save their results in XML or export to common picture formats. The BioPAX and SBML exporters can be used as part of this Web service.

Pathway Articulator
type: Resource
type: NamedIndividual
has db xref: nif-0000-20883
abbrev: PathArt
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. A comprehensive collection of manually curated information from literature as well as public domain databases on signaling and metabolic pathways. PathArt includes a dynamic pathway articulator component, which builds molecular interaction networks from curated databases. PathArt provides a tool for analysis, biological interpretation and visualization of microarray data results in these curated pathways. In addition, PathArt provides a collection of high priority disease and physiology pathways with emphasis on pathway responsive genes and knockouts. The coverage is for pathways of Human, Rat and Mouse for cell specific, tissue specific and organism specific data. The present version of PathArt covers the following: -Includes 3527 regulatory and signaling pathways across diseases and physiologies. -Provides information on 39 high priority diseases, and pathway and disease responsive genes. -Provides pathway information on 23 diverse physiologies. -Covers information on ~8783 Knockouts and ~18000 mutation data points. -Coverage of pathways for Human, Mouse and Rat for cell specificity, tissue specificity and organism specific data.

ASPicDB
type: Resource
type: NamedIndividual
has db xref: OMICS_01882
synonym: Alternative Splicing Prediction Data Base
synonym: ASPicDB - A Database tool for alternative splicing analysis
IAO_0000115: A database to access reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm (Castrignano et al. 2006), and to the functional annotation of predicted isoforms. Users may select and extract specific sets of data related to genes, transcripts and introns fulfilling a combination of user-defined criteria. Several tabular and graphical views of the results are presented, providing a comprehensive assessment of the functional implication of alternative splicing in the gene set under investigation. ASPicDB also includes information on tissue-specific splicing patterns of normal and cancer cells, based on available EST data and their library source annotation.

Pathway Commons
type: Resource
type: NamedIndividual
has db xref: biotools:PathwayCommons_web_service_API
has db xref: nif-0000-20884
has db xref: r3d100012731
abbrev: PC
IAO_0000115: Database of publicly available pathways from multiple organisms and multiple sources represented in a common language. Pathways include biochemical reactions, complex assembly, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes. Pathways were downloaded directly from source databases. Each source pathway database has been created differently, some by manual extraction of pathway information from the literature and some by computational prediction. Pathway Commons provides a filtering mechanism to allow the user to view only chosen subsets of information, such as only the manually curated subset. The quality of Pathway Commons pathways is dependent on the quality of the pathways from source databases. Pathway Commons aims to collect and integrate all public pathway data available in standard formats. It currently contains data from nine databases with over 1,668 pathways, 442,182 interactions,414 organisms and will be continually expanded and updated. (April 2013)

SAMTOOLS
type: Resource
type: NamedIndividual
has db xref: biotools:samtools
has db xref: nlx_154607
has db xref: OMICS_00090
has db xref: OMICS_01074
has db xref: SCR_018682
synonym: SAM tools
synonym: SAMtools
synonym: Samtools
synonym: samtools
synonym: Sequence Alignment Map TOOLS
IAO_0000115: Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.

HEXEvent
type: Resource
type: NamedIndividual
has db xref: OMICS_01888
synonym: HEXEvent - a database of Human EXon splicing Events
IAO_0000115: A free database that provides a list of human internal exons and reports all their known splice events based on EST information from the UCSC Genome Browser. This list can be restricted by the user to either only a specific region in the genome (by specifying the chromosome, the strand and the start and end position), to a whole chromosome or to a group of genes. Furthermore, exons can be filtered according to their splicing type (constitutive exons, cassette exons and exons with one or more alternative 3' and/or 5' splice sites). In order to extract a customized set of exons, the user-specific definitions of exon types can be fixed. The user needs to specify in what fraction of ESTs an exon is allowed to be alternatively spliced in order to still be called constitutive. Furthermore, the user can restrict the set of requested cassette exons by a certain upper inclusion level, which, for instance, is useful when only looking for low-inclusion exons.

DBASS
type: Resource
type: NamedIndividual
has db xref: OMICS_01883
IAO_0000115: A database of new exon boundaries induced by pathogenic mutations in human disease genes.

Protein Interaction Map Rider
type: Resource
type: NamedIndividual
has db xref: nif-0000-20900
synonym: PIMRider
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Web application used to exploration of protein pathways. It provides analysis and navigation within networks, overviews of biological connections between proteins, access to relevant literature and annotations, and comparisons of interaction and functional domains.

PhosphoPOINT
type: Resource
type: NamedIndividual
has db xref: nif-0000-20888
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A comprehensive human kinase interactome and phospho-protein database. PhosphoPOINT also annotates any amino acids near the phosphorylation sites where a cSNP may cause a phosphorylation site to be lost, and at the same time identifies how such alteration of the phosphorylation site may lead to human disease. PhosphoPOINT integrates 4,195 phospho-proteins, 518 serine/threonine/tyrosine kinases, and their corresponding PPI datasets with the goal of delineating the interactions among kinases, their potential substrates and their interacting (phospho)-proteins. PhosphoPOINT has integrated human protein kinases, phospho-proteins, and PPI datasets with the goal to delineate four kinds of links among kinases. These include their interacting proteins, substrates, and substrates as well as interacting phospho-proteins. Some of these interacting proteins for kinases are phospho-proteins, which might have the potential to serve as substrates for the interacting kinases.

PlantCyc
type: Resource
type: NamedIndividual
has db xref: nif-0000-20890
has db xref: nlx_15806 plant
abbrev: PMN
IAO_0000115: Multi species reference database. Comprehensive plant biochemical pathway database, containing curated information from literature and computational analyses about genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism.

ProcessDB
type: Resource
type: NamedIndividual
has db xref: nif-0000-20893
IAO_0000115: It helps molecular cell biologists manage and test their increasingly complex mechanistic hypotheses. ProcessDB does this with a bio-savvy graphical user interface that helps users formulate, visualize, compare, modify, manage and test their own mechanistic theories of cellular function. All models in ProcessDB can be automatically combined with user-specified experimental protocols and exported to the Berkeley Madonna solver for testing against experimental data. ProcessDB allows investigators to know with precision what their theories predict, and speeds discovery of mechanisms that account for all of the available data. ProcessDB, which is accessable from any Internet-connected computer, offers a highly secure and professionally maintained tool that supports mechanistic knowledge management for research laboratories working on complex biological or biomedical problems.

Protein-Small Molecule Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-20897
synonym: Protein - Small-Molecule DataBase
abbrev: PSMDB
IAO_0000115: Database of non-redundant sets of protein - small-molecule complexes that are especially suitable for structure-based drug design and protein - small-molecule interaction research. PSMB supports: * Support frequent updates - The number of new structures in the PDB is growing rapidly. In order to utilize these structures, frequent updates are required. In contrast to manual procedures which require significant time and effort per update, generation of the PSMDB database is fully automatic thereby facilitating frequent database updates. * Consider both protein and ligand structural redundancy - In the database, two complexes are considered redundant if they share a similar protein and ligand (the protein - small-molecule non-redundant set). This allows the database to contain structural information for the same protein bound to several different ligands (and vice-versa). Additionally, for completeness, the database contains a set of non-redundant complexes when only protein structural redundancy is considered (our protein non-redundant set). The following images demonstrate the structural redundancy of the protein complexes in the PDB compared to the PSMDB. * Efficient handling of covalent bonds -Many protein complexes contain covalently bound ligands. Typically, protein-ligand databases discard these complexes; however, the PSMDB simply removes the covalently bound ligand from the complex, retaining any non-covalently bound ligands. This increases the number of usable complexes in the database. * Separate complexes into protein and ligand files -The PSMDB contains individual structure files for both the protein and all non-covalently bound ligands. The unbound proteins are in PDB format while the individual ligands are in SDF format (in their native coordinate frame).

FlyFactorSurvey
type: Resource
type: NamedIndividual
has db xref: biotools:flyfactorsurvey
has db xref: OMICS_01879
IAO_0000115: Database of Drosophila transcription factor DNA binding specificity using the bacterial one-hybrid method, DNase I or SELEX methods. The database provides community access to recognition motifs and position weight matrices for transcription factors (TFs), including many unpublished motifs. Search tools and flat file downloads are provided to retrieve binding site information (as sequences, matrices and sequence logos) for individual TFs, groups of TFs or for all TFs with characterized binding specificities. Linked analysis tools allow users to identify motifs within the database that share similarity to a query matrix or to view the distribution of occurrences of an individual motif throughout the Drosophila genome. This database and its associated tools provide computational and experimental biologists with resources to predict interactions between Drosophila TFs and target cis-regulatory sequences.

AnaSpec
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_152270
synonym: AnaSpec Inc
synonym: EGT Group
IAO_0000115: Commercial supplier of antibodies, reagents, and dyes for research.

Protein families database of alignments and HMMs
type: Resource
type: NamedIndividual
has db xref: nif-0000-20898
synonym: iPfam
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. iPfam is a resource that describes physical interactions between those Pfam domains that have a representative structure in the Protein DataBank (PDB). When two or more domains occur within a single structure, the domains are analysed to see if they form an interaction. If the domains are close enough to form an interaction, the bonds that play a role in that interaction are determined. The goal has been to re-calculate iPfam interaction data for each new Pfam release, so that, as Pfam changes, the information within iPfam remains up to date.

Protein Interactions by Structural Matching
type: Resource
type: NamedIndividual
has db xref: nif-0000-20901
abbrev: P.R.I.S.M.
IAO_0000115: It is a web-server that can be used to explore protein interfaces and predict protein-protein interactions. It is a website for protein interface analysis and prediction of putative protein-protein interactions. It is composed of a database holding protein interface structures derived from the Protein Data Bank (PDB). The server also includes summary information about related proteins and an interactive protein interface viewer. A list of putative protein-protein interactions obtained by running our prediction algorithm can also be accessed. These results are applied to a set of protein structures obtained from the PDB at the time of algorithm execution. Users can browse through the non-redundant dataset of representative interfaces on which the prediction algorithm depends, retrieve the list of similar structures to these interfaces or see the results of interaction predictions for a particular protein. Another service provided is interactive prediction. This is done by running the algorithm for user input structures.

Protein Lounge
type: Resource
type: NamedIndividual
has db xref: nif-0000-20903
synonym: Protein Lounge - Redefining Biology
abbrev: ProteinLounge
IAO_0000115: Complete siRNA target database, complete Peptide-Antigen target database and a Kinase-Phosphatase database. They have also developed the largest database of illustrated signal transduction pathways, which are interconnected to their extensive protein database and online gene / protein analysis tools. The interactive web-based databases and software help life-scientists understand the complexity of systems biology. Systems biology efforts focus on understanding cellular networks, protein interactions involved in cell signaling, mechanisms of cell survival and apoptosis leading to development or identification of drug candidates against a variety of diseases. In the post-genomic era, one of the major concerns for life-science researchers is the organization of gene / protein data. Protein Lounge has met this concern by organizing all necessary data about genes / proteins into one portal.

Protein Quaternary Structure database
type: Resource
type: NamedIndividual
has db xref: nif-0000-20904
synonym: PQS
IAO_0000115: The Protein Quaternary Structure file server ( PQS ) is an internet resource that makes available coordinates for likely quaternary states for structures contained in the Brookhaven Protein Data Bank that were determined by X-ray crystallography.

PubGene
type: Resource
type: NamedIndividual
has db xref: biotools:pubgene
has db xref: nif-0000-20908
IAO_0000115: It helps users retrieve information on genes and proteins. The underlying structure of PubGene can be viewed as a gene-centric database. Gene and protein names are cross-referenced to each other and to terms that are relevant to understanding their biological function, importance in disease and relationship to chemical substances. The result is a literature network organizing information in a form that is easy to navigate.

National Center for Marine Algae and Microbiota
type: Resource
type: NamedIndividual
has db xref: nlx_154729
synonym: CCMP
synonym: Provasoli-Guillard National Center for Culture of Marine Phytoplankton
synonym: Provasoli-Guillard National Center for Marine Algae and Microbiota
abbrev: NCMA
IAO_0000115: National marine phytoplankton collection, maintaining over 2700 strains from around the world, most are marine phytoplankton but they also have benthic, macrophytic, freshwater and heterotrophic organisms - now incorporating bacteria and viruses. Strain records have (when available): * collection and isolation information * culturing medium recipes and growth conditions * photographs * GenBank accession link * collection site map * link to the taxonomic database Micro*scope The deposition of new strains are welcome if the strains are a valuable addition to the collection. Examples include strains that are referred to in publications, contain interesting molecular, biochemical or physiological properties, are the basis for taxonomic descriptions, are important for aquaculture, or are from an unusual geographical location or ecological habitat. The NCMA offers a course in phytoplankton culturing techniques and facilities for visiting scientists are available at the new laboratories in East Boothbay, Maine. Services include: Mass Culturing DNA and RNA, Purification, Private Holdings, Culture Techniques Course, Visiting Scientists, Single Cell Genomics, Flow Cytometry, Corporate Alliances and Technology Transfer.

RESNET
type: Resource
type: NamedIndividual
has db xref: nif-0000-20909
synonym: Ariadne ResNet Databases
synonym: ResNet Databases
abbrev: ResNet
IAO_0000115: Databases that represent sets of pre-compiled information on biological relationships and associations, interactions and facts which have been extracted from the biomedical literature using Ariadne's MedScan technology. ResNet databases store information harvested from the entire PubMed in a formal structure that allows searching, retrieval and updating by Pathway Studio user. ResNet is seamlessly installed when Pathway Studio is installed. There are several available ResNet databases: *ResNet Mammalian Database includes data for Human, Rat, and Mouse *ResNet Plant Database has data on Arabidopsis, Rice and several other plants. Features of ResNet: *All extracted relations have linked access to the original article or abstract *Synonyms and homologs are included to maintain gene identity and to obviate redundancy in search results *Users can update ResNet as often as required using the MedScan technology built into all Ariadne products *Updates are made available by Ariadne every quarter To purchase Pathway Studio software with ResNet database, for information, or to schedule a web demonstration, call our sales department at (240) 453-6272, or (866) 340-5040 (toll free)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Biochemical Pathways Reaction Kinetics Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-20912
has db xref: r3d100011052
synonym: Reaction Kinetics Database
synonym: SABIO-RK
synonym: System for Analysis of Biochemical Pathways Reaction Kinetics Database
synonym: System for the Analysis of Biochemical Pathways - Reaction Kinetics Database
abbrev: SABIO RK
IAO_0000115: A database based on the SABIO relational database that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. It aims to support modelers in the setting-up of models of biochemical networks, but it is also useful for experimentalists or researchers with interest in biochemical reactions and their kinetics. SABIO-RK contains and merges information about reactions such as reactants and modifiers, organism, tissue and cellular location, as well as the kinetic properties of the reactions. The type of the kinetic mechanism, modes of inhibition or activation, and corresponding rate equations are presented together with their parameters and measured values, specifying the experimental conditions under which these were determined. Links to other databases are provided for users to gather further information and to refer to the original publication. Information about reactions and their kinetic data can be exported to an SBML file. The reaction kinetics data are obtained by manual extraction from literature sources and curated.

Subtilis Protein interaction Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-20916
abbrev: SPiD
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. An online database of two-hybrid protein interactions in B. Subtilis. Interactions stored in SPID are either characterized by experimental evidence or by bibliographic references. A graphical user interface is provided to explore interaction networks as well as to view the details of each piece of evidence. The database contains 112 interactions between 79 proteins.

Target Protein Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-20918
synonym: TPDB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 29,2022. This database is an attempt to catalog in a convenient, searchable fashion the publicly available information about the identities of mammalian proteins that become covalently adducted by chemically-reactive metabolites of xenobiotic agents. At present all entries pertain to well-identified proteins that become adducted following defined exposures to known chemical agents in vivo or in cell culture experiments. Results from studies using enzymatic or chemical model systems have not been included but may be in the future. The search functions are relatively simple and intuitive, so most users can go straight to the Search page and begin searching. Additional explanations, examples and information about possible future expansions may be found.

LSPD
type: Resource
type: NamedIndividual
has db xref: nif-0000-20920
synonym: The Liver Specific Gene Promoter Database
IAO_0000115: LSPD provides liver specific gene. It lists ~300 promoter regions responsible for liver specific transcriptions, collect ~400 experimentally verified regulatory regions and elements, provide information on transcription regulation of liver genes, compare transcription regulation of functionally or evolutionarily related genes, and retrieve sequences of the promoter region. Its regulatory elements provides information on transcription regulatory elements, reports the methods for verification of the elements, records binding affinity and regulatory function, and summarizes the site distribution and sequence consensus.

The Protein Interfaceome Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-20921
synonym: InterPare
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 28,2022. InterPare is a database server for protein interaction interface information. It contains large-scale interface data of proteins whose 3D-structures are known. Protein interface information is derived from three different methods. InterPare introduces a large-scale protein domain interaction interface database called InterPare. InterPare uses three methods: 1) the Euclidean distance method for checking the distance among subunits in multidomain proteins, 2) Accessible Surface Area (ASA) for detecting the buried region of a protein that is detached from a solvent when forming multimers or complexes, 3) the Voronoi diagram, a computational geometry method, that uses a mathematical definition of interface regions. InterPare includes tools with different display modes for viewing protein interior, surface, and interaction interfaces.

SNAP - SNP Annotation and Proxy Search
type: Resource
type: NamedIndividual
has db xref: nlx_154638
has db xref: OMICS_01927
synonym: SNAP 2
synonym: SNAP (SNP Annotation and Proxy Search)
synonym: SNP Annotation and Proxy Search
abbrev: SNAP
IAO_0000115: A computer program and web-based service for the rapid retrieval of linkage disequilibrium proxy single nucleotide polymorphism (SNP) results given input of one or more query SNPs and based on empirical observations from the International HapMap Project and the 1000 Genomes Project. A series of filters allow users to optionally retrieve results that are limited to specific combinations of genotyping platforms, above specified pairwise r2 thresholds, or up to a maximum distance between query and proxy SNPs. SNAP can also generate linkage disequilibrium plots

Rice Metabolic Pathway Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-20922
synonym: Rice Metabolic Pathways
synonym: RiceCyc
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. RiceCyc is a catalog of known and/or predicted biochemical pathways from rice (Oryza sativa). Pathways and genes presented in this catalog are primarily based on the annotations carried out by Gramene database project on the release 5 of the TIGR-assembly of Oryza sativa japonica cv. Nipponbare genome sequenced by IRGSP.

SEED
type: Resource
type: NamedIndividual
has db xref: nif-0000-20923
synonym: The SEED
IAO_0000115: The SEED is a framework to support comparative analysis and annotation of genomes. The cooperative effort focuses on the development of the comparative genomics environment and, more importantly, on the development of curated genomic data. Curation of genomic data (annotation) is done via the curation of subsystems by an expert annotator across many genomes, not on a gene by gene basis. From the curated subsystems we extract a set of freely available protein families (FIGfams). These FIGfams form the core component of our RAST automated annotation technology. Answering numerous requests for automatic Seed-Quality annotations for more or less complete bacterial and archaeal genomes, we have established the free RAST-Server (RAST=Rapid Annotation using Subsytems Technology). Using similar technology, we make the Metagenomics-RAST-Server freely available. We also provide a SEED-Viewer that allows read-only access to the latest curated data sets. We currently have 58 Archaea, 902 Bacteria, 562 Eukaryota, 1254 Plasmids and 1713 Viruses in our database. All tools and datasets that make up the SEED are in the public domain and can be downloaded at ftp://ftp.theseed.org

Transcription Factor encyclopedia
type: Resource
type: NamedIndividual
has db xref: nif-0000-20924
synonym: Tfe
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.The TFe provides details of transcription factor binding sites in close collaboration with Pazar, a public database of transcription factor and regulatory sequence information. The long-term goal of TFe is to create an online encyclopedic collection of well-studied transcription factor proteins in the human, mouse, and rat genomes, combining a mixture of both expert-curated and automatically-populated content to provide users with a wide set of information relevant to a transcription factor protein of their interest.

STIFDB
type: Resource
type: NamedIndividual
has db xref: OMICS_01866
synonym: Stress Responsive Transcription Factor Database
IAO_0000115: Database of biotic and abiotic stress responsive genes in Arabidopsis thaliana and Oryza sativa L. with options to identify probable Transcription Factor Binding Sites in their promoters. In the response to biotic stress like Bacteria and abiotic stresses like ABA, drought, cold, salinity, dehydration, UV-B, high light, heat,heavy metals etc, ten specific families of transcription factors in Arabidopsis thaliana and six in Oryza sativa L. are known to be involved. HMM-based models are used to identify binding sites of transcription factors belonging to these families. They have also consulted literature reports to cross-validate the Transcription Factor Binding Sites predicted by the method.

Eukaryotic Promoter Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-20940
synonym: The Eukaryotic Promoter Database
abbrev: EPD
IAO_0000115: Collection of eukaryotic promoters derived from published articles. Annotated non-redundant collection of eukaryotic POL II promoters, for which transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. EPD is structured in a way that facilitates dynamic extraction of biologically meaningful promoter subsets for comparative sequence analysis.

Cake
type: Resource
type: NamedIndividual
has db xref: biotools:cake
has db xref: OMICS_03613
IAO_0000115: A bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone.

WikiPathways
type: Resource
type: NamedIndividual
has db xref: nif-0000-20925
has db xref: r3d100013316
synonym: Wiki Pathways
IAO_0000115: Open and collaborative platform dedicated to curation of biological pathways. Each pathway has dedicated wiki page, displaying current diagram, description, references, download options, version history, and component gene and protein lists. Database of biological pathways maintained by and for scientific community.

Yeast consensus metabolic network - A consensus reconstruction of yeast metabolism
type: Resource
type: NamedIndividual
has db xref: nif-0000-20926
synonym: Yeast consensus metabolic network
IAO_0000115: This is a portal to the consensus yeast metabolic network as reconstructed from the genome sequence and literature. It is a highly annotated metabolic map that is periodically updated by a team of collaborators from various research groups. The first version of this reconstruction was published in Herrgrd, Swainston et al. (2008) A consensus yeast metabolic reconstruction obtained from a community approach to systems biology Nature Biotechnol. 26, 1155-1160 (you can access that network here). A second version has now been released and is awaiting publication. We plan on continuing to update this resource towards a complete metabolic network of yeast. All versions will remain accessible for historical purposes, however it is highly recommended that you always use the latest one since that is the most up to date. This effort started on the shoulders of a number of reconstructions of the metabolic network of yeast based on genomic and literature data that were published separately. (iMM904 and iLL672) However, due to the different approaches utilized in them, those earlier reconstructions had a significant number of differences. In addition they suffered from the use of non-standard names and overall they were not annotated with methods that are machine-readable. A community effort in 2007, led by the Manchester Centre for Integrative Systems Biology and the YSBN resulted in a consensus network representation of yeast metabolism, reconciling the earlier results. That effort is now ongoing under the leadership of the MCISB and with collaboration with colleagues under the UNICELLSYS FP7 project. Availability The network reconstruction is primarily assembled and provided as an SBML file enriched with MIRIAM-compliant annotations (which are embedded in the SBML through RDF). All small and macro- molecules are referenced to an authoritative database (e.g. Uniprot, ChEBI, etc.). All molecules and reactions are also annotated with appropriate publications that contain support…

MPromDb
type: Resource
type: NamedIndividual
has db xref: OMICS_01876
synonym: Mammalian Promoter Database
IAO_0000115: A curated database that strives to annotate gene promoters identified from ChIP-Seq experiment results. The long term goal of the database is to provide an integrated resource for mammalian gene transcriptional regulation and epigenetics. Users can search based on Enterz gene id/symbol, or by tissue/cell specific activity and filter results based on any combination of tissue/cell specificity, known/novel, CpG/NonCpG, and protein-coding/non-coding gene promoters. It is also integrated with GBrowse genome browser for visualiztion of ChIP-seq profiles and display the annotations.

Organelle Genomics
type: Resource
type: NamedIndividual
has db xref: nif-0000-20928
has db xref: r3d100010926
synonym: Organelle Genome Megasequencing Program
abbrev: OGMP
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. It investigates mitochondrial genome diversity and evolution by systematically determining the complete mitochondrial DNA (mtDNA) sequences of a phylogenetically broad selection of protists. The mtDNAs of lower fungi and choanoflagellates are being analyzed by the Fungal Mitochondrial Genome Project (FMGP), a sister project to the OGMP.

ProTISA
type: Resource
type: NamedIndividual
has db xref: OMICS_01871
IAO_0000115: Database of confirmed translation initiation sites (TISs) for prokaryotic genomes. The confirmed data has supporting evidence from different sources, including experiments records in the public protein database Swiss-Prot, literature, conserved domain search and sequence alignment among orthologous genes. Combing with predictions from the-state-of-the-art TIS predictor MED-Start/MED-StartPlus (in release 1.0 & 1.2) and TriTISA (since release 1.4) and annotations on potential regulatory signals, the database can serve as a refined annotation resource for the public database RefSeq.

SurfRelax
type: Resource
type: NamedIndividual
has db xref: nif-0000-00347
IAO_0000115: Set of programs and Tk/Tcl scripts, with a GUI wrapper, for extracting the inner and outer cortical surfaces from a T1-weighted MR image of the human brain. It is based on the TFI C++ library and is written for a Unix-based environment (specifically 64-bit and 32-bit versions of Ubuntu). As a courtesy to Apple users a version for Apple/X11 is maintained but the OS X version will always lag the Linux version; also, because some of the third-party libraries SurfRelax relies on may not be supported in or compatible with future versions of OS X, there is no guarantee that the OS X version will be supported indefinitely. Although in principle SurfRelax could be run under Windows (using Cygwin), because of the difficulties of maintaining multiple platforms and the limited support libraries available under Cygwin, there will no longer be support for SurfRelax on this platform. The surfaces are guaranteed to be topologically equivalent to a sphere, thereby obviating the need for handle removal. SurfRelax requires no user intervention, although minor manual editing is recommended for optimal results (normally less than 10 minutes per hemisphere). SurfRelax has several properties that compare favorably with other software packages for surface reconstruction: * Free software - The binaries (written in C++ and Tcl/Tk) are in the public domain. The source code will be released once legacy code issues have been resolved (i.e. replacing with GPL code). * Uses standard public file formats: Analyze file format (SPM/FSL-compatible) for volumes and OOGL OFF binary format for surfaces (see www.geomview.org (http://www.geomview.org/docs/html/geomview_26.html#OOGLRef)) * Combines advantages of volumetric and surface-based methods for surface generation * Correct topology of output surface guaranteed * Requires little or no user intervention - no need for manual handle removal * Relatively robust to noise - multi-scale method compensates for partial volume effects and intensity inhomogene…

Leica | TCS SPE
type: Resource
type: NamedIndividual
has db xref: SciRes_000154
synonym: Leica TCS SPE confocal microscope
abbrev: TCS SPE
IAO_0000115: High resolution, compact and robust confocal that enables immunohistochemical colocalization analysis of florescent markers. Leica TCS SPE confocal point-scanning, spectral system for fluorescence imaging of live or fixed cells.

circlize
type: Resource
type: NamedIndividual
has db xref: biotools:circlize
has db xref: OMICS_04658
synonym: circlize: Circular Visualization in R
IAO_0000115: Software package that implements and enhances circular visualization in R. Due to natural born feature of R to draw statistical graphics, this package can provide more general and flexible way to visualize huge information in circular style.

SNPSTATS
type: Resource
type: NamedIndividual
has db xref: nlx_154650
synonym: SNP STATisticS
abbrev: SNPStats
IAO_0000115: A web-based application designed from a genetic epidemiology point of view to analyze association studies using single nucleotide polymorphisms (SNPs). For each selected SNP, you will receive: * Allele and genotype frequencies * Test for Hardy-Weinberg equilibrium * Analysis of association with a response variable based on linear or logistic regression * Multiple inheritance models: co-dominant, dominant, recessive, over-dominant and additive * Analysis of interactions (gene-gene or gene-environment) If multiple SNPs are selected: * Linkage disequilibrium statistics * Haplotype frequency estimation * Analysis of association of haplotypes with the response * Analysis of interactions (haplotypes-covariate)

AmiGO
type: Resource
type: NamedIndividual
has db xref: nif-0000-20935
has db xref: OMICS_02266
synonym: AmiGene Ontology
synonym: AmiGO 2
synonym: Gene Ontology Consortium
synonym: Gene Ontology Database
synonym: GO Consortium
synonym: GO Database
synonym: The Gene Ontology Consortium
IAO_0000115: Web tool to search, sort, analyze, visualize and download data of interest. Along with providing details of the ontologies, gene products and annotations, features a BLAST search, Term Enrichment and GO Slimmer tools, the GO Online SQL Environment and a user help guide.Used at the Gene Ontology (GO) website to access the data provided by the GO Consortium. Developed and maintained by the GO Consortium.

flowQB
type: Resource
type: NamedIndividual
has db xref: OMICS_05610
synonym: B and CVinstrinsic calculations
synonym: flowQB - Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q
synonym: flowQB: Automated Quadratic Characterization of Flow Cytometer Instrument Sensitivity: Q
IAO_0000115: A fully automated R Bioconductor package to calculate automatically the detector efficiency (Q), optical background (B) and intrinsic CV of the beads.

NeuroMorpho.Org
type: Resource
type: NamedIndividual
has db xref: nif-0000-00006
has db xref: r3d100010107
synonym: Neuro Morpho
synonym: NeuroMorpho
synonym: NeuroMorpho.org
IAO_0000115: Centrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications that contains some of the most complete axonal arborizations digitally available in the community. Each neuron is represented by a unique identifier, general information (metadata), the original and standardized ASCII files of the digital morphological reconstruction, and a set of morphometric features. It contains contributions from over 100 laboratories worldwide and is continuously updated as new morphological reconstructions are collected, published, and shared. Users may browse by species, brain region, cell type or lab name. Users can also download morphological reconstructions for research and analysis. Deposition and distribution of reconstruction files ultimately prevents data loss. Centralized curation and annotation aims at minimizing the effort required by data owners while ensuring a unified format. It also provides a one-stop entry point for all available reconstructions, thus maximizing data visibility and impact.

NCBI Genome Survey Sequences Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-20938
has db xref: r3d100010783
synonym: dbGSS
synonym: Entrez GSS
synonym: NCBI dbGSS
abbrev: GSS
IAO_0000115: Database of unannotated short single-read primarily genomic sequences from GenBank including random survey sequences clone-end sequences and exon-trapped sequences. The GSS division of GenBank is similar to the EST division, with the exception that most of the sequences are genomic in origin, rather than cDNA (mRNA). It should be noted that two classes (exon trapped products and gene trapped products) may be derived via a cDNA intermediate. Care should be taken when analyzing sequences from either of these classes, as a splicing event could have occurred and the sequence represented in the record may be interrupted when compared to genomic sequence. The GSS division contains (but is not limited to) the following types of data: * random single pass read genome survey sequences. * cosmid/BAC/YAC end sequences * exon trapped genomic sequences * Alu PCR sequences * transposon-tagged sequences Although dbGSS sequences are incorporated into the GSS Division of GenBank, annotation in dbGSS is more comprehensive and includes detailed information about the contributors, experimental conditions, and genetic map locations.

Cinteny
type: Resource
type: NamedIndividual
has db xref: OMICS_00931
synonym: Cinteny Server for Synteny Identification and Analysis of Genome Rearrangement
IAO_0000115: Online database for finding and analyzing syntenic regions across multiple genomes and measuring the extent of genome rearrangement using reversal distance as a measure.

Gene Index Project
type: Resource
type: NamedIndividual
has db xref: biotools:tigr_gene_indices
has db xref: nif-0000-20942
synonym: DFCI
synonym: DFCI Gene Index Project
abbrev: DFCI TGI
abbrev: TGI
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 19,2019.The goal of The Gene Index Project is to use the available Expressed Sequence Transcript (EST) and gene sequences, along with the reference genomes wherever available, to provide an inventory of likel…

RegPrecise
type: Resource
type: NamedIndividual
has db xref: OMICS_01869
IAO_0000115: Collection of manually curated inferences of regulons in prokaryotic genomes. Database for capturing, visualization and analysis of transcription factor regulons that were reconstructed by comparative genomic approach in wide variety of prokaryotic genomes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

High Throughput Genomic Sequences Division
type: Resource
type: NamedIndividual
has db xref: nif-0000-20943
synonym: High-Throughput Genomic Sequences
synonym: HTG database
synonym: HTG GenBank Division
synonym: HTG Sequence
synonym: NCBI High-Throughput Genomic Sequences
abbrev: HTG Division
abbrev: HTG Sequences
IAO_0000115: Database of high-throughput genome sequences from large-scale genome sequencing centers, including unfinished and finished sequences. It was created to accommodate a growing need to make unfinished genomic sequence data rapidly available to the scientific community in a coordinated effort among the International Nucleotide Sequence databases, DDBJ, EMBL, and GenBank. Sequences are prepared for submission by using NCBI's software tools Sequin or tbl2asn. Each center has an FTP directory into which new or updated sequence files are placed. Sequence data in this division are available for BLAST homology searches against either the htgs database or the month database, which includes all new submissions for the prior month. Unfinished HTG sequences containing contigs greater than 2 kb are assigned an accession number and deposited in the HTG division. A typical HTG record might consist of all the first-pass sequence data generated from a single cosmid, BAC, YAC, or P1 clone, which together make up more than 2 kb and contain one or more gaps. A single accession number is assigned to this collection of sequences, and each record includes a clear indication of the status (phase 1 or 2) plus a prominent warning that the sequence data are unfinished and may contain errors. The accession number does not change as sequence records are updated; only the most recent version of a HTG record remains in GenBank.

NextGen Sequence Databases
type: Resource
type: NamedIndividual
has db xref: nif-0000-20944
synonym: NextGen
IAO_0000115: Informational portal that aggregates information about databases for next gen sequencing.

New Energy and Industrial Technology Development Organization
type: Resource
type: NamedIndividual
has db xref: nif-0000-20945
synonym: NEDO Database
synonym: New Energy and Industrial Technology Development Database
abbrev: NEDO
IAO_0000115: A database of sequence data of cDNA clones from the Kazusa DNA Research Institute human spleen cDNA library, which was determined by the NEDO human cDNA sequencing project. The cDNAs supplied by Kazusa DNA Research Institute were generated by conventional methods and strictly size-selected from a cDNA library of adult human spleen. Consequently, not all of the cDNAs may be full-length, though all possess relatively long cDNA inserts, whose average size is about 4.5 kb. cDNAs having unknown end sequences and high protein-coding probability at their 5-prime ends were selected and sequenced. The physical maps were constructed on the basis of the sequence data of the cDNA clones. RepeatMasker, which is a program that screens DNA sequences for interspersed repeats known to exist in mammalian genomes, was applied to detect repeat sequences in cDNA sequences. The predicted protein sequences were examined for motifs present in the PROSITE database. Because weakly defined sequence motifs appear too many times in the HUGE database and are, thus, unlikely to be informative, several motifs were excluded from the analysis, including amidation site, N-glycosylation site, and cAMP- and cGMP-dependent protein kinase phosphorylation site.

neuRosim
type: Resource
type: NamedIndividual
has db xref: SciRes_000194
synonym: neuRosim: Functions to Generate fMRI Data Including Activated Data Noise Data and Resting State Data
IAO_0000115: Software package that allows users to generate fMRI time series or 4D data. Some high-level functions are created for fast data generation with only a few arguments and a diversity of functions to define activation and noise. For more advanced users it is possible to use the low-level functions and manipulate the arguments.

SVA
type: Commercial Organization
type: NamedIndividual
has db xref: biotools:sequencevariantanalyzer
has db xref: nlx_154666
has db xref: OMICS_00190
synonym: Sequence Variant Analyzer
synonym: SVA: Sequence Variant Analyzer
IAO_0000115: Software package to annotate, visualize, and analyze the genetic variants identified through next-generation sequencing studies, including whole-genome sequencing (WGS) and exome sequencing studies. SVA aims to provide the research community with a user-friendly and efficient tool to analyze large amount of genetic variants, and to facilitate the identification of the genetic causes of human diseases and related traits.

Sequence Tag Alignment and Consensus Knowledgebase Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-20946
synonym: STACKdb
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The STACKdb is knowledgebase generated by processing EST and mRNA sequences obtained from GenBank through a pipeline consisting of masking, clustering, alignment and variation analysis steps. The STACK project aims to generate a comprehensive representation of the sequence of each of the expressed genes in the human genome by extensive processing of gene fragments to make accurate alignments, highlight diversity and provide a carefully joined set of consensus sequences for each gene. The STACK project is comprised of the STACKdb human gene index, a database of virtual human transcripts, as well as stackPACK, the tools used to create the database. STACKdb is organized into 15 tissue-based categories and one disease category. STACK is a tool for detection and visualization of expressed transcript variation in the context of developmental and pathological states. The data system organizes and reconstructs human transcripts from available public data in the context of expression state. The expression state of a transcript can include developmental state, pathological association, site of expression and isoform of expressed transcript. STACK consensus transcripts are reconstructed from clusters that capture and reflect the growing evidence of transcript diversity. The comprehensive capture of transcript variants is achieved by the use of a novel clustering approach that is tolerant of sub-sequence diversity and does not rely on pairwise alignment. This is in contrast with other gene indexing projects. STACK is generated at least four times a year and represents the exhaustive processing of all publicly available human EST data extracted from GenBank. This processed information can be explored through 15 tissue-specific categories, a disease-related category and a whole-body index

SYZYGY
type: Resource
type: NamedIndividual
has db xref: nlx_154668
has db xref: OMICS_02166
synonym: Syzygy - SNP and indel calling for pooled and individual targeted resequencing studies
abbrev: Syzygy
IAO_0000115: A targeted sequencing post processing analysis software tool that allows: 1. SNP and indel detection; 2. Allele frequency estimation; 3. Single-marker association test; 4. Group-wise marker test association; 5. Experimental QC summary (%dbSNP, Ts/Tv, Ns/S); 6. Power to detect variant. (entry from Genetic Analysis Software)

TcoF
type: Resource
type: NamedIndividual
has db xref: biotools:tcof-db
has db xref: OMICS_01865
synonym: Dragon Database for Human Transcription Co-Factors and Transcription Factor Interacting Proteins
synonym: TcoF - Dragon database of transcription co-factors and transcription factor interacting proteins
synonym: TcoF-DB
IAO_0000115: Database that facilitates the exploration of proteins involved in the regulation of transcription in humans by binding to regulatory DNA regions (transcription factors) and proteins involved in the regulation of transcription in humans by interacting with transcription factors and not binding to regulatory DNA regions (transcription co-factors).

BD Biosciences | LSR II Flow Cytometer
type: Resource
type: NamedIndividual
has db xref: Model_Number_BD LSR II
has db xref: SciRes_000152
abbrev: LSR II Flow Cytometer
IAO_0000115: Benchtop high-performance cell sorter with multiple lazer, detector and fluoroscrome options. Allows detection of 12 parameters (10 color conjugates, forward and sideward scatter).

WD repeat Family of Proteins
type: Resource
type: NamedIndividual
has db xref: nif-0000-20949
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. This website contains a library of WD-repeat containing proteins in which the repeats appear as multi-aligned sets. WD-repeat-containing proteins are those that contain 4 or more copies of the WD-repeat (tryptophan-aspartate repeat), a sequence motif approximately 31 amino acids long, that encodes a structural repeat. This repeat is described by the following profile, where x is ANY amino acid. By clicking on each high-lighted character you will obtain the distribution of amino acids found at that position of the repeat among an aligned set of WD-repeat containing proteins. The tertiary structure of only one member of this family has been determined, that of the G protein beta subunit, which contains 7 WD-repeats. Each of the 7 repeats folds into a small antiparallel beta-sheet. The over-lines above indicate the position of these strands, with a being the strand closest to the central pore and d at the external surface of the folded protein. These sheets are arranged around a central pseudosymmetry axis into a beta propeller. The WD-repeat-containing proteins form a very large family that is diverse in both its function and domain structure. Within all these proteins the WD-repeat domains are thought to have two common features: the domain folds into a beta propeller; and the domains form a platform without any catalytic activity on which multiple protein complexes assemble reversibly. The fact that these proteins play such key roles in the formation of protein-protein complexes in nearly all the major pathways and organelles unique to eukaryotic cells has two important implications. It supports both their ancient and proto eukaryotic origins and supports a likely association with many genetic diseases.

Protein Structure Initiative
type: Resource
type: NamedIndividual
has db xref: nif-0000-20950
synonym: PSI
IAO_0000115: The Structural Genomics Project aims at determination of the 3D structure of all proteins. It also aims to reduce the cost and time required to determine three-dimensional protein structures. It supports selection, registration, and tracking of protein families and representative targets. This aim can be achieved in four steps : -Organize known protein sequences into families. -Select family representatives as targets. -Solve the 3D structure of targets by X-ray crystallography or NMR spectroscopy. -Build models for other proteins by homology to solved 3D structures. PSI has established a high-throughput structure determination pipeline focused on eukaryotic proteins. NMR spectroscopy is an integral part of this pipeline, both as a method for structure determinations and as a means for screening proteins for stable structure. Because computational approaches have estimated that many eukaryotic proteins are highly disordered, about 1 year into the project, CESG began to use an algorithm. The project has been organized into two separate phases. The first phase was dedicated to demonstrating the feasibility of high-throughput structure determination, solving unique protein structures, and preparing for a subsequent production phase. The second phase, PSI-2, has focused on implementing the high-throughput structure determination methods developed in PSI-1, as well as homology modeling and addressing bottlenecks like modeling membrane proteins. The first phase of the Protein Structure Initiative (PSI-1) saw the establishment of nine pilot centers focusing on structural genomics studies of a range of organisms, including Arabidopsis thaliana, Caenorhabditis elegans and Mycobacterium tuberculosis. During this five-year period over 1,100 protein structures were determined, over 700 of which were classified as unique due to their < 30% sequence similarity with other known protein structures. The primary goal of PSI-1 was to develop methods to streamline the structure determi…

University of Cantabria; Cantabria; Spain
type: Organization
type: NamedIndividual
has db xref: nlx_158275
synonym: Unican
synonym: Universidad de Cantabria
synonym: University of Cantabria
abbrev: UC
IAO_0000115: Public university in Cantabria, Spain that offers undergraduate, graduate and post graduate degree programs in areas including sciences, humanities, law, medicine, and tourism.

Matchprot
type: Resource
type: NamedIndividual
has db xref: OMICS_03666
IAO_0000115: A pairwise protein structure alignment software.

Marine Geoscience Data System
type: Resource
type: NamedIndividual
has db xref: DOI:10.26022/
has db xref: nlx_154713
has db xref: r3d100010273
abbrev: MGDS
IAO_0000115: Repository providing free access to marine geophysical data (e.g. bathymetry, seismic data, magnetics, gravity, images) and related land-based data from NSF-funded research conducted throughout the global oceans. Data Portals include GeoPRISMS, MARGINS, Ridge 2000, Antarctic and Southern Ocean Data Synthesis, the Global Multi-Resolution Topography Synthesis, and Seismic Reflection Field Data Portal. Primary data types served are multibeam bathymetric data from the ocean floor, seismic reflection data imaging below the seafloor, and multi-disciplinary ship based data from the Southern Ocean. Other holdings include deep-sea photographic transects, and ultra-high resolution bathymetry, temperature probe data, biological species compilations, MAPR and CTD data. Derived data products and sets include microseismicity catalogs, images, visualization scenes, magnetic and gravity compilations, grids of seismic layer thickness, velocity models, GIS project files, and 3D visualizations. Tools to discover, explore, and visualize data are available. They deliver catalogs, maps, and data through standard programmatic interfaces. GeoMapApp, a standalone data visualization and analysis tool, permits dynamic data exploration from a map interface and the capability to generate and download custom grids and maps and other data. Through GeoMapApp, users can access data hosted at the MGDS, at other data repositories, and import their own data sets. Global Multi-Resolution Topography (GMRT) is a continuously-updated compilation of seafloor bathymetry integrated with global land topography. It can be used to create maps and grids and it can be accessed through several standard programmatic interfaces including GeoMapApp and Google Earth. The GMRT compilation can also be explored in 3D using Virtual Ocean. The MGDS MediaBank contains high quality images, illustrations, animations and video clips that are organized into galleries. Media can be sorted by category, and keyword and map-based s…

WebGeSTer DB
type: Resource
type: NamedIndividual
has db xref: biotools:webgester_db
has db xref: OMICS_01862
synonym: Web Genome Scannner for Terminators Database
synonym: WebGesTer Database
synonym: WebGeSTer DB - A Transcription Terminator Database
IAO_0000115: Database of intrinsic terminators of transcription that is comprized of >2,200,000 bacterial terminators identified from a total of 2036 chromosomes and 1508 plasmids. Information about structural parameters of individual terminators such as sequence, length of stem and loop, mismatches and gaps, U-trail, genomic coordinates and gene name and accession number is available in both tabular form and as a composite figure. Summary statistics for terminator profiles of whole genome can be also obtained. Raw data files for individual genomes can be downloaded (.zip files) for detailed investigations. Data is organized into different tiers such that users can fine-tune their search by entering name of the species, or taxon ID or genomes with a certain number of terminators. To visualize the occurrence of the terminators, an interactive map, with the resolution to single gene level, has been developed.

VoxBo
type: Resource
type: NamedIndividual
has db xref: nif-0000-00353
IAO_0000115: Software package for brain image manipulation and analysis, focusing on fMRI and lesion analysis. VoxBo can be used independently or in conjunction with other packages. It provides GLM-based statistical tools, an architecture for interoperability with other tools (they encourage users to incorporate SPM and FSL into their processing pipelines), an automation system, a system for parallel distributed computing, numerous stand-alone tools, decent wiki-based documentation, and lots more.

pfSNP
type: Resource
type: NamedIndividual
has db xref: OMICS_01854
synonym: pfSNP Search Engine
synonym: Potentially Functional SNP Search Engine
IAO_0000115: Search engine integrating various bio-informatic resources and algorithims to produce a one-stop resource for biologists to identify potentially functional SNPs. It caters to different groups of scientists interested in SNPs including those working in the following areas: * Whole-genome association studies * Gene-based association studies * Designing experiments to address the functionality of specific SNPs * Determining potentially functionally significant SNPs that are in LD with non-pfSNPs of interest. Users may add published SNP functions.

Cell Centered Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-00007
has db xref: r3d100000018
synonym: CCDB
synonym: Cell-Centered Database
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented June 5, 2017. It has been merged with Cell Image Library. Database for sharing and mining cellular and subcellular high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging that makes unique and valuable datasets available to the scientific community for visualization, reuse and reanalysis. Techniques range from wide field mosaics taken with multiphoton microscopy to 3D reconstructions of cellular ultrastructure using electron tomography. Contributions from the community are welcome. The CCDB was designed around the process of reconstruction from 2D micrographs, capturing key steps in the process from experiment to analysis. The CCDB refers to the set of images taken from microscope the as the Microscopy Product. The microscopy product refers to a set of related 2D images taken by light (epifluorescence, transmitted light, confocal or multiphoton) or electron microscopy (conventional or high voltage transmission electron microscopy). These image sets may comprise a tilt series, optical section series, through focus series, serial sections, mosaics, time series or a set of survey sections taken in a single microscopy session that are not related in any systematic way. A given set of data may be more than one product, for example, it is possible for a set of images to be both a mosaic and a tilt series. The Microscopy Product ID serves as the accession number for the CCDB. All microscopy products must belong to a project and be stored along with key specimen preparation details. Each project receives a unique Project ID that groups together related microscopy products. Many of the datasets come from published literature, but publication is not a prerequisite for inclusion in the CCDB. Any datasets that are of high quality and interest to the scientific community can be included in the CCDB.

shinyTANDEM
type: Resource
type: NamedIndividual
has db xref: OMICS_03517
IAO_0000115: Software package that provides a GUI interface for rTANDEM, an R/Bioconductor package for MS/MS protein identification. The GUI is primarily designed to visualize rTANDEM result object or result xml files. But it will also provides an interface for creating parameter objects, launching searches or performing conversions between R objects and xml files.

AREX
type: Resource
type: NamedIndividual
has db xref: nif-0000-20955
synonym: Arabidopsis Gene Expression Database
synonym: The Arabidopsis Gene Expression Database
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. The Arabidopsis gene Expression Database collects Arabidopsis gene expression data from genome-wide and gene-specific sources and integrative search tools are provided. Currently the database contains only root gene expression data, but has the capability to contain data from any part of the plant. The aim of Arabidopsis gene Expression Database is to: (1) Integrate genome-wide and gene-specific ("traditional") types of expression pattern data, using ontologies to describe data whenever possible, in particular to describe expression patterns. (2) Provide user-friendly search tools, for example to search for genes expressed with a certain pattern, or to search for the expression pattern of specific genes (from gene-specific experiments and from microarray data). Expression pattern predicted from the microarray data is called digital in situ.

NITRC Computational Environment
type: Resource
type: NamedIndividual
has db xref: nlx_155889
synonym: NITRC Computational Environment in Amazon Marketplace
abbrev: NITRC-CE
IAO_0000115: An on-demand, cloud based computational virtual machine pre-installed with popular NITRC neuroimaging tools built using NeuroDebian. For a listing of current NITRC-CE packages visit: http://www.nitrc.org/ce-packages. You can also use the "public Amazon Machine Interface (AMI)" to conduct your analyses on the Amazon EC2 platform.

Genoscope
type: Organization
type: NamedIndividual
has db xref: grid.434728.e
has db xref: ISNI: 0000 0004 0641 2997
has db xref: nif-0000-20957
has db xref: Wikidata: Q3100800
synonym: French National Sequencing Center
synonym: Genoscope - Centre National de Sequencage
synonym: Genoscope - Centre National de S�quen�age
synonym: Genoscope - French National Sequencing Center
IAO_0000115: French national sequencing center with the following resources: * Sequencing ** Genoscope Projects * Environmental genomics ** Microbial diversity in wastewater ** Metabolic genomics * Bioinformatics ** Atelier for comparative genomics ** Computational Systems Biology ** Servers resources *** GGB for Generic Genome Browser: graphic interface for various databases (sequence, annotation, syntenies...) for a given organism. *** MaGe for Magnifying Microbial Genomes: annotation system for microbial genomes.

CistromeMap
type: Resource
type: NamedIndividual
has db xref: OMICS_01853
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A knowledgebase of all of the publicly available ChIP-Seq and DNase-Seq data in mouse and human. They have also manually curated metadata to ensure annotation consistency, and developed a user-friendly display matrix for quick navigation and retrieval of data for specific factors, cells, and papers. The community can contribute to this resource.

metaRNASeq
type: Resource
type: NamedIndividual
has db xref: OMICS_03527
synonym: metaRNASeq: Meta-analysis of RNA-seq data
IAO_0000115: Software package for meta-analysis of RNA-seq data. This package implements two p-value combination techniques (inverse normal and Fisher methods). It also provides a vignette explaining how to combine data from multiple RNA-seq experiments.

ZOOM
type: Commercial Organization
type: NamedIndividual
has db xref: biotools:zoom
has db xref: OMICS_01852
synonym: ZOOM: Next Gen Sequencing
IAO_0000115: Software to map the Illumina/Solexa reads of 15x coverage of a human genome to the reference human genome in one CPU-day, allowing two mismatches, at full sensitivity.

NASCs Bioinformatics Webservices
type: Resource
type: NamedIndividual
has db xref: nif-0000-20959
synonym: SOAPLAB
IAO_0000115: The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community. SOAPLAB, was developed in the European Bioinformatics Institute (EBI), and is a SOAP-based analysis web service that is used to wrap command-line applications so they can be used as web service. NASC provides most of its data via SOAPLAB.

flowPlots
type: Resource
type: NamedIndividual
has db xref: OMICS_05608
synonym: flowPlots: analysis plots and data class for gated flow cytometry data
IAO_0000115: Software for analysis plots and data class for gated flow cytometry data.

ImaGene
type: Resource
type: NamedIndividual
has db xref: biotools:ImaGene
has db xref: OMICS_00841
IAO_0000115: Software tool as convolutional neural network to quantify natural selection from genomic data.Supervised machine learning algorithm to predict natural selection and estimate selection coefficients from population genomic data. Can be used to estimate any parameter of interest from evolutionary population genetics model., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

VAAST
type: Resource
type: NamedIndividual
has db xref: biotools:vaast
has db xref: nlx_154686
has db xref: OMICS_02134
has db xref: SciRes_000138
synonym: Variant Annotation Analysis & Search Tool
synonym: Variant Annotation Analysis and Search Tool
abbrev: VAAST 2
IAO_0000115: A probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST combines elements of phylogenetic conservation, amino acid substitution, and aggregative approaches to variant prioritization into a single unified likelihood-framework that allows users to accurately identify damaged genes and deleterious variants. The software can score both coding (SNV, indel and splice site) and non-coding variants (SNV), evaluating the cumulative impact of both types of variants simultaneously. It can identify rare variants causing rare genetic diseases and can also use both rare and common variants to identify genes responsible for common diseases.

ARACNE
type: Resource
type: NamedIndividual
has db xref: OMICS_01851
synonym: Algorithm for the Reconstruction of Accurate Cellular Networks
IAO_0000115: An algorithm, using microarray expression profiles, to scale up to the complexity of regulatory networks in mammalian cells, yet general enough to address a wider range of network deconvolution problems. This method uses an information theoretic approach to eliminate the vast majority of indirect interactions typically inferred by pairwise analysis.

FR-HIT
type: Resource
type: NamedIndividual
has db xref: OMICS_01850
synonym: FR-HIT: Metagenome Fragment Recruitment at High Identity with Tolerance
synonym: Fragment Recruitment at High Identity with Tolerance
synonym: Metagenome Fragment Recruitment at High Identity with Tolerance
IAO_0000115: An efficient fragment recruitment software program for next generation sequences against microbial reference genomes. It produces similar sensitivity of BLASTN, but runs at a 100 times higher speed. The algorithm adopts a seeding heuristic strategy with overlapping k-mer hashing to locate candidate matching blocks on the reference sequences, and then apply an effective filtering within the candidate blocks to filter out blocks that do not meet the minimum criteria for containing an alignment with specified parameters. For each candidate block that passed the filter, the best matching sub-regions between a candidate block and a read are determined, and used subsequently by the banded Smith-Waterman algorithm to carry out the actual alignment efficiently, which will finally verify if this can be a valid recruitment hit.

PROVEAN
type: Resource
type: NamedIndividual
has db xref: OMICS_01849
synonym: Protein Variation Effect Analyzer
IAO_0000115: A software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein.

flowPhyto
type: Resource
type: NamedIndividual
has db xref: OMICS_05606
synonym: flowPhyto - Methods for Continuous Flow Cytometry
IAO_0000115: An R package that performs aggregate statistics on virtually unlimited collections of raw flow cytometry files and provides a memory efficient, parallelized solution for analyzing high-throughput flow cytometric data.

Mini Analysis Program
type: Resource
type: NamedIndividual
has db xref: SciRes_000143
has db xref: SCR_014441
synonym: Mini Analysis
synonym: MiniAnalysis
IAO_0000115: Software tool that detects peaks of any type, any shape, any direction, and any size for neuroscientists who are studying spontaneous activities. Allows detection of virtually any kind of peaks including spontaneous miniature synaptic currents and potentials, action potential spikes, calcium imaging peaks, amperometric peaks, ECG peaks etc. It includes the complex and multiple peak detection algorithm. Has post-detection analyses including essential plots and statistical parameters. Group Analysis provides specialized and detailed analysis options for action potentials, decay fitting, fEPSP/population spikes, amperometry, etc., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

MEDLINE
type: Resource
type: NamedIndividual
has db xref: nlx_53277
IAO_0000115: A premier bibliographic database that contains over 18 million references to journal articles in life sciences with a concentration on biomedicine. A distinctive feature is that the records are indexed with NLM Medical Subject Headings (MeSH). PubMed provides free access to MEDLINE and links to full text articles when possible. The great majority of journals are selected for MEDLINE based on the recommendation of the Literature Selection Technical Review Committee (LSTRC), an NIH-chartered advisory committee of external experts analogous to the committees that review NIH grant applications. Some additional journals and newsletters are selected based on NLM-initiated reviews, e.g., history of medicine, health services research, AIDS, toxicology and environmental health, molecular biology, and complementary medicine, that are special priorities for NLM or other NIH components. These reviews generally also involve consultation with an array of NIH and outside experts or, in some cases, external organizations with which NLM has special collaborative arrangements. MEDLINE is the primary component of PubMed, part of the Entrez series of databases provided by the NLM National Center for Biotechnology Information (NCBI). MEDLINE may also be searched via the NLM Gateway. Time coverage: generally 1946 to the present, with some older material. Source: Currently, citations from approximately 5,516 worldwide journals in 39 languages; 60 languages for older journals. Citations for MEDLINE are created by the NLM, international partners, and collaborating organizations.

Midas Platform
type: Resource
type: NamedIndividual
has db xref: nlx_154696
synonym: Midas Platform - The Multimedia Digital Archiving System
abbrev: Midas
IAO_0000115: Open-source toolkit that enables the rapid creation of tailored, web-enabled data storage and provides a cohesive system for data management, visualization, and processing. At its core, Midas Platform is implemented as a PHP modular framework with a backend database (PostGreSQL, MySQL and non-relational databases). While the Midas Platform system can be installed and deployed without any customization, the framework has been designed with customization in mind. As building one system to fit all is not optimal, the framework has been extended to support plugins and layouts. Through integration with a range of other open-source toolkits, applications, or internal proprietary workflows, Midas Platform offers a solid foundation to meet the needs of data-centric computing. Midas Platform provides a variety of data access methods, including web, file system and DICOM server interfaces, and facilitates extending the methods in which data is stored to other relational and non-relational databases.

Integrated
type: Resource
type: NamedIndividual
has db xref: nlx_154697
synonym: Integrated through SciCrunch
synonym: SciCrunch Integrated
IAO_0000115: Virtual database of individual data sources, maintained by SciCrunch participating groups. Database topics are varied, including animals, grants, software, brain gene expression, and clinical trials.

CINERGI
type: Resource
type: NamedIndividual
has db xref: nlx_154714
synonym: Community Inventory of EarthCube Resources for Geosciences Interoperability
IAO_0000115: A project constructing a community inventory and knowledge base on geoscience information resources to meet the challenge of finding resources across disciplines, assessing their fitness for use in specific research scenarios, and providing tools for integrating and re-using data from multiple domains. The project team envisions a comprehensive system linking geoscience resources, users, publications, usage information, and cyberinfrastructure components. This system would serve geoscientists across all domains to efficiently use existing and emerging resources for productive and transformative research.

National Oceanographic Data Center
type: Resource
type: NamedIndividual
has db xref: nlx_154699
synonym: National Oceanographic Data Center (NODC)
abbrev: NODC
IAO_0000115: Accepts and provides access to biology data, buoy data, chlorophyll, nutrients, ocean currents, oxygen, plankton, profile data, salinity, satellite data, sea level, snow and ice, temperature, waves. Please note that routine underway oceanographic shipboard data collected with standard equipment aboard the UNOLS fleet (e.g. CTD, ADCP, XBT, MET, TSG) are routinely transmitted to NODC via Rolling Deck to Repository (R2R). NODC Provides: * The World's largest collection of freely available oceanographic data * Water temperatures dating back to the late 1700's and measuring thousands of meters deep * A State of the Ocean Climate from NODC's Ocean Climate Lab and Satellite Team's scientific analyses * Scientific journals, rare books, historical photo collections and maps through the NOAA Central Library, a division of NODC * Data management expertise including metadata training through NODC's National Coastal Data Development Center

Neotoma Paleoecology Database
type: Resource
type: NamedIndividual
has db xref: nlx_154700
has db xref: r3d100011761
synonym: Neotoma DB
synonym: NeotomaDB
abbrev: Neotoma
IAO_0000115: Paleoecology database for plio-pleistocene to holocene fossil data with a centralized structure for interdisciplinary, multiproxy analyses and common tool development; discipline-specific data can also be easily accessed. Data currently include North American Pollen (NAPD) and fossil mammals (FAUNMAP). Other proxies (plant macrofossils, beetles, ostracodes, diatoms, etc.) and geographic areas (Europe, Latin America, etc.) will be added in the near future. Data are derived from sites from the last 5 million years.

BCO-DMO
type: Resource
type: NamedIndividual
has db xref: nlx_154701
synonym: Biological & Chemical Oceanography Data Management Office
synonym: Biological and Chemical Oceanography Data Management Office
IAO_0000115: Accepts and provides access to marine biogeochemical and ecological data sets from NSF-funded research programs. BCO-DMO is also the data repository for the US GLOBEC and JGOFS programs.

Exomiser
type: Resource
type: NamedIndividual
has db xref: SciRes_000142
synonym: Exomiser2: Annotate and Filter Variants
synonym: Exomiser 2.0
synonym: The Exomiser2: Annotate and Filter Variants
abbrev: Exomiser2
IAO_0000115: A Java program that functionally annotates variants from whole-exome sequencing data starting from a VCF (Variant Call Format) file (version 4). The functional annotation code is based on Annovar and uses UCSCKnownGene transcript definitions and hg19 genomic coordinates. Variants are prioritized according to user-defined criteria on variant frequency, pathogenicity, quality, inheritance pattern, phenotype data from human and model organisms, and proximity in the interactome to phenotypically similar genes.

Antarctic and Southern Ocean Data Portal
type: Resource
type: NamedIndividual
has db xref: nlx_154703
synonym: Antarctic & Southern Ocean Data Portal
abbrev: ASODS
IAO_0000115: Accepts and provides access to geoscience data, primarily marine, collected from oceanographic expeditions in the Antarctic region. The synthesis began in 2003 as the Antarctic Multibeam Bathymetry and Geophysical Data Synthesis (AMBS) with a focus on multibeam bathymetry field data and other geophysical data from the Southern Ocean collected with the R/V N. B. Palmer. In 2005, the effort was expanded to include all routine underway geophysical and oceanographic data collected with both the R/V N. B. Palmer and R/V L. Gould, the two primary research vessels serving the US Antarctic Program. Data available include seafloor bathymetry, subbottom profiling, trackline gravity and magnetics, meteorological, and water column data as well as basic cruise information for all Palmer and Gould expeditions. Seafloor bathymetry data are provided both as raw swath data as well as in gridded form through the Global Multi-Resolution Topography (GMRT) synthesis. This gridded compilation of seafloor bathymetry data can be accessed through GeoMapApp, Create Maps and Grids and through an OGC-compliant Web Map Service. GeoMapApp is an integrated mapping application that provides access to many additional regional bathymetric grids, seismic, radar, gravity and magnetics profiles as well as other map and grid compilations for the Antarctic continent including LIMA.

Academic Seismic Portal at LDEO
type: Resource
type: NamedIndividual
has db xref: nlx_154704
has db xref: r3d100010644
abbrev: ASP-LDEO
IAO_0000115: Seismic Reflection Field Data from the academic research community. Their partner Academic Seismic Portal at UTIG offers additional seismic resources, http://www.ig.utexas.edu/sdc/

National Center for Earth-Surface Dynamics
type: Resource
type: NamedIndividual
has db xref: nlx_154715
has db xref: r3d100011295
synonym: NCED Data Repository
abbrev: NCED
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Field, laboratory, and model data related to earth-surface dynamics created or compiled by NCED-funded scientists. NCED is a Science and Technology Center developed to predict the coupled dynamics and co-evolution of landscapes and their ecosystems in order to transform management and restoration of the Earth-surface environment.

Community Surface Dynamics Modeling System
type: Resource
type: NamedIndividual
has db xref: nlx_154705
has db xref: r3d100012544
abbrev: CSDMS
IAO_0000115: Model repository and data related to earth-surface dynamics modeling. The CSDMS Modeling Tool (CMT) allows you to run and couple CSDMS model components on the CSDMS supercomputer in a user-friendly software environment. Components in the CMT are based on models, originally submitted to the CSDMS model repository, and now adapted to communicate with other models. The CMT tool is the environment in which you can link these components together to run new simulations. The CMT software runs on your own computer; but it communicates with the CSDMS HPCC, to perform the simulations. Thus, the CMT also offers you a relatively easy way of using the CSDMS supercomputer for model experiments. CSDMS deals with the Earth's surface - the ever-changing, dynamic interface between lithosphere, hydrosphere, cryosphere, and atmosphere. They are a diverse community of experts promoting the modeling of earth surface processes by developing, supporting, and disseminating integrated software modules that predict the movement of fluids, and the flux (production, erosion, transport, and deposition) of sediment and solutes in landscapes and their sedimentary basins. CSDMS: * Produces protocols for community-generated, continuously evolving, open software * Distributes software tools and models * Provides cyber-infrastructure to promote the quantitative modeling of earth surface processes * Addresses the challenging problems of surface-dynamic systems: self-organization, localization, thresholds, strong linkages, scale invariance, and interwoven biology & geochemistry * Enables the rapid development and application of linked dynamic models tailored to specific landscape basin evolution (LBE) problems at specific temporal and spatial scales * Partners with related computational and scientific programs to eliminate duplication of effort and to provide an intellectually stimulating environment * Supports a strong linkage between what is predicted by CSDMS codes and what is observed, both in natur…

CUAHSI Hydrologic Information System
type: Resource
type: NamedIndividual
has db xref: nlx_154706
has db xref: r3d100010082
synonym: Consortium of Universities for the Advancement of Hydrologic Science Hydrologic Information System
abbrev: CUAHSI HIS
abbrev: CUAHSI-HIS
IAO_0000115: An internet-based system for sharing hydrologic data. It is comprised of databases and servers, connected through web services, to client applications, allowing for the publication, discovery and access of data.

Spatially Constrained Parcellation
type: Resource
type: NamedIndividual
has db xref: nlx_155533
IAO_0000115: A set of tools for deriving region of interest (ROI) atlases by whole brain clustering of task or resting state data. This resource also contains several atlases derived by parcellating publicly available resting state fMRI datasets. The initial release will include python scripts and ROI atlases developed to perform the analyses described in Craddock et. al., A whole brain fMRI atlas generated via spatially constrained spectral clustering, which is currently in revision in Human Brain Mapping. The scripts provide all of the tools necessary to derive an ROI atlases using spatially constrained Ncut spectral clustering. The scripts require python, numpy and scipy to run. Source code and parcellations now available! Go to http://ccraddock.github.io/cluster_roi/ for more information.

Critical Zone Observatories
type: Resource
type: NamedIndividual
has db xref: nlx_154707
synonym: National CZO
synonym: US NSF National CZO program
abbrev: CZO
IAO_0000115: Data related to the National Critical Zone Observatory Program including in-situ environmental sensors, field instruments, remote sensing, and surface and subsurface imaging. The Program serves the international scientific community through research, infrastructure, data, and models. They focus on how components of the Critical Zone interact, shape Earth's surface, and support life. A primary goal is to develop high-resolution 4D datasets that inform our theoretical framework, constrain our conceptual and coupled systems models, and test our model-generated hypotheses. They are developing cross-CZO capabilities to easily share, integrate, analyze and preserve the wide range of multi-disciplinary data generated by CZOs.

Neisseria meningitidis MC58 Genome Page
type: Resource
type: NamedIndividual
has db xref: nif-0000-20964
synonym: NMMGP
IAO_0000115: Portal contains detailed information for Neisseria meningitidis MC58. Information include DNA molecule summary, primary annotation summary, and taxonomy. It is a tool that allows the researcher to access all of the bacterial genome sequences completed to date. Users may access information on all of the bacterial genomes or any subset of them. Information in the website about its DNA molecule includes: total number of DNA molecules, total size of all DNA molecules, number of primary annotation coding bases, and number of G + C bases. Its primary annotation summary include: total genes, protein coding genes, tRNA genes, and rRNA genes. Sponsors: The CMR was previously funded by two grants, one from the U.S. Department of Energy (DOE) and one from the National Science Foundation (NSF). It is currently partially funded by a Microbial Sequence Center (MSC) grant from the National Institute of Allergy and Infectious Diseases (NIAID)

Incorporated Research Institutions for Seismology
type: Organization
type: NamedIndividual
has db xref: DOI:10.7914
has db xref: DOI:10.17611
has db xref: DOI:10.17616/R3X607
has db xref: DOI:10.25504/FAIRsharing.x9rqf7
has db xref: grid.300201.0
has db xref: ISNI: 0000 0004 6078 0424
has db xref: nlx_154710
has db xref: Wikidata: Q16074398
synonym: IRIS Consortium
abbrev: IRIS
IAO_0000115: Passive and active source waveform data, event (earthquake) catalog, channel response data is available. This comprehensive data store of raw geophysical time-series data is collected from a large variety of sensors, courtesy of a vast array of US and International scientific networks, including seismometers (permanent and temporary), tilt and strain meters, infrasound, temperature, atmospheric pressure and gravimeters, to support basic research aimed at imaging the Earth's interior. IRIS also provides data and software for educational purposes. This consortium of over 100 US universities is dedicated to the operation of science facilities for the acquisition, management, and distribution of seismological data. IRIS programs contribute to scholarly research, education, earthquake hazard mitigation, and verification of the Comprehensive Nuclear-Test-Ban Treaty. Data is stored at the IRIS Data Management Center in Seattle, Washington. They currently manage a large archive from over tens of thousands of seismic stations and ship hundreds of terabytes of data yearly.

Library of Experimental Phase Relations
type: Resource
type: NamedIndividual
has db xref: nlx_154711
has db xref: r3d100012548
synonym: LEPR - Library of Experimental Phase Relations
abbrev: LEPR
IAO_0000115: Database of results of published experimental studies involving liquid-solid phase equilibria relevant to natural magmatic systems.

Tokyo Metropolitan Institute of Medical Science; Tokyo; Japan
type: Organization
type: NamedIndividual
has db xref: grid.272456.0
has db xref: nlx_144090
synonym: RINSHOKEN
synonym: Tokyo Metropolitan Institute of Medical Science
IAO_0000115: Scientific institute in Japan that promotes project-based research, targeted research initiatives for clinically-relevant questions on cancer, and dissemination of information to the research community and public.

OpenTopography
type: Resource
type: NamedIndividual
has db xref: nlx_154717
has db xref: r3d100010655
synonym: NSF OpenTopography Facility
synonym: Open Topography
synonym: OpenTopography Facility
abbrev: OpenTopo
IAO_0000115: Accepts and provides access to high-resolution (meter to sub-meter scale) Earth science-oriented topography data (e.g. LiDAR) and bathymetric data, and related tools and resources. The OpenTopography Tool Registry provides a community populated clearinghouse of software, utilities, and tools oriented towards high-resolution topography data (e.g. collected with LiDAR technology) handling, processing, and analysis. Tools registered range from source code to full-featured software applications. Contributions to the registry via the Contribute a Tool page are welcome. OpenTopography also hosts a dataset catalog to which users can register datasets hosted elsewhere; these entries are discoverable by users alongside OpenTopography hosted datasets. Lidar point cloud data are available in LAS, LAZ and ASCII formats. Raster datasets and derived products can be downloaded in Arc ASCII, IMG, and GeoTIFF formats. Derived products and visualizations are available in Google Earth KML format. The OpenTopography user community and advisory committee provides feedback to define the scope of collaborations on data hosting and cyberinfrastructure development

flowCore
type: Resource
type: NamedIndividual
has db xref: OMICS_05596
synonym: flowCore: Basic structures for flow cytometry data
IAO_0000115: A Bioconductor software package for high throughput flow cytometry that provides S4 data structures and basic functions.

Community Structure-Activity Resource
type: Resource
type: NamedIndividual
has db xref: nlx_154720
abbrev: CSAR
IAO_0000115: Experimental datasets of crystal structures and binding affinities for diverse protein-ligand complexes. Some datasets are generated in house while others are collected from the literature or deposited by academic labs, national centers, and the pharmaceutical industry. For the community to improve their approaches, they need exceptional datasets to train scoring functions and develop new docking algorithms. They aim to provide the highest quality data for a diverse collection of proteins and small molecule ligands. They need input from the community in developing target priorities. Ideal targets will have many high-quality crystal structures (apo and 10-20 bound to diverse ligands) and affinity data for 25 compounds that range in size, scaffold, and logP. It is best if the ligand set has several congeneric series that span a broad range of affinity, with low nanomolar to mid-micromolar being most desirable. They prefer Kd data over Ki data over IC50 data (no % activity data). They will determine solubility, pKa, logP/logD data for the ligands whenever possible. They have augmented some donated IC50 data by determining Kon/Koff and ITC data.

EarthChem
type: Resource
type: NamedIndividual
has db xref: nlx_154721
has db xref: r3d100011538
synonym: IEDA: EarthChem
IAO_0000115: Accepts and makes available geochemical, geochronlogical, and petrological data (analytical and synthesis) through this community-driven effort to facilitate the preservation, discovery, access and visualization of data generated. * PetDB holds geochemical data from sub-oceanic igneous and metamorphic rocks generated at mid-ocean ridges including back-arc basins, young seamounts, and old oceanic crust. Data are compiled primarily from the published literature. * SedDB integrates marine and terrestrial sediment geochemical data compiled primarily from the published literature. * Deep Lithosphere Data Set contains geochemical and petrological data from lower crust and upper mantle xenoliths. (more info) * VentDB contains hydrothermal spring geochemistry that hosts and serves the full range of compositional data acquired on seafloor hydrothermal vents from all tectonic settings. * NAVDAT - The Western North American Volcanic and Intrusive Rock Database * Geochron is an application that helps with the onerous task of data management for geochronological and thermochronological studies. * EarthChemPortal is the one-stop-shop for geochemical data that gives users the ability to search federated databases PetDB, NAVDAT, and GEOROC simultaneously, integrated into a common output format. (more info) * The EarthChem Library is a repository for geochemical datasets (analytical data, experimental data, synthesis databases) and other digital resources relevant to the field of geochemistry, contributed by the geochemistry community. * SESAR - System for Earth SAmple Registration

MetPetDB
type: Resource
type: NamedIndividual
has db xref: nlx_154722
has db xref: r3d100012514
IAO_0000115: Database / data repository for metamorphic petrology that is being designed and built by a global community of metamorphic petrologists in collaboration with computer scientists at Rensselaer Polytechnic Institute as part of the National Cyberinfrastructure Initiative.

PetDB
type: Resource
type: NamedIndividual
has db xref: nlx_154723
has db xref: r3d100011235
synonym: PetDB - the Petrological Database
IAO_0000115: Accepts and provides access to geochemical and petrological data for ocean floor igneous and metamorphic rocks, (whole rock, volcanic, glass, mineral, and melt inclusion analyses), and mantle and lower-crustal xenolith samples. Data are compiled primarily from the published literature. Authors are encouraged to submit their datasets and databases to EarthChem.

SedDB
type: Resource
type: NamedIndividual
has db xref: nlx_154724
has db xref: r3d100011534
IAO_0000115: Geochemical database for marine and terrestrial sediments primarily from the published literature containing a full range of analytical values for sediment samples, primarily from marine sediment cores. It includes major and trace element concentrations, radiogenic and stable isotope ratios, and data for a plethora of materials such as organic and inorganic components, leachates, and size fractions. SedDB also archives a vast array of metadata relating to the individual sample.

UCL Medical School; London; United Kingdom
type: Organization
type: NamedIndividual
has db xref: nlx_143837
synonym: UCL Medical School
synonym: University College London Medical School
IAO_0000115: Medical school at the University College London that provides undergraduate and postgraduate medical education programs, educational research, and specializations in variety of medical subfields.

Polar Rock Repository
type: Resource
type: NamedIndividual
has db xref: nlx_154740
has db xref: r3d100011627
synonym: Polar Rock Repository Database
synonym: U.S. Polar Rock Repository
abbrev: PRR
IAO_0000115: National facility for permanent curatorial preservation of rock collections from Antarctica and Southern Ocean. Repository preserves existing rock/dredge/unconsolidated/terrestrial core/photo archive collections for research use. Database allows online requests for sample loans. Mapping tool combines existing PRR database with high resolution satellite images of Antarctica, REMA or USGS topographic layers. PRR created Polar Rock Boxes for educators who are teaching about Earth science and Antarctica. Each Polar Rock Box contains samples with binder full of teaching information about Earth science and Antarctica. These boxes are freely available as short loans to US schools.

Antarctic Marine Geology Research Facility
type: Resource
type: NamedIndividual
has db xref: nlx_154735
synonym: Antarctic Research Facility
abbrev: AMGRF
abbrev: ARF
IAO_0000115: National repository for geological materials collected in polar regions housing over 20,000 meters of deep-sea core sediment and over 5,000 kg of dredge, trawl, and grab samples, the largest such Southern Ocean collection in the world. These materials have been acquired from over 90 USAP research vessel cruises. The Facility also houses and curates nearly 3,000 meters of rotary cored geological material acquired by NSF supported drilling programs in the Antarctic. Replacement cost of this core inventory in terms of ship and ice-based drilling is conservatively estimated to be in the range of $150 to $200M. SESAR or the the System for Earth Sample Registration is a service provided by the IDEA. SESAR operates the registry that distributes the International Geo Sample Number IGSN. SESAR catalogs and preserves sample metadata profiles, and provides access to the sample catalog via the Global Sample Search. Facility services include: * curation of the existing collections at the facility * onsite ship and land based curatorial services * receipt and processing of new cores * core description and publication of core descriptions * distribution of samples from the collection to authorized scientists * hosting of scientific meetings and workshops * tours, lectures, and student education and training in Antarctic geoscience * maintenance of: ** a core and sample database ** an Antarctic geology and marine geology reference library and a searchable End Note computer database of the entire collection ** a satellite IODP/MRC for nannofossils and diatoms

ARK-Genomics: Centre for Functional Genomics
type: Resource
type: NamedIndividual
has db xref: nif-0000-20966
has db xref: SciEx_157
synonym: ARK Genomics
synonym: Roslin Institute ARK-Genomics
IAO_0000115: Portal for studies of genome structure and genetic variation, gene expression and gene function. Provides services including DNA sequencing of model and non-model genomes using both Next Generation and Sanger sequencing , Gene expression analysis using both microarrays and Next Generation Sequencing, High throughput genotyping of SNP and copy number variants, Data collection and analysis supported in-house high performance computing facilities and expertise, Extensive EST clone collections for a number of animal species, all of commercially available microarray tools from Affymetrix, Illumina, Agilent and Nimblegen, Parentage testing using microsatellites and smaller SNP panels. ARK-Genomics has developed network of researchers whom they support through each stage of their genomics research, from grant application, experimental design and technology selection, performing wet laboratory protocols, through to analysis of data often in conjunction with commercial partners.

National Lacustrine Core Facility
type: Resource
type: NamedIndividual
has db xref: nlx_154737
synonym: Limnological Research Center LacCore Facility
synonym: LRC LacCore Facility
abbrev: LacCore
IAO_0000115: Archive of almost 20,000 meters of high quality sediment cores from large and small expeditions to lakes all around the world. LacCore advocates for, coordinates, and facilitates core-based research on Earth's continents through collaborative support for logistics, field and laboratory, and data and sample curation and dissemination. They provide a wide variety of fee-based analytical services, as well as offer training and instrument time to lab visitors. They also develop Standard Operating Procedures (SOPs) for local training and adoption by individuals at other labs.

Lamont-Doherty Core Repository
type: Resource
type: NamedIndividual
has db xref: DOI:10.17616/R3PV10
has db xref: DOI:10.26022
has db xref: nlx_154738
synonym: Lamont -Doherty Earth Observatory
synonym: LDEO Core Repository
synonym: LDEO-Deep Sea Sample Repository
abbrev: LDCR
abbrev: LDEO-DSSR
IAO_0000115: Core repository and one of the world's most unique and important collections of scientific samples from the deep sea. Sediment cores from every major ocean and sea are archived at the Core Repository. The collection contains approximately 72,000 meters of core composed of 9,700 piston cores; 7,000 trigger weight cores; and 2,000 other cores such as box, kasten, and large diameter gravity cores. They also hold 4,000 dredge and grab samples, including a large collection of manganese nodules, many of which were recovered by submersibles. Over 100,000 residues are stored and are available for sampling where core material is expended. In addition to physical samples, a database of the Lamont core collection has been maintained for nearly 50 years and contains information on the geographic location of each collection site, core length, mineralogy and paleontology, lithology, and structure, and more recently, the full text of megascopic descriptions. Samples from cores and dredges, as well as descriptions of cores and dredges (including digital images and other cruise information), are provided to scientific investigators upon request. Materials for educational purposes and museum displays may also be made available in limited quantities when requests are adequately justified. Various services and data analyses, including core archiving, carbonate analyses, grain size analyses, and RGB line scan imaging, GRAPE, P-wave velocity and magnetic susceptibility runs, can also be provided at cost. The Repository operates a number of labs and instruments dedicated to making fundamental measurements on material entering the repository including several non-destructive methods. Instruments for conducting and/or assisting with analyses of deep-sea sediments include a GeoTek Multi-Sensor Core Logger, a UIC coulometer, a Micromeritics sedigraph, Vane Shear, X-radiograph, Sonic Sifter, freeze dryer, as well as a variety of microscopes, sieves, and sampling tools. They also make these ins…

Smithsonian Mineral Sciences Collections
type: Resource
type: NamedIndividual
has db xref: nlx_154739
synonym: Smithsonian Institution Mineral Sciences Collections
synonym: Smithsonian Institution National Museum of Natural History Mineral Sciences Collections
IAO_0000115: National facility for curating meteorite, rock, ore, gem, and mineral specimens that are available to the public via a standard web interface. New records and associated images are added continuously and are made available on an approximately monthly basis. There are currently over 350,000 records available. Every year hundreds of specimens are loaned to scientists around the world for research projects in geology, materials science, health, chemistry, physics, etc.

Cluster reporter
type: Resource
type: NamedIndividual
has db xref: nlx_155532
IAO_0000115: This matlab script and associated files will take resultant statistical images and essentially output everything you could ever want to know. It can work off of images that were previously corrected for multiple comparisons, but it can actually do the correction itself. This is because the cluster_correct script is incorporated within. It will iterate through atlases (borrowed from other software) to tell you the location of significant results. It outputs an extremely detailed report as well as a summary table for quick investigation. In addition, it will output statistics for each surviving cluster, and the image as a whole. Feedback would be much appreciated.

Antarctic Glaciological Data Center
type: Resource
type: NamedIndividual
has db xref: nlx_154741
has db xref: r3d100011579
synonym: Antarctic Glaciological Data Center at NSIDC
synonym: Antarctic Glaciological Data Center at the National Snow and Ice Data Center
abbrev: AGDC
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2, 2025. Archives and distributes Antarctic glaciological and cryospheric system data collected by the U.S. Antarctic Program. The Data Catalog contains data sets collected by individual investigators and products assembled from many different PI data sets, published literature, and other sources. The catalog provides useful compilations of important geophysical parameters, such as accumulation rate or ice velocity. The NSF OPP Guidelines and Award Conditions for Scientific Data state that PIs should submit data collected as a result of their OPP grant to a designated data center as soon as possible, but no later than two years after the data are collected.

National Snow and Ice Data Center
type: Resource
type: NamedIndividual
has db xref: DOI:10.5067/
has db xref: DOI:10.7265
has db xref: DOI:10.17616/R3HP4V
has db xref: DOI:10.25504/FAIRsharing.k9vqye
has db xref: nlx_154742
synonym: National Snow & Ice Data Center
abbrev: NSIDC
IAO_0000115: National data center / repository for snow and ice data including snow, ice, glaciers, frozen ground, and climate interactions that make up Earth's cryosphere. The center manages and distributes scientific data, creates tools for data access, supports data users, performs scientific research, and educates the public about the cryosphere. Users may explore the Earth's frozen places in the collection of photographs and images. Photographs from field research trips, images captured by satellites of the changing cryosphere, and photos and images are available. Data sets are organized into the following groups: sea ice, frozen ground, snow cover, snow hydrology, glaciers and ice sheets, arctic people.

U.S. Antarctic Program Data Coordination Center
type: Resource
type: NamedIndividual
has db xref: nlx_154744
has db xref: r3d100010660
abbrev: USAP-DCC
IAO_0000115: Assists scientists in finding Antarctic scientific data of interest and submitting data for long-term preservation in accordance with their obligations under the National Science Foundation (NSF) Office of Polar Programs (OPP) Data Policy.

System for Earth Sample Registration
type: Resource
type: NamedIndividual
has db xref: nlx_154747
has db xref: r3d100010420
abbrev: SESAR
IAO_0000115: Sample Catalog and Registry for the International Geo Sample Number. SESAR catalogs and preserves sample metadata profiles, and provides access to the sample catalog via the Global Sample Search.

Arvados
type: Resource
type: NamedIndividual
has db xref: OMICS_01835
abbrev: arvados
IAO_0000115: Bioinformatics platform for storing, organizing, processing, and sharing genomic and other biomedical big data. Designed to make it easier for bioinformaticians to develop analyses, developers to create genomic web applications and IT administers to manage large-scale compute and storage genomic resources. Designed to run on top of cloud operating systems such as Amazon Web Services and OpenStack. Currently, there are implementations that work on AWS and Xen+Debian/Ubuntu. Functionally, Arvados has two major sets of capabilities: (a) data management and (b) compute management.

flowMerge
type: Resource
type: NamedIndividual
has db xref: OMICS_05605
synonym: flowMerge - Cluster Merging for Flow Cytometry Data
IAO_0000115: Software for merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework.

RankAggreg
type: Resource
type: NamedIndividual
has db xref: OMICS_03526
synonym: RankAggreg: Weighted rank aggregation
IAO_0000115: Software package that performs aggregation of ordered lists based on the ranks using several different algorithms: Borda count, Cross-Entropy Monte Carlo algorithm, Genetic algorithm, and a brute force algorithm.

Cluster Extent Correction
type: Resource
type: NamedIndividual
has db xref: nlx_155531
IAO_0000115: This script will take any .img file and correct it based on a cluster extent, cluster definition and voxelwise threshold. The threshold entered will be applied to positive and negative values separately, and separate pos and neg corrected images will be output. This script requires a license for the matlab image processing toolbox.

4D Atlases Construction
type: Resource
type: NamedIndividual
has db xref: nlx_155688
synonym: 4D Atlas Construction
synonym: 4D Atlas Construction Toolbox
IAO_0000115: Software package for constructing longitudinal atlases, which are the necessary steps for many brain-related applications.

GRBio
type: Resource
type: NamedIndividual
has db xref: nlx_155523
synonym: Global Registry of Biorepositories
IAO_0000115: Database of biological collections in natural history museums, herbaria, and other biorepositories resulting from a merger of Index Herbariorum (IH), Biodiversity Collections Index (BCI) and biorepositories.org. It contains more than 14,000 records for biorepository institutions, their collections, and staff members. Their two main goals are to improve access to information about biorepositories, the collections and specimens they house, and the researchers and collection managers who work there; and to facilitate electronic linkages to this information through web services that will rely on unique identifiers assigned to biorepositories and collections. The Consortium for the Barcode of Life (CBOL) has developed and will manage GRBio in collaboration with IH and BCI and in consultation with GBIF and NCBI. GRBio includes four categories of data records that provide information on: * Institutional repositories such as museums, herbaria, botanical gardens, zoos, biomedical research institutes and culture centers; * Institutional collection records such as the bird, algal or insect collections within an institutional repository; * Personal collections such as field samples held by a researcher before they have been accessioned into an institutional collection, or privately owned specimens held by non-researchers; and * Staff members at institutional repositories GRBio operates as a moderated community-curated resource. The community is invited to check and update their records and to register institutions, collections and staff members that have not already been registered. GRBio offers registration of institutional collections, "personal" research collections that have not yet been accessioned into an institutional repository, and privately owned collections.

OpenBioinformatics.org
type: Resource
type: NamedIndividual
has db xref: nlx_155524
synonym: OpenBioinformatics.org: An open bioinformatis software repository
IAO_0000115: An open bioinformatis software repository with no tie to any organization or institution. Contact them to host your software.

NIfTImatlab
type: Resource
type: NamedIndividual
has db xref: nlx_155526
synonym: NYU CBI NIfTI Matlab tool
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28, 2025. Software tool that allows the user to operate on NIfTI image files from Matlab.

ConsensusPathDB
type: Resource
type: NamedIndividual
has db xref: nif-0000-02684
has db xref: OMICS_01903
has db xref: r3d100012822
synonym: ConsensusPathDB-human
abbrev: CPDB
IAO_0000115: An integrative interaction database that integrates different types of functional interactions from heterogeneous interaction data resources. Physical protein interactions, metabolic and signaling reactions and gene regulatory interactions are integrated in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. With human, yeast and mouse complex functional interactions, it currently constitutes the most comprehensive publicly available interaction repository for these species. Different ways of utilizing these integrated interaction data, in particular with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways is offered.

CIGAL
type: Resource
type: NamedIndividual
has db xref: nlx_155528
synonym: Compilable Imaging Graphics and Analytical Language
IAO_0000115: Software program that provides accurate real-time stimulus control, behavioral and physiological recording, and synchronization with external devices. It can also provide continuous real-time feedback of task performance and physiological responses. Task programming typically involves a simple text file specifying basic parameter settings (e.g. screen color) and a list of stimulus events, which can include images, animated movies, sound files, text stimuli, video graphics, or commands that communicate with external hardware devices. Multiple video and auditory stimuli can be presented simultaneously. Multi-channel response recording and real-time feedback features require no user programming. Advanced users can add customized stimulus events using CIGAL's real-time programming capabilities. Output files can be automatically created in a variety of output formats (e.g. FSL 3-column files, XML Events files, CSV trial tables).

CleanLine
type: Resource
type: NamedIndividual
has db xref: nlx_155529
IAO_0000115: An EEGLAB plugin which adaptively estimates and removes sinusoidal artifacts from independent component analysis (ICA) components or scalp channels using a frequency-domain (multi-taper) regression technique with a Thompson F-statistic for identifying significant sinusoidal artifacts. This approach has been advocated by Partha Mitra and Hemant Bokil (Observed Brain Dynamics, Chapter 7.3.4., 2007) and CleanLine utilizes modified routines from the Mitra Lab's Chronux Toolbox (www.chronux.org). Sinusoidal noise can be a prominent artifact in recorded electrophysiological data. This can stem from AC power line fluctuations (e.g. 50/60 Hz line noise + harmonics), power suppliers (e.g. in medical equipment), fluorescent lights, etc. Notch filtering is generally undesirable due to creation of band-holes, and significant distortion of frequencies around the notch frequency (as well as phase distortion at other frequencies and Gibbs rippling in the time-domain).

Computational Morphometry Toolkit
type: Resource
type: NamedIndividual
has db xref: nlx_155536
synonym: Computational Morphometry Toolkit (CMTK)
abbrev: CMTK
IAO_0000115: A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O. The command line tools primarily provide the following functionality: registration (affine and nonrigid; single and multi-channel; pairwise and groupwise), image correction (MR bias field estimation; interleaved image artifact correction; EPI unwarping), processing (filters; combination of segmentations via voting and STAPLE; shape-based averaging), statistics (t-tests; general linear model). CMTK is implemented in C++ with parallel processing using POSIX Threads (SMP), OpenMP (SMP), Grand Central Dispatch (SMP), and CUDA (GPU). Supported file formats include Analyze (r/w), NIFTI (r/w), Nrrd (r/w), DICOM (read), BioRad (read). Data exchange with other toolkits, such as ITK, FSL, AFNI, SPM, etc. is thus easily accomplished.

Cognitive Paradigm Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_155537
abbrev: CogPO
IAO_0000115: Ontology used to describe the experimental conditions within cognitive and behavioral experiments, primarily in humans for application and use in the functional neuroimaging community. CogPO has been developed through the integration of the Functional Imaging Biomedical Informatics Research Network (FBIRN) Human Imaging Database (HID) and the BrainMap Database. The design of CogPO concentrates on what can be observed directly: categorization of each paradigm in terms of (1) the stimulus presented to the subjects, (2) the requested instructions, and (3) the returned response.

UD Chick EST Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-20971
synonym: U.D. Chick EST Database
synonym: University of Delaware Chick EST Database
synonym: University of Delaware Chick EST Project
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. A chicken EST Web site has been created to provide access to the data, and a set of unique sequences has been deposited with GenBank. This site contains over 40,000 EST sequences from the chicken cDNA libraries in the University of Delaware collection. Users can perform keyword searches, BLAST nucleotide sequences against our database, view clusters of similar or overlapping clones, and order clones. The cDNA and gene sequences of many mammalian cytokines and their receptors are known. However, corresponding information on avian cytokines is limited due to the lack of cross-species activity at the functional level or strong homology at the molecular level. To improve the efficiency of identifying cytokines and novel chicken genes, a directionally cloned cDNA library from T-cell-enriched activated chicken splenocytes was constructed, and the partial sequence of 5251 clones was obtained. Sequence clustering indicates that 2357 (42%) of the clones are present as a single copy, and 2961 are distinct clones, demonstrating the high level of complexity of this library. Comparisons of the sequence data with known DNA sequences in GenBank indicate that approximately 25% of the clones match known chicken genes, 39% have similarity to known genes in other species, and 11% had no match to any sequence in the database. Several previously uncharacterized chicken cytokines and their receptors were present in our library. This collection provides a useful database for cataloging genes expressed in T cells and a valuable resource for future investigations of gene expression in avian immunology. Therefore, the Chick EST database was created.

Zebrafish Information Server
type: Resource
type: NamedIndividual
has db xref: nif-0000-21003
abbrev: ZIS
IAO_0000115: A portal to different zebrafish resources such as jobs, book, journals, database, meetings, and K-12 programs. Most information leads to ZFIN: The Zebrafish Model Organism Database.

aBEAT
type: Resource
type: NamedIndividual
has db xref: nlx_155542
has db xref: nlx_155840
synonym: aBEAT: A Toolbox for Consistent Analysis of Longitudinal Adult Brain MRI
synonym: Adult Brain Extraction and Analysis Toolbox
IAO_0000115: A 4D adult brain extraction and analysis toolbox with graphical user interfaces to consistently analyze 4D adult brain MR images. Single-time-point images can also be analyzed. Main functions of the software include image preprocessing, 4D brain extraction, 4D tissue segmentation, 4D brain labeling, ROI analysis. Linux operating system (64 bit) is required. A computer with 8G memory (or more) is recommended for processing many images simultaneously. The graphical user interfaces and overall framework of the software are implemented in MATLAB. The image processing functions are implemented with the combination of C/C++, MATLAB, Perl and Shell languages. Parallelization technologies are used in the software to speed up image processing.

MAIA (Microarray Image Analysis)
type: Resource
type: NamedIndividual
has db xref: OMICS_00843
synonym: Microarray Image Analysis
abbrev: MAIA
IAO_0000115: Software package for automatic processing of the one- and two- (typically, Cy3-green/Cy5-red) color images produced in cDNA, CGH (comparative genome hybridization) or protein microarray technologies. It incorporates the following modules: * The spot localization module (i) identifies the position of each spot on the array, so that the name of the spotted clone can be associated with the correspondent spot; and (ii) establishes the borders between the neighborhood spots letting one to perform further data processing procedures (i.e. to extract quantitative information) for each spot independently of the other neighborhood spots. Visually this results in the generation of a grid covering the image. The spot localization algorithm is fully automatic and robust with respect to deviations from perfect spot alignment and contamination. As an input, it requires only the common array design parameters: number of blocks and number of spots in the x and y directions of the array. * The spot quantification module for one-color images performs segmentation of the spots and estimates the averaged spot and local background intensities. The spot quantification module for two-color images estimates the ratio of the measured intensities in the two color channels at each spot reflecting differential gene (cDNA technology) or protein expression or a change in DNA copy number (CGH experiments) between the test and control samples for the corresponding gene. This module includes algorithms based on the linear regression and segmentation of the spots. A special procedure for detection and removal of the aberrant pixels has been developed to make ratio estimates more resistant to array contamination. It ensures more consistent ratio estimates obtained from different algorithms, and allows delivery of a single trustable ratio value. * The quality control module provides a value of spot quality reflecting the level of confidence in the obtained quantitative estimates at each spot. These qua…

edX
type: Resource
type: NamedIndividual
has db xref: nlx_155551
IAO_0000115: Massive, open, online courses (MOOCs) and interactive online classes in subjects including law, history, science, engineering, business, social sciences, computer science, public health, and artificial intelligence (AI). This non-profit was created by founding partners Harvard and MIT bringing the best of higher education to students around the world. Online courses are designed to be interesting, fun and rigorous. They are the best online courses, from the best professors and the best schools, spanning dozens of subjects. Some edX courses now offer ID verified Certificates of Achievement. A new way to demonstrate your achievement and showcase your knowledge.

Human Brain Project EU
type: Resource
type: NamedIndividual
has db xref: nlx_155553
synonym: European Human Brain Project
abbrev: European HBP
abbrev: HBP
abbrev: HBP EU
IAO_0000115: Global, collaborative effort for neuroscience, medicine and computing to understand brain, its diseases and its computational capabilities. Goal is to obtain access to research, data sources, platforms and infrastructures offered by other organisations, and enabling organizations outside HBP to use HBP platforms to pursue their own research. Coordinating these activities is the responsibility of the European Research Programme.

Fly EM
type: Resource
type: NamedIndividual
has db xref: nlx_155555
synonym: Fly EM Project
abbrev: FlyEM
IAO_0000115: A project producing datasets, software, and algorithms that is developing the technology to produce connectomes at the electron microscopic level of behaviorally-relevant neural circuits as well as the entire Drosophila nervous system. This technology will enable them to create a map of every neuron and synapse in the Drosophila nervous system, using novel approaches to electron microscopy (EM) as the foundation. In the same way that the fly genome paved the way for larger projects, including sequencing the human genome, Fly EM may ultimately contribute to our understanding of the human brain by establishing a fly "connectome" a map that shows how all neurons in the fly brain are connected to each other. They began their entry into EM reconstruction with the fly's adult visual system, where much is known about cell types from previous EM and histological studies, as well as ongoing studies in the Fly Light Project. In addition to establishing and publishing a fly connectome, Fly EM will make technology and methodology available that is needed to perform large-scale EM reconstructions. Fly EM will generally pursue an open policy with their datasets, software, and algorithms after relevant publications. When an EM reconstruction is published, the derived connectome and reconstructed neuronal skeletons will be made available online. The raw data and annotatations will be made available upon request as logistics dictate. To encourage further collaboration and scientific discovery, a small fraction of their raw data and corresponding segmentation will be made available independent of publication. Their goal is to enable others who wish to approach the many algorithmic challenges, but who do not have access to an EM facility, to have the data they need to support methods development, as well as their results to use as a benchmark. Fly EM emphasizes publication of supporting techniques and software approaches before major EM reconstruction releases to encourage rapid feedb…

Connectomes.org
type: Resource
type: NamedIndividual
has db xref: nlx_155556
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. Project mapping whole mouse brain connectivity using serial block face scanning electron microscopy (SBF-SEM) with a specially-designed whole-brain microtome (WBM). With any luck, the whole mouse brain will be mapped ultrastructurally in the near term, which will then open the door to more serious problems; reliable automated segmentation and circuit reconstruction. These will undoubtedly require advances in machine learning methods and their application. Connectomics Software and a Multiresolution Image Viewer (MIV) is also available.

RDoC
type: Resource
type: NamedIndividual
has db xref: nlx_155557
synonym: Research Domain Criteria
IAO_0000115: NIMH Strategic Plan developing, for research purposes, new ways of classifying psychopathology based on dimensions of observable behavior and neurobiological measures. In brief, the effort is to define basic dimensions of functioning (such as fear circuitry or working memory) to be studied across multiple units of analysis, from genes to neural circuits to behaviors, cutting across disorders as traditionally defined. The intent is to translate rapid progress in basic neurobiological and behavioral research to an improved integrative understanding of psychopathology and the development of new and/or optimally matched treatments for mental disorders. The various domains of functioning, and their constituent elements, are being defined by an ongoing series of consensus workshops; input from the research community and other interested stakeholders is encouraged.

Hycult Biotech
type: Resource
type: NamedIndividual
has db xref: nlx_152377
synonym: Hycult Biotech inc.
synonym: Hycult Biotechnology
IAO_0000115: Commercial supplier of antibodies and assay kits for biomedical research.

Connectomic reconstruction of the inner plexiform layer in the mouse retina
type: Resource
type: NamedIndividual
has db xref: nlx_155563
abbrev: MPIN Connectomics
IAO_0000115: Data set of the dense reconstruction of 950 neurons and their mutual contacts for the mouse inner plexiform layer--the main computational neuropil region in the mammalian retina. This was achieved by applying a combination of crowd-sourced manual annotation and machine-learning-based volume segmentation to serial block-face electron microscopy data. They characterize a new type of retinal bipolar interneuron and show that they can subdivide a known type based on connectivity. Circuit motifs that emerge from their data indicate a functional mechanism for a known cellular response in a ganglion cell that detects localized motion, and predict that another ganglion cell is motion sensitive. A Data browser is also available for download

QUEST Project
type: Resource
type: NamedIndividual
synonym: QUEST: Quesnellia Exploration Strategy
abbrev: QUEST
IAO_0000115: A program of regional geochemical and geophysical surveys designed to attract the mineral exploration industry to an under-explored region of British Columbia between Williams Lake and Mackenize. The QUEST Project is focused on the Quesnel Terrane, which has good potential for copper and gold porphyry deposits, but in this region is covered by a thick layer of sand and gravel left behind by glaciers. Geoscience BC's QUEST Project included two airborne geophysical surveys: an airborne electromagnetic (EM) survey and an airborne gravity survey, which give insight into the conductivity and density of the rocks. The results of the two airborne surveys are an important tool for industry looking to understand the geology in the QUEST Project area. The QUEST Project also included the reanalysis of almost 5000 archived regional geochemical samples from parts of NTS sheets 93A, B, G, H, K and N, and the collection of 2200 new geochemical samples north and west of Prince George. This new geochemical data is helping industry to identify new exploration targets. Subsequent follow-up work has included analysis and inversion of datasets and updating the regional bedrock geology map.

Brain Bee
type: Resource
type: NamedIndividual
has db xref: nlx_155566
synonym: International Brain Bee
abbrev: IBB
IAO_0000115: A world-wide neuroscience competition for high school students that aims to motivate them to learn about the brain and to pursue neuroscience careers. Brain Bee tests knowledge of the human brain, including topics like intelligence, emotions, memory, sleep, vision, hearing, sensations, Alzheimer's disease, Parkinson's disease, stroke, schizophrenia, epilepsy, depression, addictions and brain research.

Virtual brain
type: Resource
type: NamedIndividual
has db xref: nlx_155567
synonym: The Virtual Brain
synonym: thevirtualbrain
synonym: thevirtualbrain.org
abbrev: tvb
IAO_0000115: Simulation software for modeling the entire human brain by combining structural and functional data from empirical neuroimaging data. It can generate local field potentials, EEG, MEG and fMRI BOLD data based on neural mass models. The user can also modify the model parameters to match clinical conditions from focal lesions or degenerative disorders.

OMICtools
type: Resource
type: NamedIndividual
has db xref: nlx_155571
has db xref: r3d100012426
synonym: genOMIC tools
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented Jul 19, 2024. Metadatabase manually curated that provides web accessible tools related to genomics, transcriptomics, proteomics and metabolomics. Used as informative directory for multi-omic data analysis.

University of Alaska Fairbanks; Alaska; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100005921
has db xref: grid.70738.3b
has db xref: ISNI:0000 0004 1936 981X
has db xref: nlx_156102
has db xref: Wikidata:Q1285262
synonym: UA Fairbanks
synonym: University of Alaska Fairbanks
abbrev: UAF
IAO_0000115: Public research university in Fairbanks, Alaska that offers degree programs in engineering, liberal arts, fisheries and ocean sciences, and rural and community development.

MR Connectome Automated Pipeline
type: Resource
type: NamedIndividual
has db xref: nlx_155575
synonym: Magnetic Resonance Connectome Automated Pipeline
synonym: MR Connectome Automated Pipeline (MRCAP)
abbrev: MRCAP
IAO_0000115: Based on JIST and MIPAV, this pipeline combines structural magnetic resonance data with diffusion tensor imaging to estimate a connectome, which is a comprehensive description of the wiring diagram of the brain.

Influential references dataset
type: Resource
type: NamedIndividual
has db xref: nlx_155576
IAO_0000115: A dataset of 100 annotated papers for use in text mining applications, that includes the importance of each reference compared to other references. Useful for natural language processing, machine learning or bibliometrics. To collect the annotations, authors of a paper were asked to determine whether a given reference had a strong influence on their research. In a blog post on March 20th 2012, authors were invited to help create a gold-standard dataset of labeled references. Data are available for download.

CORUM
type: Resource
type: NamedIndividual
has db xref: nif-0000-02688
has db xref: OMICS_01904
has db xref: r3d100011272
synonym: CORUM - the Comprehensive Resource of Mammalian protein complexes
synonym: CORUM the Comprehensive Resource of Mammalian protein complexes
IAO_0000115: Database of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, but data from high-throughput experiments is excluded. The majority of protein complexes in CORUM originates from man (65%), followed by mouse (14%) and rat (14%)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

CoryneRegNet
type: Resource
type: NamedIndividual
has db xref: biotools:coryneregnet
has db xref: nif-0000-02689
has db xref: OMICS_01858
IAO_0000115: Reference database and analysis platform for corynebacterial transcription factors and gene regulatory networks. It generates links to genome annotations, to identified transcription factors and to the corresponding cis-regulatory elements. CoryneRegNet is based on a multi-layered, hierarchical and modular concept of transcriptional regulation and was implemented by using the relational database management system MySQL and an ontology-based data structure.

NHGRI Dog Genome Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-20975
synonym: National Human Genome Research Institute Dog Genome Project
IAO_0000115: The Dog Genome Project at the National Human Genome Research Institute is working to develop resources necessary to map and clone canine genes in an effort to utilize dogs as a model system for genetics and cancer research. The US National Human Genome Research Institute (NHGRI) agreed to fund a project to sequence the entire genome of a boxer dog named Tasha, because it recognized the value of the dog as an unrivaled model for the study of human disease. The National Human Genome Research Institute (NHGRI) led the National Institutes of Health's (NIH) contribution to the International Human Genome Project, which had as its primary goal the sequencing of the human genome. This project was successfully completed in April 2003. Now, the NHGRI's mission has expanded to encompass a broad range of studies aimed at understanding the structure and function of the human genome and its role in health and disease. To that end NHGRI supports the development of resources and technology that will accelerate genome research and its application to human health. A critical part of the NHGRI mission continues to be the study of the ethical, legal and social implications (ELSI) of genome research. NHGRI also supports the training of investigators and the dissemination of genome information to the public and to health professionals.

FlyMove
type: Resource
type: NamedIndividual
has db xref: nif-0000-20976
synonym: Fly Move
IAO_0000115: Database combining movies, animated schemata, interactive modules and pictures that will greatly facilitate the understanding of Drosophila development. The resource is aimed at university students and teachers of developmental biology classes. Contribute your own movies, images and illustrations to FlyMove. Illustrating developmental processes using first hand research data will allow students to gain a better understanding of the real organism, and it will allow you to draw their attention to your field of research and to your group. All donors of media integrated in FlyMove will be cited and links to their homepages will be made.

Kindai University School of Medicine; Osaka; Japan
type: Organization
type: NamedIndividual
has db xref: nlx_149307
synonym: Kinki University School of Medicine
IAO_0000115: Medical school division of Kindai University with a resident-centered approach to medicine.

miso-lims
type: Resource
type: NamedIndividual
has db xref: OMICS_01007
synonym: MISO: An open source LIMS for small-to-large scale sequencing centres
synonym: MISO: An open-source LIMS for NGS sequencing centres
abbrev: MISO
IAO_0000115: Open source software for a Laboratory Information Management System (LIMS) for NGS sequencing centres.

COSMIC - Catalogue Of Somatic Mutations In Cancer
type: Resource
type: NamedIndividual
has db xref: biotools:cosmic
has db xref: nif-0000-02690
has db xref: OMICS_00082
synonym: Catalogue Of Somatic Mutations In Cancer
abbrev: COSMIC
IAO_0000115: Database to store and display somatic mutation information and related details and contains information relating to human cancers. The mutation data and associated information is extracted from the primary literature. In order to provide a consistent view of the data a histology and tissue ontology has been created and all mutations are mapped to a single version of each gene. The data can be queried by tissue, histology or gene and displayed as a graph, as a table or exported in various formats. Some key features of COSMIC are: * Contains information on publications, samples and mutations. Includes samples which have been found to be negative for mutations during screening therefore enabling frequency data to be calculated for mutations in different genes in different cancer types. * Samples entered include benign neoplasms and other benign proliferations, in situ and invasive tumours, recurrences, metastases and cancer cell lines.

CPDB - the Circular Permutation Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02693
synonym: Circular Permutation Database
abbrev: CPDB
IAO_0000115: A database of circular permutation (CP) in proteins that provides resources for studying circular permutation (CP) and circular permutation relationships among protein structures. This site also offers viable CP site predictions in order to facilitate the application of CP in academic researches and biotechnological developments.<BR / The organizational principle of CPDB is a hierarchical categorization in which pairs of circular permutants are grouped into CP clusters, which are further grouped into folds and in turn classes. Additions to CPDB include a useful set of tools and resources for the identification, characterization, comparison and visualization of CP. Besides, several viable CP site prediction methods are implemented and assessed in CPDB. This database can be useful in protein folding and evolution studies, the discovery of novel protein structural and functional relationships, and facilitating the production of new CPs with unique biotechnical or industrial interests.

Parasite Databases of Clustered ESTs
type: Resource
type: NamedIndividual
has db xref: nif-0000-20980
synonym: PDCEST
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. These databases were constructed by extracting the organism specific ESTs from dbEST, removing polyA sequences from the ends and trimming 5' and 3' regions with greater than 25% N's in a 20 base pair window. These quality sequences were then aligned using the cap2 program and the consensus sequences thus generated put into a database that is available on the web. A number of parasitic organisms were chosen that have between 3000 and 15000 ESTs. The attempt here is to provide useful information and analyses to the scientific community without curating the results in any way. A total of 55192 ESTs, deposited into dbEST/GenBank, were included in the analyses. The resulting sequences have been clustered into nonredundant gene assemblies and deposited into a relational database that supports a variety of sequence and text searches. This database has been used to compare the gene assemblies using BLAST similarity comparisons to the public protein databases to identify putative genes. Of these new entries, approximately 15%-20% represent putative homologs with a conservative cutoff of p < 10(-9), thus identifying many conserved genes that are likely to share common functions with other well-studied organisms. Gene assemblies were also used to identify strain polymorphisms, examine stage-specific expression, and identify gene families. An interesting class of genes that are confined to members of this phylum and not shared by plants, animals, or fungi, was identified. These genes likely mediate the novel biological features of members of the Apicomplexa and hence offer great potential for biological investigation and as possible therapeutic targets.

cpnDB: A Chaperonin Database
type: Resource
type: NamedIndividual
has db xref: biotools:cpndb
has db xref: nif-0000-02694
has db xref: OMICS_01511
abbrev: cpnDB
IAO_0000115: A curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. Users can search the database by Chaperonin type, group (I or II), BLAST, or other options, and can also enter and analyze FASTA sequences.

NCI Mouse Repository
type: Resource
type: NamedIndividual
has db xref: nif-0000-20985
synonym: MMHCC
synonym: MMHCC Repository
synonym: Mouse Models of Human Cancers Consortium (MMHCC) Repository
synonym: Mouse Models of Human Cancers Consortium Repository
abbrev: NCIMR
IAO_0000115: The NCI Mouse Repository cryoarchives and distributes strains of genetically engineered mice that are of immediate interest to the cancer research community. These are either gene-targeted or transgenic mice that display a cancer-related phenotype, or tool strains (e.g., cre transgenics) that can be used to develop new cancer models. You do not have to be a member of the NCI Mouse Repository or a recipient of NCI funding to have your mouse model distributed through the NCI Mouse Repository. NCI Mouse Repository strains are maintained as live colonies or cryoarchived as frozen embryos, depending on demand. Up to three breeder pairs may be ordered from live colonies. Cryoarchived strains are supplied as frozen embryos or recovery of live mice by the NCI Mouse Repository may be requested.

Takifugu rubripes Genome
type: Resource
type: NamedIndividual
has db xref: nif-0000-20989
synonym: Fugu genome
abbrev: Fugu
abbrev: Fugu rubripes
abbrev: Takifugu
IAO_0000115: Genome of Takifugu, the Japanese puffer fish. The Fugu genome was sequenced and assembled using the whole genome shotgun method.

Genetic Maps of the Rat Genome
type: Resource
type: NamedIndividual
has db xref: nif-0000-20990
abbrev: Genetic Maps of the Rat
IAO_0000115: Data set of pictures representing genetic linkage maps of the rat resulting from the integration of two F2 intercrosses (SHRSP x BN and FHH x ACI). Markers in common between the two crosses are connected by a line to define integration points. There are a total of 4,786 markers on these maps; 4375 WIBR/MIT CGR markers; 223 markers from the previously released Mit/Mgh rat maps and 188 markers from the National Institute of Arthritis and Musculoskeletal and Skin Diseases Arb rat maps. Pictures are drawn to a scale of 5cm (Kosombi) per inch. The changes in color of the backbone of the chromosome for each cross represents the space between any two framework loci. Markers in blue type are framework loci. Markers in green type are unique placement loci. Markers in black type are bouncy placement loci.

NIH Rat Genomics and Genetics
type: Resource
type: NamedIndividual
has db xref: nif-0000-20991
synonym: RGS
IAO_0000115: The Rat Genome Program was launched after the National Institutes of Health (NIH) realized the potential of rat models in understanding basic biology and human health and disease. The purpose of this NIH Rat Genomics and Genetics web site is to serve as a central point for information on NIH sponsored and related rat genetic and genomic activities and resources. It will provide information on: the follow up to recommendations made to the NIH; funding opportunities for rat genomic and genetic tools and resources; major rat genomic resources available and/or produced in response to the NIH Rat Program; courses and meetings related to rat genomics and genetics; and selected reports and publications. These programs have produced a wide variety of resources and a way to link and capitalize upon the data and resources of other model organisms and the human. In conjunction with and in addition to these programs, the NIH, through the RGWG, has convened advisory groups and workshops to discuss the opportunities that rat models offer and provide recommendations on the investments that are needed to capitalize on these opportunities.

Rice Genome Research Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-20992
IAO_0000115: Rice Genome Research Program (RGP) is an integral part of the Japanese Ministry of Agriculture, Forestry and Fisheries (MAFF) Genome Research Project. RGP now aims to completely sequence the entire rice genome and subsequently to pursue integrated goals in functional genomics, genome informatics and applied genomics. It is jointly coordinated by the National Institute of Agrobiological Sciences (NIAS), a government research institute under MAFF and the Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF), a semi-private research organization managed and supported by MAFF and a consortium of some twenty Japanese companies. The research is funded with yearly grants from MAFF and additional funds from the Japan Racing Association (JRA). It is now the leading member of the International Rice Genome Sequencing Project (IRGSP), a consortium of ten countries sharing the sequencing of the 12 rice chromosomes. The IRGSP adopts the clone-by-clone shotgun sequencing strategy so that each sequenced clone can be associated with a specific position on the genetic map and adheres to the policy of immediate release of the sequence data to the public domain. In December 2004, the IRGSP completed the sequencing of the rice genome. The high-quality and map-based sequence of the entire genome is now available in public databases.

flowMap
type: Resource
type: NamedIndividual
has db xref: OMICS_05600
synonym: flowMap - A probabilistic algorithm for matching and comparing multiple flow cytometry samples
IAO_0000115: Software package that quantifies the similarity of cell populations across multiple flow cytometry samples using a nonparametric multivariate statistical test. The algorithm allows the users to specify a reference sample for comparison or to construct a reference sample from the available data. The output of the algorithm is a set of text files where the cell population labels are replaced by a metaset of population labels, generated from the matching process.

rmeta
type: Resource
type: NamedIndividual
has db xref: OMICS_00245
synonym: rmeta: Meta-analysis
IAO_0000115: Package of software functions for simple fixed and random effects meta-analysis for two-sample comparisons and cumulative meta-analyses. Draws standard summary plots, funnel plots, and computes summaries and tests for association and heterogeneity.

Washington University School of Medicine Neuroscience Tutorial
type: Resource
type: NamedIndividual
has db xref: nif-0000-00113
abbrev: Neuroscience Tutorial
IAO_0000115: An illustrated guide to the essential basics of clinical neuroscience created in conjunction with the first-year course for medical students. Topics covered: * Coronal and horizontal sections * Basic visual pathway * Basic somatosensory pathway * Basic motor pathway * Eye and retina * Central visual pathways * Auditory and vestibular systems * Somatosensory pathways from the body * Somatosensory pathways from the face * Spinal motor structures * Brainstem nuclei of cranial nerves * Basal ganglia and cerebellum * Hypothalamus and autonomic nervous system * Medial temporal lobe and memory * Sleep and language * Where is...?

UK Sheep Genome Mapping Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-20995
synonym: UKSGMP
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The project aims to apply genome mapping research to sheep, utilizing previous research in sheep (in other countries) and in other species (in the UK and abroad) to the benefit of the UK sheep industry. The project itself uses existing breeding structures, knowledge of the sheep genome and experimental resources. It has three main aims: i) To use the Suffolk, Texel and Charollais Sire Referencing Schemes to detect and verify quantitative trait loci (QTLs) for growth and carcass composition traits ii) To investigate candidate genes and/or chromosomal regions for associations with production traits. iii) To investigate approaches for optimizing future genotyping strategies within the sire referencing schemes for practical and cost effective application of marker-assisted selection By using commercial breeding populations for the research, immediate application of beneficial results is possible. Potential benefits include increased genetic progress through marker assisted selection which utilizes the genotype information, correction of possible parentage errors (ultimately leading to additional genetic progress) and opportunities for using marker information for product certification. The project will benefit the UK sheep industry by the use of Marker Assisted Selection (MAS) utilizing QTL or gene variants identified in the project. Additional benefits may arise from parentage verification and correction of errors e.g. misallocation of lamb to ewe. In the longer term, opportunities may exist to use markers for quality control, tracing products to their source. The major advantage of the design of this project is that the results are immediately applicable to the breeding schemes within which the QTLs and/or genes are detected. The time lag in the application of the results that is often seen with experimental populations is minimized. The project requires close involvement with the Sire Reference Scheme…

Phevor
type: Resource
type: NamedIndividual
has db xref: SciRes_000139
synonym: Phenotype Driven Variant Ontological Re-Ranking Tool
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. Tool that integrates phenotype, gene function, and disease information with personal genomic data for improved power to identify disease-causing alleles. It works by combining knowledge resident in multiple biomedical ontologies with the outputs of variant prioritization tools. It does so using an algorithm that propagates information across and between ontologies. This process enables Phevor to accurately reprioritize potentially damaging alleles identified by variant prioritization tools in light of gene function, disease, and phenotype knowledge. Phevor is especially useful for single exome and family trio-based diagnostic analyses, the most commonly occurring clinical scenarios, and ones for which existing personal-genomes diagnostic tools are most inaccurate and underpowered. Phevor not only improves diagnostic accuracy for individuals presenting with established disease phenotypes, but also for those with previously undescribed and atypical disease presentations. Importantly, Phevor is not limited to known diseases, or known disease-causing alleles.

Nonhuman Primate HIV/SIV Vaccine Trials Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-20999
synonym: HIV/SIV Trials Vaccine Database
synonym: HIV/SIV Trials Vaccine DB
IAO_0000115: An overview of HIV and SIV vaccine trials and their outcomes. It was developed as a tool for compilation, search and comparison of published studies on SIV, HIV and SHIV vaccine trials in nonhuman primates. We used a set of criteria to scan Pubmed for relevant studies to enter into the database. In selecting studies for entry, priority was given to recently published studies in journals generally regarded as the primary source of information pertaining to HIV and SIV vaccine research in nonhuman primates. In most cases, we give priority to challenge studies, where the animals received a live virus to measure the "efficacy" of the immunogen(s) inoculated during the course of the investigation. The HIV Sequence Database focuses on five primary goals: *Collecting HIV and SIV sequence data (all sequences since 1987) *Curating and annotating this data, and making it available to the scientific community *Computer analysis of HIV and related sequences *Production of software for the analysis of (sequence) data *Publication of the data and analyses on this site and in a yearly printed publication, the HIV sequence Compendium, which is available free of charge

flowMeans
type: Resource
type: NamedIndividual
has db xref: OMICS_05603
synonym: flowMeans - Non-parametric Flow Cytometry Data Gating
synonym: flowMeans: Non-parametric Flow Cytometry Data Gating
IAO_0000115: Software that identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection.

ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters
type: Resource
type: NamedIndividual
has db xref: biotools:alggen
has db xref: nif-0000-21006
synonym: A database of Annotated regulatory Binding Sites from orthologous promoters
abbrev: ABS
IAO_0000115: Public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. For each gene, TFBSs conserved in orthologous sequences from at least two different species must be available. Promoter sequences as well as the original GenBank or RefSeq entries are additionally supplied in case of future identification conflicts. The final TSS annotation has been refined using the database dbTSS. Up to this release, 500 bps upstream the annotated transcription start site (TSS) according to REFSEQ annotations have been always extracted to form the collection of promoter sequences from human, mouse, rat and chicken. For each regulatory site, the position, the motif and the sequence in which the site is present are available in a simple format. Cross-references to EntrezGene, PubMed and RefSeq are also provided for each annotation. Apart from the experimental promoter annotations, predictions by popular collections of weight matrices are also provided for each promoter sequence. In addition, global and local alignments and graphical dotplots are also available.

AceView
type: Resource
type: NamedIndividual
has db xref: nif-0000-21007
has db xref: r3d100010651
synonym: AceView genes
synonym: AceView/WormGenes
synonym: The AceView Genes
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented August 29, 2016. AceView offers an integrated view of the human, nematode and Arabidopsis genes reconstructed by co-alignment of all publicly available mRNAs and ESTs on the genome sequence. Our goals are to offer a re…

Digress.it
type: Resource
type: NamedIndividual
has db xref: nif-0000-02700
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented October 5, 2018. Digress.it is a tool (plugin) that offers paragraph-level commenting in the margins of a text. Digress.it is based on the WordPress blogging architecture, but is geared toward in-depth discussions of longer documents: article, essay or even book-length. Digress.it allows you run blog-style comment threads digressions, if you will off of individual paragraphs. To do this efficiently, we've re-jiggered the conventional post-discussion hierarchy of blogs, moving the comment area from beneath the post to beside it (floating to the right) hearkening back to the age-old practice of scribbling in page margins. We see great possibilities for educators, literary groups, political or civic activists, legal scholars, and pretty much anyone who wants to do a communal close reading. Since its initial launch Digress.it has been used by universities, publishers and governments across the world and is cited on various academic and scientific journals as an exemplary online collaboration tool. Digress.it is first an foremost a public service. The source code is completely free software and open to be used and customized by anyone without restriction. The hosting service is also free and has no ads. The project is primarily funded by grants, donations and people interested in seeing the project stay alive.

CTCFBSDB
type: Resource
type: NamedIndividual
has db xref: nif-0000-02703
has db xref: OMICS_00530
synonym: CTCFBSDB 2.0: A database for CTCF binding sites and genome organization
synonym: CTCFBSDB: a CTCF binding site database for characterization of vertebrate genomic insulators
abbrev: CTCFBSDB 2.0
IAO_0000115: A comprehensive collection of experimentally determined and computationally predicted CCCTC-binding factor (CTCF) binding sites (CTCFBS) from the literature. The database is designed to facilitate the studies on insulators and their roles in demarcating functional genomic domains. The CTCFBS Prediction Tool allows users to scan sequences for the single best match to CTCF position weight matrices. Currently (March 2014), the database contains almost 15 million experimentally determined CTCF binding sites across several species. CTCF binding sites were collected from published papers containing CTCF binding sites identified using ChIPSeq or similar methods, data from the ENCODE project, and a set of approximately 100 manually curated binding sites identified by low-throughput experiments. Users can browse insulator sequence features, function annotations, genomic contexts including histone methylation profiles, flanking gene expression patterns and orthologous regions in other mammalian genomes. Users can also retrieve data by text search, sequence search and genomic range search.

spliceR
type: Resource
type: NamedIndividual
has db xref: OMICS_03514
synonym: spliceR - Classification of alternative splicing and prediction of coding potential from RNA-seq data
IAO_0000115: An easy-to-use R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.

Automatic Generated Test-Sets Database for Protein-Protein Docking
type: Resource
type: NamedIndividual
has db xref: nif-0000-21012
abbrev: AGT-SDP
IAO_0000115: Database providing automatic test cases for protein-protein docking. A consensus-type approach is proposed processing the whole PDB and classifying protein structures into complexes and unbound proteins by combining information from three different approaches. Out of this classification test cases are generated automatically. All calculations were run on the database. The information stored is available via a web interface. The user can choose several criteria for generating his own subset out of the test cases, e.g. for testing docking algorithms. In unbound protein--protein docking, the complex of two proteins is predicted using the unbound conformations of the proteins (Halperin et al.,2002). For testing of docking algorithms, two unbound proteins which form a known complex have to be identified, so that the result of the docking algorithm can be compared to the known complex. For the identification of test cases, the structures taken from the PDB have to be classified as unbound proteins or complexes and unbound proteins with a 100% sequence identity to one complex part have to be searched. By now, most groups use handpicked test sets. The largest collection of test cases used so far is described by Chen et al. (Chen et al.,2003) and contains 31 test cases for unbound docking. Because of the exponential growth of available protein structures in the PDB, automatic generation of test cases will become more and more important in the future.

International Neuroinformatics Coordinating Facility
type: Organization
type: NamedIndividual
has db xref: grid.498423.0
has db xref: ISNI: 0000 0004 6107 939X
has db xref: nif-0000-00365
synonym: INCF
synonym: The International Neuroinformatics Coordinating Facility
IAO_0000115: Independent international facilitator catalyzing and coordinating global development of neuroinformatics aiming to advance data reuse and reproducibility in global brain research. Integrates and analyzes diverse data across scales, techniques, and species to understand brain function and positively impact the health and well being of society.

flowMatch
type: Resource
type: NamedIndividual
has db xref: OMICS_05602
synonym: flowMatch - Matching and meta-clustering in flow cytometry
IAO_0000115: Software for matching cell populations and building meta-clusters and templates from a collection of flow cytometry (FC) samples.

AMEDEO: The Medical Literature Guide
type: Resource
type: NamedIndividual
has db xref: nif-0000-21024
synonym: Amedeo - The Medical Literature Guide
synonym: The AMADEO Literature Guide
abbrev: AMEDEO
IAO_0000115: A service created to allow healthcare professionals to access timely, relevant information within their respective fields. Users can subscribe to receive weekly emails with bibliographic lists about new scientific publications, personal web pages for one-time download of available abstracts, and an overview of the medical literature published in relevant journals over the past 12 to 24 months.

Fiji
type: Resource
type: NamedIndividual
has db xref: biotools:Fiji
has db xref: SciRes_000137
synonym: Fiji is just ImageJ
IAO_0000115: Software package as distribution of ImageJ and ImageJ2 together with Java, Java3D and plugins organized into coherent menu structure. Used to assist research in life sciences.

flowFit
type: Resource
type: NamedIndividual
has db xref: OMICS_05601
synonym: flowFit - Estimate proliferation in cell-tracking dye studies
IAO_0000115: A Bioconductor package designed to perform quantitative analysis of cell proliferation in tracking dye-based experiments. The package uses an R implementation of the Levenberg-Marquardt algorithm (minpack.lm) to fit a set of peaks (corresponding to different generations of cells) over the proliferation-tracking dye distribution in a FACS experiment.

The Basics of MRI
type: Resource
type: NamedIndividual
has db xref: nif-0000-00115
IAO_0000115: An interesting and exhaustive explanation of how the technology works and is applied. It is an online book on principles and practice of magnetic resonance imaging. This educational package requires a hyper text markup language (HTML) 3.0 compatible browser, such as Mozilla Firefox, Microsoft Internet Explorer, or Apple Safari. This type of browser allows the user to view frames. Three frames will be used in this package to simultaneously display text, graphics, and navigation aids. You are reading this in the text window. The graphics window is in the upper left hand corner of your screen. This window will be used to display animations, static figures, references, symbol definitions, and the glossary. The navigation window appears in the lower left corner of the screen and has one line of options. To experience the full potential of the frames, a screen capable of displaying at least 1024 by 768 pixels with 256 colors is recommended. You may be able to gain a few extra pixels in the vertical direction on your monitor by turning off the show toolbar, show location, and show directory buttons under options at the top of your browser. A computer mouse is necessary to access the contents of this package. The mouse allows you to move up and down in a frame by either moving the slider, or holding the mouse button down on the up or down arrows located at the right of the frame.

CMEList.com
type: Resource
type: NamedIndividual
has db xref: nif-0000-21030
synonym: Annotated List of Online Continuing Medical Education (CME)
synonym: Online Continuing Medical Education (CME)
IAO_0000115: Links to, and descriptions of, every web site that offers AMA-approved Continuing Medical Education (CME) online. At this time, there are over 325 sites listed. These sites offer over 16,000 separate activities and over 26,000 hours of credit. Using this list, you can find online CME web sites arranged by their: # dominant medical specialty or medical topic; or # alphabetically by the first letter of the site name; or # you can scroll this list until you find a course or site of interest. Find sites by medical specialty or topic: Allergy, Anesthesia, Bioterrorism, Cardiology, Critical Care, Dermatology, Diabetes/Endocrinology, Ear, Nose and Throat, Emergency Medicine, Family Practice, Gastroenterology, Genetics, Geriatrics, Hematology / Oncology, HIV / Infectious Disease, Imaging / Radiology, Internal Medicine, Neurology, Neurosurgery, Obstetrics / Gynecology, Oncology/Hematology, Ophthalmology, Orthopedic Surgery, Pain Management, Pathology / Lab Medicine, Pediatrics, Psychiatry, Pulmonary, Quality/Management, Radiology / Imaging, Rheumatology, Surgery, Urology, Wellness / Prevention.

CYGD - Comprehensive Yeast Genome Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02713
synonym: Comprehensive Yeast Genome Database
synonym: MIPS Comprehensive Yeast Genome Database
synonym: MIPS Saccharomyces cerevisiae genome database
abbrev: CYGD
IAO_0000115: The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition, the data of various projects on related yeasts are used for comparative analysis.

Autosomal Recessive Polycystic Kidney Disease Mutation Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-21038
synonym: Mutation Database Autosomal Recessive Polycystic Kidney Disease (ARPKD/PKHD1)
IAO_0000115: Catalog of all changes detected in PKHD1 (Polycystic Kidney and Hepatic Disease 1) in a locus specific database. Investigators are invited to submit their novel data to this database. These data should be meaningful for clinical practice as well as of relevance for the reader interested in molecular aspects of polycystic kidney disease (PKD). There are also some links and information for ARPKD patients and their parents. Autosomal recessive polycystic kidney disease (ARPKD/PKHD1) is an important cause of renal-related and liver-related morbidity and mortality in childhood. This study reports mutation screening in 90 ARPKD patients and identifies mutations in 110 alleles making up a detection rate of 61%. Thirty-four of the detected mutations have not been reported previously. Two underlying mutations in 40 patients and one mutation in 30 cases are disclosed, and no mutation was detected on the remaining chromosomes. Mutations were found to be scattered throughout the gene without evidence of clustering at specific sites. PKHD1 mutation analysis is a powerful tool to establish the molecular cause of ARPKD in a given family. Direct identification of mutations allows an unequivocal diagnosis and accurate genetic counseling even in families displaying diagnostic challenges.

DEMI
type: Resource
type: NamedIndividual
has db xref: OMICS_03438
synonym: demi: Differential Expression from Multiple Indicators
synonym: Differential Expression from Multiple Indicators
IAO_0000115: R package for estimating differential expression from multiple indicators that capitalizes on the high number of concurrent measurements. It extends to various experimental designs and target categories (transcripts, genes, genomic regions) as well as small sample sizes.

Deja Vu: a Database of Highly Similar and Duplicate Citations
type: Resource
type: NamedIndividual
has db xref: nif-0000-02718
synonym: Deja Vu
synonym: Deja Vu: a Database of Highly Similar Citations
IAO_0000115: Deja vu is a database of extremely similar Medline citations. Many, but not all, of which contain instances of duplicate publication and potential plagiarism. Deja vu is a dynamic resource for the community, with manual curation ongoing continuously, and we welcome input and comments. In the scientific research community plagiarism and multiple publications of the same data are considered unacceptable practices and can result in tremendous misunderstanding and waste of time and energy. Our peers and the public have high expectations for the performance and behavior of scientists during the execution and reporting of research. With little chance for discovery and decreasing budgets, yet sustained pressure to publish, or without a clear understanding of acceptable publication practices, the unethical practices of duplicate publication and plagiarism can be enticing to some. Until now, discovery has been through serendipity alone, so these practices have largely gone unchecked.

Functional Regression Analysis of DTI Tract Statistics
type: Resource
type: NamedIndividual
has db xref: nlx_155629
synonym: Functional Regression Analysis of DTI
abbrev: FRATS
IAO_0000115: Software for the analysis of multiple diffusion properties along fiber bundle as functions in an infinite dimensional space and their association with a set of covariates of interest, such as age, diagnostic status and gender, in real applications. The resulting analysis pipeline can be used for understanding normal brain development, the neural bases of neuropsychiatric disorders, and the joint effects of environmental and genetic factors on white matter fiber bundles.

Binding MOAD
type: Resource
type: NamedIndividual
has db xref: nif-0000-21048
has db xref: OMICS_01900
synonym: Binding Mother of All Databases
synonym: BindingMOAD.org
IAO_0000115: Database of protein-ligand crystal structures that is a subset of the Protein Data Bank (PDB), containing every high-quality example of ligand-protein binding. The resolved protein crystal structures with clearly identified biologically relevant ligands are annotated with experimentally determined binding data extracted from literature. A viewer is provided to examine the protein-ligand structures. Ligands have additional chemical data, allowing for cheminformatics mining. The binding-affinity data ranges 13 orders of magnitude. The issue of redundancy in the data has also been addressed. To create a nonredundant dataset, one protein from each of the 1780 protein families was chosen as a representative. Representatives were chosen by tightest binding, best resolution, etc. For the 1780 best complexes that comprise the nonredundant version of Binding MOAD, 475 (27%) have binding data. This collection of protein-ligand complexes will be useful in elucidating the biophysical patterns of molecular recognition and enzymatic regulation. The complexes with binding-affinity data will help in the development of improved scoring functions and structure-based drug discovery techniques.

BioAfrica HIV Informatics in Africa
type: Resource
type: NamedIndividual
has db xref: nif-0000-21050
synonym: HIV Informatics in Africa
IAO_0000115: The BioAfrica HIV-1 Proteomics Resource is a website that contains detailed information about the HIV-1 proteome and protease cleavage sites, as well as data-mining tools that can be used to manipulate and query protein sequence data, a BLAST tool for initiating structural analyses of HIV-1 proteins, and a proteomics tools directory. HIV Proteomics Resource contains information about each HIV-1 gene product in regard to expression, post-transcriptional / post-translational modifications, localization, functional activities, and potential interactions with viral and host macromolecules. The Proteome section contains extensive data on each of 19 HIV-1 proteins, including their functional properties, a sample analysis of HIV-1HXB2, structural models and links to other online resources. The HIV-1 Protease Cleavage Sites section provides information on the position, subtype variation and genetic evolution of Gag, Gag-Pol and Nef cleavage sites.

Biological Magnetic Resonance Data Bank (BMRB)
type: Resource
type: NamedIndividual
has db xref: nif-0000-21058
has db xref: r3d100010191
synonym: Biological Magnetic Resonance DataBank
synonym: BioMag Res Bank
synonym: BioMagResBank
synonym: BMRB
IAO_0000115: Public depository that collects, annotates, archives, and disseminates important spectral and quantitative data derived from nuclear magnetic resonance spectroscopic investigations of biological macromolecules and metabolites. Provides reference information and maintains a collection of NMR pulse sequences and computer software for biomolecular NMR.

Blood Group Antigen Gene Mutation Database
type: Resource
type: NamedIndividual
has db xref: biotools:bgmut
has db xref: nif-0000-21064
synonym: BGMUT - Blood Group Antigen Gene Mutation Database
synonym: Blood Group Antigen Gene Mutation Database (BGMUT)
abbrev: BGMUT
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23, 2019.BGMUT was database that provided publicly accessible platform for DNA sequences and curated set of blood mutation information. Data Archive are available at ftp://ftp.ncbi.nlm.nih.gov/pub/mhc/rbc/Final Archive.

BioCyc
type: Resource
type: NamedIndividual
has db xref: nif-0000-00369
has db xref: r3d100011259
synonym: BioCyc Database Collection
IAO_0000115: A collection of Pathway/Genome Databases which describes the genome and metabolic pathways of a single organism. The BioCyc collection of Pathway/Genome Databases (PGDBs) provides an electronic reference source on the genomes and metabolic pathways of sequenced organisms. BioCyc PGDBs are generated by software that predicts the metabolic pathway complements of completely sequenced organisms from their genome sequences. They also include the results of a number of other computational inference procedures applied to these genomes, including predictions of which genes code for missing enzymes in metabolic pathways, and predicted operons. The BioCyc Web site provides a suite of software tools for database searching and visualization, for omics data analysis, and for comparative genomics and comparative pathway questions. The databases within the BioCyc collection are organized into tiers according to the amount of manual review and updating they have received. Tier 1 PGDBs have been created through intensive manual efforts, and receive continuous updating. Tier 2 PGDBs were computationally generated by the PathoLogic program, and have undergone moderate amounts of review and updating. Tier 3 PGDBs were computationally generated by the PathoLogic program, and have undergone no review and updating. There are 967 DBs in Tier 3. The downloadable version of BioCyc that includes the Pathway Tools software provides more speed and power than the BioCyc Web site.

CampyDB: Campylobacter Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-21075
synonym: CampyDB
IAO_0000115: CampyDB is a database for comparative genome analysis of For Campylobacter, Helicobacter and Wolinella. The database contains information on: -Campylobacter coli RM2228 -Campylobacter concisus 13826 -Campylobacter curvus 525.92 -Campylobacter fetus subsp. fetus 82-40 -Campylobacter hominis ATCC BAA-381 -Campylobacter jejuni RM1221 -Campylobacter jejuni subsp. doylei 269.97 -Campylobacter jejuni subsp. jejuni 260.94 -Campylobacter jejuni subsp. jejuni 81-176 -Campylobacter jejuni subsp. jejuni 81-176 -Campylobacter jejuni subsp. jejuni 84-25 -Campylobacter jejuni subsp. jejuni CF93-6 -Campylobacter jejuni subsp. jejuni CG8486 -Campylobacter jejuni subsp. jejuni HB93-13 -Campylobacter jejuni subsp. jejuni NCTC 11168 -Campylobacter lari RM2100 -Campylobacter upsaliensis RM3195 -Helicobacter acinonychis str. Sheeba -Helicobacter hepaticus ATCC 51449 -Helicobacter pylori 26695 -Helicobacter pylori HPAG1 -Helicobacter pylori J99 -Thiomicrospira denitrificans ATCC 33889 -Wolinella succinogenes DSM 1740 Sponsors: The project was originally conceived in 2002 by Roy Chaudhuri and Mark Pallen at the University of Birmingham, as part of a BBSRC funded Exploiting Genomics (ExGen) consortium. CampyDB is developed and maintained by Nick Loman and Lori Snyder working in the Pallen Research Group at University of Birmingham and is supported by a 5 year BBSRC grant until Feburary 2012.

DBD: Transcription factor prediction database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02726
has db xref: OMICS_00531
synonym: DNA-binding domain
abbrev: DBD
IAO_0000115: Database of predicted transcription factors in completely sequenced genomes. The predicted transcription factors all contain assignments to sequence specific DNA-binding domain families. The predictions are based on domain assignments from the SUPERFAMILY and Pfam hidden Markov model libraries. Benchmarks of the transcription factor predictions show they are accurate and have wide coverage on a genomic scale. The DBD consists of predicted transcription factor repertoires for 930 completely sequenced genomes.

Center for the Neural Basis of Cognition
type: Resource
type: NamedIndividual
has db xref: nif-0000-00370
synonym: CNBC
IAO_0000115: CNBC is joint venture of University of Pittsburgh and Carnegie Mellon University. Our center leverages the strengths of the University of Pittsburgh in basic and clinical neuroscience and those of Carnegie Mellon in cognitive and computational neuroscience to support a coordinated cross-university research and educational program of international stature. In addition to our Ph.D. program in Neural Computation, we sponsor a graduate certificate program in cooperation with a wide variety of affiliated Ph.D. programs.

dbMHC
type: Resource
type: NamedIndividual
has db xref: nif-0000-02729
has db xref: r3d100010881
synonym: Major Histocompatibility Complex Database
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23, 2019 Database was open, publicly accessible platform for DNA and clinical data related to human Major Histocompatibility Complex (MHC). Data from IHWG workshops were provided as well., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

CGSC
type: Resource
type: NamedIndividual
has db xref: nif-0000-21083
synonym: CGSC - The Coli Genetic Stock Center
synonym: Coli Genetic Stock Center
synonym: E. coli Genetic Stock Center
synonym: The Coli Genetic Stock Center
IAO_0000115: The CGSC Collection contains only non-pathogenic BSL-1 laboratory strains, primarily genetic derivatives of Escherichia coli K-12, the laboratory strain widely used in genetic and molecular studies, but a few B strains. The CGSC Database of E. coli genetic information includes genotypes and reference information for the strains in the CGSC collection, the names, synonyms, properties, and map position for genes, gene product information, and information on specific mutations and references to primary literature. The public version of the database includes this information and can be queried directly via this CGSC DB WebServer. The collection includes cultures of wild-type contributed from a number of laboratories and a few thousand derivatives carrying one or up to 29 mutations from among 3500 mutations in (or included in deletions spanning) more than 1300 different loci. Some combinations were constructed particularly for mapping purposes and are still used for teaching and for rapid localization, some for manifestation of a particular phenotype, some strains for transferring a particular region or for complementation analysis. Some plasmids, e.g., the Clarke and Carbon collection, F-primes, a number of toolkit plasmids, and a few classic plasmids are included, but it is not a comprehensive collection of plasmids. Additionally, we have recently acquired most of the strains from the Keio Collection of systematic individual gene knockout (deletion/kan insertion) strains.

CodonCodes TraceViewer
type: Commercial Organization
type: NamedIndividual
has db xref: OMICS_01822
synonym: CodonCode''s TraceViewer
abbrev: TraceViewer
IAO_0000115: A Java program that allows you to see, print, and edit DNA sequencing traces.

International Gene Trap Consortium
type: Resource
type: NamedIndividual
has db xref: nif-0000-00036
abbrev: IGTC
IAO_0000115: Consortium represents all publicly available gene trap cell lines, which are available on non-collaborative basis for nominal handling fees. Researchers can search and browse IGTC database for cell lines of interest using accession numbers or IDs, keywords, sequence data, tissue expression profiles and biological pathways, can find trapped genes of interest on IGTC website, and order cell lines for generation of mutant mice through blastocyst injection. Consortium members include: BayGenomics (USA), Centre for Modelling Human Disease (Toronto, Canada), Embryonic Stem Cell Database (University of Manitoba, Canada), Exchangeable Gene Trap Clones (Kumamoto University, Japan), German Gene Trap Consortium provider (Germany), Sanger Institute Gene Trap Resource (Cambridge, UK), Soriano Lab Gene Trap Resource (Mount Sinai School of Medicine, New York, USA), Texas Institute for Genomic Medicine - TIGM (USA), TIGEM-IRBM Gene Trap (Naples, Italy).

Chemistry Molecular Models
type: Resource
type: NamedIndividual
has db xref: nif-0000-21087
IAO_0000115: A collection of chemical structure files in Protein Data Bank format that may be displayed in 3D by a plug-in called Chemscape Chime. These files may be saved locally and displayed outside of a browser with the programs RasMol or iMol. In addition, the cross-platform Java Viewer, Jmol, may be used to display the files locally or in web pages. Structures Collected at UW-Stevens Point Chemistry Department include: biochemical structures, amino acids, carbohydrates, coenzymes and vitamins, glycolysis enzymes and metabolites, krebs cycle enzymes and metabolites, neutral lipids, amphipathic lipids, isoprenoid lipids, nucleic acids, nucleotides, peptides and proteins, organic chemistry, aliphatic compounds, aromatic compounds, polymers, drugs, sweeteners, general chemistry, bioinorganic compounds, norganic compounds (crystals), and VSEPR structures

CIBEX: Center for Information Biology gene EXpression database
type: Resource
type: NamedIndividual
has db xref: nif-0000-21088
synonym: Center for Information Biology gene EXpression database
abbrev: CIBEX
IAO_0000115: Gene expression database system in compliance with MIAME, which is a standard that the MGED Society has developed for comparing and data produced in microarray experiments at different laboratories worldwide. It serves as a public repository for a wide range of high-throughput experimental data in gene expression research, including microarray-based experiments measuring mRNA, serial analysis of gene expression (SAGE tags), and mass spectrometry proteomic data.

RelocaTE
type: Resource
type: NamedIndividual
has db xref: OMICS_03506
IAO_0000115: Software toolkit of a collection of scripts in which short reads (paired or unpaired), a fasta containing the sequences of transposable elements and a reference genome sequence, are the input and the output is a series of files containing the locations of TE insertions in the reference and short reads.

ClinicalTrials.gov
type: Resource
type: NamedIndividual
has db xref: nif-0000-21091
has db xref: OMICS_01792
has db xref: r3d100010211
synonym: Clinical Trials Database
synonym: Clinical Trials gov
synonym: ClinicalTrials
synonym: Clinicaltrials.gov: A Service Of The National Institutes Of Health
IAO_0000115: Registry and results database of federally and privately supported clinical trials conducted in United States and around world. Provides information about purpose of trial, who may participate, locations, and phone numbers for more details. This information should be used in conjunction with advice from health care professionals.Offers information for locating federally and privately supported clinical trials for wide range of diseases and conditions. Research study in human volunteers to answer specific health questions. Interventional trials determine whether experimental treatments or new ways of using known therapies are safe and effective under controlled environments. Observational trials address health issues in large groups of people or populations in natural settings. ClinicalTrials.gov contains trials sponsored by National Institutes of Health, other federal agencies, and private industry. Studies listed in database are conducted in all 50 States and in 178 countries.

MCIC
type: Resource
type: NamedIndividual
has db xref: nlx_155657
IAO_0000115: Expertly collected, well-curated data sets consisting of comprehensive clinical characterization and raw structural, functional and diffusion-weighted DICOM images in schizophrenia patients and gender and age-matched controls are now accessible to the scientific community through an on-line data repository (coins.mrn.org). This data repository will be useful to 1) educators in the fields of neuroimaging, medical image analysis and medical imaging informatics who need exemplar data sets for courses and workshops; 2) computer scientists and software algorithm developers for testing and validating novel registration, segmentation, and other analysis software; and 3) scientists who can study schizophrenia by further analysis of this cohort and/or by pooling with other data.

MGDM: Multi Geometric Deformable Model
type: Resource
type: NamedIndividual
has db xref: nlx_155658
synonym: Multi Geometric Deformable Model
abbrev: MGDM
IAO_0000115: An efficient level set framework for multi-object segmentation. Its representation inherently prevents overlaps and gaps and it readily preserves object topology and object relationships. MGDM is efficient, storing only a fixed number of functions for any number of objects, and therefore scales well to segmentation problems with many classes and large images. It's representation also avoids some instabilities in other multi-class level set methods. MGDM is cross-platform; MATLAB wrappers, Java source and API are provided, with MIPAV plugins forthcoming.

MIAS Registration Toolkit
type: Resource
type: NamedIndividual
has db xref: nlx_155659
abbrev: MIAS Toolkit
IAO_0000115: Software toolkit that provides the following libraries and functions on linux platform: # Multi-resolution registration of MR images include T1, multimodality, and DTI images. # The registration model is B-spline, and users can custermize their own image similarity measures by writing a plugin function and recompile the program.

MAGE
type: Resource
type: NamedIndividual
has db xref: OMICS_01783
synonym: MicroArray and Gene Expression
synonym: MicroArray and Gene Expression - MAGE
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 27,2023. Group providing a standard for the representation of microarray expression data that would facilitate the exchange of microarray information between different data systems.

Cogprints: Cognitive Sciences EPrint Archive
type: Resource
type: NamedIndividual
has db xref: nif-0000-21093
synonym: Cogprints
IAO_0000115: An electronic archive for self-archive papers in any area of Psychology, neuroscience, and Linguistics, and many areas of Computer Science, Philosophy, Biology, Medicine, Anthropology, cognitive ethnology, archeology, paleontology, as well as any other portions of the physical, social and mathematical sciences that are pertinent to the study of cognition.

Medical Image Visualization and Analysis
type: Resource
type: NamedIndividual
has db xref: nlx_155664
abbrev: MIVA
IAO_0000115: Software package that is a powerful graphical interface that displays, segments, aligns, manipulates, and blends image (pixel) and geometry (real-world coordinates) data simultaneously. Several applications are directly built into MIVA. Registration modes include interactive affine transformations. Fiducial registration tools facilitate rapid alignments for inter-modality volumes. Interactive Region of Interst (ROI) and Volume-of-Interest (VOI) tools exist to segment medical images. Virtually unique to MIVA are its 3D geometry tools and their compatibility with pixel based medical images. A full 3D interactive rat brain atlas is in an fMRI module which walks one through the necessary steps of fMRI. A multiple material surface routine takes segmented medical slices and creates 3D triangulated surfaces that align along all region boarders without overlap or gaps. These surfaces are the direct input into the MIVA tetrahedral mesh generator.

Microstructural correlation toolbox
type: Resource
type: NamedIndividual
has db xref: nlx_155665
abbrev: MSC
IAO_0000115: A Matlab-based software library to perform independent component analysis on group white matter skeleton generated by FSL TBSS. The script produces stable estimates of the white matter tract or tract segments that resemble highly correlated variation profiles across a group of subjects.

MisterI
type: Resource
type: NamedIndividual
has db xref: nlx_155666
abbrev: Mr I
abbrev: Mr. I
IAO_0000115: A powerful and modular medical image viewer/editor. It should be particularly useful to Undergraduates, Postdocs and Researchers in Medical Imaging to visualize data and to easily make attractive figures (for papers or presentations). It will also in a near future offer a number of advanced algorithms for medical image processing. Look at the video to get an idea ! http://www.benoitscherrer.com/MisterI/videos.html

MriWatcher
type: Resource
type: NamedIndividual
has db xref: nlx_155667
IAO_0000115: This simple visualization tool allows to load several images at the same time. The cursor across all windows are coupled and you can move/zoom on all the images at the same time. Very useful for quality control, image comparison.

flowCyBar
type: Resource
type: NamedIndividual
has db xref: OMICS_05597
synonym: flowCyBar - Analyze flow cytometric data using gate information
IAO_0000115: A software package to analyze flow cytometric data using gate information to follow population / community dynamics.

ConSurf Database
type: Resource
type: NamedIndividual
has db xref: BioTools:consurf-db
has db xref: nif-0000-02685
has db xref: nif-0000-21098
has db xref: SCR_007609
synonym: ConSurf Server Database
synonym: ConSurf- Data Base
synonym: ConSurf-DataBase
synonym: ConSurf-DB
synonym: consurf-db
synonym: ConSurfDataBase
synonym: ConSurfDB
IAO_0000115: Provides pre-calculated evolutionary conservation profiles for proteins of known structure in the PDB. Enables flexibility in setting the parameters of the calculation, and accepts optional uploads of atomic coordinates, multiple sequence alignments, and phylogenetic trees for use in the calculation of conservation profiles.

Multiple Correlation Function Tool
type: Resource
type: NamedIndividual
has db xref: nlx_155670
IAO_0000115: Software tool that provides a convenient environment to simulate NMR diffusion in closed pores. It builds on the eigenfunction expansion of the magnetization.

dbRES: A web-oriented database for annotated RNA Editing Site
type: Resource
type: NamedIndividual
has db xref: nif-0000-02732
synonym: dbRES
IAO_0000115: dbRES is a web-oriented comprehensive database for RNA Editing Site. dbRES contain only experimental validated RNA Editing Site. All the data in dbRES was manually collected from literatures reporting related experiment result or the GeneBank database. dbRES now contains all together 5437 RNA edit site data. dbRES covers altogether 95 organisms from 251 transcripts. RNA editing is a post-transcriptional modification of RNA and markedly increases the complexity of the transcriptome. RNA editing occurs in the nucleus, as well as in mitochondria and plastids. To date such changes have been observed in prokaryotes, plants, animals and virus. The diversity of this widespread phenomenon includes nucleoside modifications, nucleotide additions and insertions, either in coding or non-coding sequences of RNA, which can occur concomitantly with transcription and splicing processes.

NITRC Community Conferences Workshops and Meetings
type: Resource
type: NamedIndividual
has db xref: nlx_155672
synonym: NITRC / INCF Community Conferences Workshops and Meetings
abbrev: Conferences Workshops and Meetings
IAO_0000115: Project to assist the community in the support of information about upcoming Conferences, Workshops and Meetings. Such support may be documents, news, files, etc. To see a listing of upcoming Events, please use the NITRC Community Events Page at http://www.nitrc.org/incf/event_list.php (and tab at right). To announce an Event, please use the Submit an Event at the NITRC Community Events Page, http://www.incf.org/Events/events/createObject?type_name=Event (and tab at right). Note, INCF account is currently required. All users are encouraged to check this site for upcoming meetings, and promote future meetings here.

glycosciences.de
type: Resource
type: NamedIndividual
has db xref: nif-0000-21103
synonym: Glycosciences
abbrev: GLYCOSCIENCES.de
IAO_0000115: Portal of glycoinformatics resources including databases and bioinformatics tools for glycobiology and glycomics research. Databases include a bibliography, structure, nuclear magnetic resonance (NMR), mass spectroscopy (ms) and a PDB search.

Current Controlled Trials
type: Resource
type: NamedIndividual
has db xref: nif-0000-21104
synonym: Current Controlled Trials Ltd
abbrev: CCT
IAO_0000115: Free-to-view clinical trials register of clinical trials worldwide, it allows users to search, register and share information about randomized controlled trials. Publication services are also available via the range of open access peer-reviewed journals published by BioMed Central. Current Controlled Trials is run by an editorial and technical in-house team. It receives advice from an international Advisory Group, including academics, doctors and health care specialists of international renown. The Advisory Group provides valuable guidance on the current activities and possible new directions of Current Controlled Trials' two databases, the metaRegister of Controlled Trials (mRCT) and the International Standard Randomised Controlled Trial Number (ISRCTN) scheme.

Developmental and Reproductive Toxicology Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-21110
abbrev: DART
IAO_0000115: Bibliographic database providing references to developmental and reproductive toxicology literature on the National Library of Medicine's Toxicology Data Network. It covers teratology and other aspects of developmental and reproductive toxicology. It contains over 200,000 references to literature published since 1965. DART/ETIC is easily accessible and free of charge. Search by subject terms, title words, chemical name, Chemical Abstracts Service Registry Number (RN), and author. Search results can easily be viewed, printed or downloaded. Search results are displayed in relevancy ranked order, but may be sorted by publication date, author or title.

Iterative Signature Algorithm
type: Resource
type: NamedIndividual
has db xref: biotools:isa
has db xref: OMICS_03487
synonym: isa2: The Iterative Signature Algorithm
abbrev: ISA
abbrev: isa2
IAO_0000115: A biclustering algorithm that finds modules in an input matrix. A module or bicluster is a block of the reordered input matrix.

Advanced Targeting Systems
type: Organization
type: NamedIndividual
has db xref: grid.422052.3
has db xref: nlx_152256
abbrev: ATS
IAO_0000115: Commercial supplier of antibodies, assay kits, conjugates and various toxins for biomedical research. ATS's product line is designed to assist scientists in the study of system functions, cell functionality, diseases and disorders.

Variant Reporter Software
type: Resource
type: NamedIndividual
has db xref: OMICS_01818
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 28, 2017. Software that performs comparative sequencing, also known as direct sequencing, medical sequencing, PCR sequencing and resequencing with DNA sequencing files. The software is designed for reference based and non-reference based analysis such as mutation detection and analysis, SNP discovery and validation and sequence confirmation.

UPR Analysis Resource Center Confocal Microscopy Core Laboratory
type: Resource
type: NamedIndividual
has db xref: nlx_156592
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented June 26, 2017. Lab that provides resources for researchers such as image analysis and access to confocal microscopes.

Directory of Health Organizations Online
type: Resource
type: NamedIndividual
has db xref: nif-0000-21122
synonym: Directory of Information Resources Online
abbrev: DIRLINE
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented July 15, 2016. Database containing location and descriptive information about a wide variety of information resources including organizations, research resources, projects, and databases concerned with health and biomedicine. This information may not be readily available in bibliographic databases. Each record may contain information on the publications, holdings, and services provided. These information resources fall into many categories including federal, state, and local government agencies; information and referral centers; professional societies; self-help groups and voluntary associations; academic and research institutions and their programs; information systems and research facilities. Topics include HIV/AIDS, maternal and child health, most diseases and conditions including genetic and other rare diseases, health services research and technology assessment. DIRLINE can be searched using subject words (such as disease or condition) including Medical Subject Headings (MeSH) or for the name or location of a resource. It now offers an A to Z list of over 8,500 organizations.

DogMap
type: Resource
type: NamedIndividual
has db xref: nif-0000-21123
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. An international collaboration between 46 labs from 20 different countries towards a low resolution canine marker map under the auspices of the International Society for Animal Genetics (ISAG). The map under development should achieve a resolution of about 20 cM and some of the markers should be mapped physically. The participants have agreed to use microsatellites as markers on a common panel of reference families which will provide the backbone of the marker map. It is foreseen to also include type I markers in the mapping effort and to produce cosmid derived microsatellites for physical mapping. For this purpose part of the effort focuses on the standardization of the canine karyotype. Special attention is payed to hereditary diseases where efforts are under way to establish resource families either by collecting families or by specific breeding. A point of emphasis of the DogMap project is the setting up of an internationally accessible database for handling the mapping data. The structure of the DogMap collaboration includes a managing committee and scientific advisers. The managing committee is responsible for the overall coordination of the activities within the collaboration, for the dissemination of relevant information to all of the participants and for the representation of DogMap outside the collaboration., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

RepARK
type: Resource
type: NamedIndividual
has db xref: OMICS_03446
synonym: Repetitive motif detection by Assembly of Repetitive K-mers
IAO_0000115: Software using a de novo repeat assembly method which avoids potential biases by using abundant k-mers of next-generation sequencing (NGS) whole genome sequencing (WGS) reads without requiring a reference genome.

Database of Transcribed Sequences
type: Resource
type: NamedIndividual
has db xref: nif-0000-21125
synonym: DoTs
IAO_0000115: DoTS (Database Of Transcribed Sequences) is a human and mouse transcript index created from all publicly available transcript sequences. The input sequences are clustered and assembled to form the DoTS Consensus Transcripts that comprise the index. These transcripts are assigned stable identifiers of the form DT.123456 (and are often referred to as dots). The transcripts are in turn clustered to form putative DoTS Genes. These are assigned stable identifiers of the form DG.1234356. As of September 1, 2004, the DoTS annotation team has manually annotated 43,164 human and 78,054 mouse DoTS Transcripts (DTs), corresponding to 3,939 human and 7,752 mouse DoTS Genes (DGs). Use the manually annotated gene query to see the DoTS Transcripts that have been manually annotated. The focus of the DoTS project is integrating the various types of data (e.g., EST sequences, genomic sequence, expression data, functional annotation) in a structured manner which facilitates sophisticated queries that are otherwise not easy to perform. DoTS is built on the GUS Platform which includes a relational database that uses controlled vocabularies and ontologies to ensure that biologically meaningful queries can be posed in a uniform fashion. An easy way to start using the site is to search for DoTS Transcripts using an existing cDNA or mRNA sequence. Click on the BLAST tab at the top of the page and enter your sequence in the form provided. All the transcripts with significant sequence similarity to your query sequence will be displayed. Or use one of the provided queries to retrieve transcripts using a number of criteria. These queries are listed on the query page, which can also be reached by clicking on the tab marked query at the top of the page. Finally, the boolean query page allows these queries to be combined in a variety of ways. Sponsors: Funding provided by -NIH grant RO1-HG-01539-03 -DOE grant DE-FG02-00ER62893

DPDx: Laboratory Identification of Parasites of Public Health Concern
type: Resource
type: NamedIndividual
has db xref: nif-0000-21126
abbrev: DPDx
IAO_0000115: Parasite-related portal including concise reviews of parasites and parasitic diseases, an image library, a review of recommended procedures for collecting, shipping, processing, and examining biologic specimens, and a diagnostic assistance function, in which laboratorians and other health professionals desiring assistance in parasite identification can ask questions and/or send digital images of specimens for expedited review and consultation with DPD staff. This assistance is free of charge. The portal is hoped to strengthen diagnosis of, and enhance the capacity to address the global problem of parasitic diseases, both in the United States and abroad. Potential DPDx applications include: * training and continuing education of laboratorians, using material collected by CDC or contributed by other institutions * provision to health facilities worldwide of diagnostic assistance by CDC staff backed up when needed by experts from other institutions * diagnostic quizzes for self-assessment of laboratorians skills * informal, early detection of unusually clustered, atypical or emerging parasitic diseases

Drug-Interactions
type: Resource
type: NamedIndividual
has db xref: nif-0000-21132
synonym: Cytochrome P450 Drug Interaction Table
synonym: Cytochrome P450 Drug Interactions
synonym: P450 Drug Interactions
abbrev: Drug Interactions
IAO_0000115: Table designed as a hypothesis testing, teaching and reference tool for physicians and researchers interested in drug interactions that are the result of competition for, or effects on the human cytochrome P450 system. The table contains lists of drugs in columns under the designation of specific cytochrome P450 isoforms. A drug appears in a column if there is published evidence that it is metabolized, at least in part, via that isoform. It does not necessarily follow that the isoform is the principal metabolic pathway in vivo, or that alterations in the rate of the metabolic reaction catalyzed by that isoform will have large effects on the pharmacokinetics of the drug., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

PolyPhred
type: Resource
type: NamedIndividual
has db xref: biotools:polyphred
has db xref: OMICS_01815
IAO_0000115: Software program that compares fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions. Its functions are integrated with the use of three other programs: Phred (Brent Ewing and Phil Green), Phrap (Phil Green), and Consed (David Gordon and Phil Green). PolyPhred identifies potential heterozygotes using the base calls and peak information provided by Phred and the sequence alignments provided by Phrap. Potential heterozygotes identified by PolyPhred are marked for rapid inspection using the Consed tool.

dbSNP
type: Resource
type: NamedIndividual
has db xref: biotools:dbsnp
has db xref: nif-0000-02734
has db xref: OMICS_00264
has db xref: r3d100010652
synonym: dbSNP: Database for Short Genetic Variations
synonym: Entrez SNP
synonym: Entrez SNP - Single Nucleotide Polymorphism
synonym: NCBI Short Genetic Variations
synonym: NCBI Short Genetic Variations (SNV) database
synonym: NCBI Short Genetic Variations Database
synonym: NCBI Single Nucleotide Polymorphism
synonym: NCBI SNV Database
synonym: SNV Database
IAO_0000115: Database as central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. Distinguishes report of how to assay SNP from use of that SNP with individuals and populations. This separation simplifies some issues of data representation. However, these initial reports describing how to assay SNP will often be accompanied by SNP experiments measuring allele occurrence in individuals and populations. Community can contribute to this resource.

DBSubLoc - Database of protein Subcellular Localization
type: Resource
type: NamedIndividual
has db xref: nif-0000-02735
abbrev: DbSubLoc
IAO_0000115: A database of protein subcellular localization containing proteins from primary protein database SWISS-PROT and PIR. By collecting the subcellular localization annotation, these information are classified and categorized by cross references to taxonomies and Gene Ontology database. Annotations were taken from primary protein databases, model organism genome projects and literature texts, and then were analyzed to dig out the subcellular localization features of the proteins. The proteins are also classified into different categories. Based on sequence alignment, nonredundant subsets of the database have been built, which may provide useful information for subcellular localization prediction. The database now contains >60 000 protein sequences including 30 000 protein sequences in the nonredundant data sets. Online download, SOAP server, Blast tools and prediction services are also available.

BRAINSFit
type: Resource
type: NamedIndividual
has db xref: nlx_155701
IAO_0000115: A program for registering images with with mutual information based metric. Several registration options are given for 3,6, 9,12,16 parameter (i.e. translate, rigid, scale, scale/skew, full affine) based constraints for the registration. The program uses the Slicer3 execution model framework to define the command line arguments and can be fully integrated with Slicer3 using the module discovery capabilities of Slicer3

BEETL-fastq
type: Resource
type: NamedIndividual
has db xref: biotools:beetl
has db xref: OMICS_04900
IAO_0000115: Software tool that not only compresses FASTQ-formatted DNA reads more compactly than gzip but also permits rapid search for k-mer queries within the archived sequences. The full FASTQ record of each matching read or read pair is returned, allowing the search results to be piped directly to any of the many standard tools that accept FASTQ data as input. Searchable compressed archive for DNA reads.

DWGSIM
type: Resource
type: NamedIndividual
has db xref: OMICS_00249
IAO_0000115: Whole Genome Simulator for Next-Generation Sequencing.

Evolutionary Lineage Inferred from Structural Analysis
type: Resource
type: NamedIndividual
has db xref: nif-0000-21141
synonym: ELISA
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. ELISA is an online database that combines functional annotation with structure and sequence homology modeling to place proteins into sequence-structure-function neighborhoods. The atomic unit of the database is a set of sequences and structural templates that those sequences encode. A graph that is built from the structural comparison of these templates is called PDUG (protein domain universe graph). It introduces a method of functional inference through a probabilistic calculation done on an arbitrary set of PDUG nodes. Further, all PDUG structures are mapped onto all fully sequenced proteomes allowing an easy interface for evolutionary analysis and research into comparative proteomics. ELISA is the first database with applicability to evolutionary structural genomics explicitly in mind.

Ensembl
type: Resource
type: NamedIndividual
has db xref: biotools:ensembl
has db xref: nif-0000-21145
has db xref: OMICS_01647
has db xref: r3d100010228
synonym: ENSEMBL
IAO_0000115: Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.

DBTBS
type: Resource
type: NamedIndividual
has db xref: nif-0000-02736
has db xref: OMICS_01859
synonym: DBTBS: a database of Bacillus subtilis promoters and transcription factors
synonym: DBTBS: a database of Bacillus subtilis promoters and transcription factors.
IAO_0000115: Database of experimentally validated gene regulatory relations and the corresponding transcription factor binding sites upstream of Bacillus subtilis genes. The database allows the comparison of systematic experiments with individual experimental results in order to facilitate the elucidation of the complete B. subtilis gene regulatory network. The current version is constructed by surveying 947 references and contains the information of 120 binding factors and 1475 gene regulatory relations. For each promoter, all of its known cis-elements are listed according to their positions, while these cis-elements are aligned to illustrate the consensus sequence for each transcription factor. All probable transcription factors coded in the genome were classified using Pfam motifs. The DBTBS database was reorganized to show operons instead of individual genes as the building blocks of gene regulatory networks. It now contains 463 experimentally known operons, as well as their terminator sequences if identifiable. In addition, 517 transcriptional terminators were identified computationally. (De Hoon, M.J.L. et al., PLoS Comput. Biol. 1, e25 (2005)). A new section was added under "Motif conservation", which presents hexameric motifs found to be conserved to different extents between upstream intergenic regions of genus-specific subgroups of homologous proteins.

Familial Hypertrophic Cardiomyopathy DNA Mutation Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-21151
synonym: FHC Mutation Database
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The aim of this locus-specific mutation database was to provide an online resource that contains summarized and updated information on familial hypertrophic cardiomyopathy (FHC)-associated mutations and related data, for researchers and clinicians. It also serves as a means of publishing previously unpublished data, which could be of value in understanding genotype/phenotype correlations. This database contains mutations in various genes known to cause familial hypertrophic cardiomyopathy, a genetic disorder associated with defects in the sarcomere [1]. Only gene symbols approved by HUGO are used and mutations are reported in accordance with guidelines recommended by the Mutation Database Initiative of HUGO and EBI.

INCF Software Center
type: Resource
type: NamedIndividual
has db xref: nif-0000-00372
synonym: International Neuroinformatics Coordinating Facility Software Center
IAO_0000115: Software repository that makes it easy for neuroscientists to find, use and share software tools. The Software Center is accessible to everyone: you can browse and download available software tools without registering. However, by creating an account, you will be able to post comments, and request to join development teams. The INCF Software Center and the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) are sharing content. Software tools hosted by NITRC also appear at the INCF Software Center. Your software tool will be available to all users of the Software Center. You will be able to upload documentation, executables and related files; track use of your software; create a wiki; and establish a development team. Registered Software Center users will be able to comment on and post reviews about your software, and can request to join your development team. INCF's vision of the Software Center is that it will become a communication enabler for software users as well as developers. Accordingly, future system features to be added include communication and collaboration functions. We also plan to include support services to allow software developers organize their software, track the use, and receive feedback for further improvement and development. Further development of the Software Center will be strongly driven by the user needs. Please let us know what features you would like to see added.

Full-Malaria: Malaria Full-Length cDNA Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-21157
synonym: Full-Malaria
IAO_0000115: FULL-malaria is a database for a full-length-enriched cDNA library from the human malaria parasite Plasmodium falciparum. Because of its medical importance, this organism is the first target for genome sequencing of a eukaryotic pathogen; the sequences of two of its 14 chromosomes have already been determined. However, for the full exploitation of this rapidly accumulating information, correct identification of the genes and study of their expression are essential. Using the oligo-capping method, this database has produced a full-length-enriched cDNA library from erythrocytic stage parasites and performed one-pass reading. The database consists of nucleotide sequences of 2490 random clones that include 390 (16%) known malaria genes according to BLASTN analysis of the nr-nt database in GenBank; these represent 98 genes, and the clones for 48 of these genes contain the complete protein-coding sequence (49%). On the other hand, comparisons with the complete chromosome 2 sequence revealed that 35 of 210 predicted genes are expressed, and in addition led to detection of three new gene candidates that were not previously known. In total, 19 of these 38 clones (50%) were full-length. From these observations, it is expected that the database contains approximately 1000 genes, including 500 full-length clones. It should be an invaluable resource for the development of vaccines and novel drugs. Full-malaria has been updated in at least three points. (i) 8934 sequences generated from the addition of new libraries added so that the database collection of 11,424 full-length cDNAs covers 1375 (25%) of the estimated number of the entire 5409 parasite genes. (ii) All of its full-length cDNAs and GenBank EST sequences were mapped to genomic sequences together with publicly available annotated genes and other predictions. This precisely determined the gene structures and positions of the transcriptional start sites, which are indispensable for the identification of the promoter regio…

MIAME
type: Resource
type: NamedIndividual
has db xref: OMICS_01785
synonym: Minimum Information About a Microarray Experiment
IAO_0000115: Standard specification for the Minimum Information About a Microarray Experiment that is needed to enable the interpretation of the results of the experiment unambiguously and potentially to reproduce the experiment.

Fungal Databases
type: Resource
type: NamedIndividual
has db xref: nif-0000-21158
IAO_0000115: This website contains a list of five fungal genome databases from The J. Craig Venter Institute. Aspergillus genomes: -Aspergillus fumigatus (strain-Af 293) -Aspergillus clavatus -Neosartorya fischeri Other Fungal Genomes: -Cryptococcus neoformans (strain-JEC21) -Coccidioides posadasii

MAQC
type: Resource
type: NamedIndividual
has db xref: OMICS_01784
synonym: MicroArray Quality Control
IAO_0000115: Project to improve the microarray and next-generation sequencing technologies and foster their proper applications in discovery, development and review of FDA regulated products by developing standards and quality measures. Microarrays and next-generation sequencing represent core technologies in pharmacogenomics and toxicogenomics; however, before these technologies can successfully and reliably be used in clinical practice and regulatory decision-making, standards and quality measures need to be developed. Everyone is invited to participate in the MAQC project.

NeuroHub: the information environment for Neuroscientists
type: Resource
type: NamedIndividual
has db xref: nif-0000-21160
synonym: NeuroHub
synonym: The Neuro Hub
IAO_0000115: Online aggregation portal of neuroscience research services that clients can use as a tool to contact, refer, and utilize such as medical services, neuropsychology assessments, and speech pathology.

HaploClique
type: Resource
type: NamedIndividual
has db xref: OMICS_03442
IAO_0000115: Software providing a computational approach to reconstruct the structure of a viral quasispecies from next-generation sequencing data as obtained from bulk sequencing of mixed virus samples.

DBTSS: Database of Transcriptional Start Sites
type: Resource
type: NamedIndividual
has db xref: biotools:dbtss
has db xref: nif-0000-02738
has db xref: OMICS_01860
synonym: DataBase of Transcriptional Start Sites
abbrev: DBTSS
IAO_0000115: Database of transcriptional start sites (TSSs) representing exact positions in the genome based on a unique experimentally validated TSS sequencing method, TSS Seq. A major part of human adult and embryonic tissues are covered. DBTSS contains 491 million TSS tag sequences collected from a total of 20 tissues and 7 cell cultures. Also integrated is generated RNA-seq data of subcellular- fractionated RNAs and ChIP Seq data of histone modifications, RNA polymerase II and several transcriptional regulatory factors in cultured cell lines. Also included is external epigenomic data, such as chromatin map of the ENCODE project. They associated those TSS information with public and original SNV data, in order to identify single nucleotide variations (SNVs) in the regulatory regions.

SCETI
type: Organization
type: NamedIndividual
has db xref: nlx_152251
has db xref: nlx_152454
synonym: Actif SCETI
synonym: SCETI K.K.
IAO_0000115: Commercial marketer, distributor and importer of industrial, medical, pharmaceutical and biological research and health innovation products.

BrainVision Analyzer
type: Resource
type: NamedIndividual
has db xref: nlx_155717
synonym: BrainVision Analyzer 2
abbrev: BVA
IAO_0000115: Software to manage the daily work of analyzing various neurophysiological data. Features include a history tree, automated analysis, various data format readers, and more.

GENESIS Neural Database and Modelers Workspace
type: Resource
type: NamedIndividual
has db xref: nif-0000-21168
synonym: GENESIS Neural Database and Modeler's Workspace
abbrev: Modeler's Workspace
abbrev: Modelers Workspace
IAO_0000115: Software system to assist computational neuroscientists in interacting with databases of models and with neural simulation packages such as GENESIS. There are three components in the system: a user interface, a database server, and a global registry and repository. The collection of software tools with a graphical user interface enables users to interact over the WWW with databases of models and data. It provides facilities for searching multiple remote databases for model components based on various criteria; visualizing the characteristics of the components retrieved; creating new components, either from scratch or derived from existing models; combining components into new models; linking models to experimental data as well as online publications; and interacting with simulation packages such as GENESIS to simulate the new constructs. Although the initial version uses GENESIS as the simulator, the design permits the use of multiple simulation systems, with or without the use of a database. This allows modeling at multiple levels of scale from the molecular level, through the subcellular (e.g. ion channel), single cell, and network levels, to the systems level (e.g. relating models to fMRI studies). The system is intended to help users create and organize models and to interact with databases of models and neuronal simulation software. More specifically, the Modeler's Workspace is designed to provide the following: * Search and retrieval facilities for interacting with databases of models and other information; * Facilities for creating, editing and visualizing the characteristics of models; * Facilities for combining model components together and translating them into formats suitable for simulation systems such as GENESIS and NEURON; * Facilities for managing a personal database where a user can collect models and other objects; and * Collaboration facilities for connecting one or more users together, to allow them to simultaneously edit objects in a shared data…

Genevestigator
type: Commercial Organization
type: NamedIndividual
has db xref: nif-0000-21172
has db xref: OMICS_00763
IAO_0000115: A high performance search engine for gene expression that integrates thousands of manually curated public microarray and RNAseq experiments and nicely visualizes gene expression across different biological contexts (diseases, drugs, tissues, cancers, genotypes, etc.). There are two basic analysis approaches: # for a gene of interest, identify which conditions affect its expression. # for condition(s) of interest, identify which genes are specifically expressed in this/these conditions. Genevestigator builds on the deep integration of data, both at the level of data normalization and on the level of sample annotations. This deep integration allows scientists to ask new types of questions that cannot be addressed using conventional tools.

DNA DataBank of Japan (DDBJ)
type: Resource
type: NamedIndividual
has db xref: biotools:ddbj
has db xref: nif-0000-02740
has db xref: OMICS_01644
has db xref: r3d100010218
synonym: DDBJ
synonym: DDBJ - DNA Data Bank of Japan
synonym: DNA Data Bank of Japan
synonym: DNA DataBank of Japan
IAO_0000115: Maintains and provides archival, retrieval and analytical resources for biological information. Central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation. Database content is exchanged with EBI and NCBI within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). In 2011, DDBJ launched two new resources: DDBJ Omics Archive and BioProject. DOR is archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between the ArrayExpress at EBI and DOR in the common MAGE-TAB format. BioProject provides organizational framework to access metadata about research projects and data from projects that are deposited into different databases.

GoMiner
type: Resource
type: NamedIndividual
has db xref: nif-0000-21181
IAO_0000115: GoMiner is a tool for biological interpretation of "omic" data including data from gene expression microarrays. Omic experiments often generate lists of dozens or hundreds of genes that differ in expression between samples, raising the question, What does it all mean biologically? To answer this question, GoMiner leverages the Gene Ontology (GO) to identify the biological processes, functions and components represented in these lists. Instead of analyzing microarray results with a gene-by-gene approach, GoMiner classifies the genes into biologically coherent categories and assesses these categories. The insights gained through GoMiner can generate hypotheses to guide additional research. GoMiner displays the genes within the framework of the Gene Ontology hierarchy in two ways: * In the form of a tree, similar to that in AmiGO * In the form of a "Directed Acyclic Graph" (DAG) The program also provides: * Quantitative and statistical analysis * Seamless integration with important public databases GoMiner uses the databases provided by the GO Consortium. These databases combine information from a number of different consortium participants, include information from many different organisms and data sources, and are referenced using a variety of different gene product identification approaches.

Relevance Voxel Machine
type: Resource
type: NamedIndividual
has db xref: SciRes_000134
abbrev: RVoxM
IAO_0000115: A Bayesian image-based prediction algorithm that is based on the Relevance Vector Machine and Automatic Relevance Detection frameworks, which are popular approaches in Machine Learning. RVoxM adapts this framework to handle images and explicitly models the spatial smoothness in images. RVoxM can be used to learn to predict a binary or continuous variable from image data.

COGNISION
type: Resource
type: NamedIndividual
has db xref: nlx_155724
synonym: COGNISION (TM) System
IAO_0000115: A portable, highly integrated, internet-enabled, hardware / software platform and patient management system, which includes an online Patient Manager module which complies with the HIPAA Final Security Rule, an event-related potential (ERP) Viewer module to view and analyze raw and average ERP waves, and a Protocol Editor module to simplify the choice and administration of selected ERP protocols. It is also easy to train and administer with non-specialized personnel, and is designed to be used in an out-patient setting. COGNISION TM with auditory or visual event-related potential (ERP) technology, provides a direct physiologic measure of patients' cognitive processing (i.e., a cognitive biomarker).

ISO
type: Resource
type: NamedIndividual
has db xref: OMICS_01782
synonym: International Organization for Standardization
IAO_0000115: An independent, non-governmental organization made up of members from the national standards bodies of 161 countries that develop and publish International Standards covering almost all aspects of technology and business. From food safety to computers, and agriculture to healthcare, ISO International Standards impact all our lives. The Central Secretariat in Geneva, Switzerland, coordinates the system. The standards are developed by the people that need them, through a consensus process. Experts from all over the world develop the standards that are required by their sector. This means they reflect a wealth of international experience and knowledge.

Hardin MD
type: Resource
type: NamedIndividual
has db xref: nif-0000-21186
has db xref: r3d100011208
synonym: Hardin Meta Directory
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 2, 2025. A medical database with lists, or directories, of information in health and medicine and images of medical conditions. Users may search Hardin MD, browse through the Medical picture gallery, and sort search results by disease or alphabetical letter.

Haz-Map: Occupational Exposure to Hazardous Agents
type: Resource
type: NamedIndividual
has db xref: nif-0000-21187
synonym: Haz-Map: Information on Hazardous Chemicals and Occupational Diseases
abbrev: Haz-Map
IAO_0000115: Occupational health database designed for health and safety professionals and for consumers seeking information about the adverse effects of workplace exposures to chemical and biological agents. The main links in Haz-Map are between chemicals and occupational diseases. These links have been established using current scientific evidence. Haz-Map shows the diseases linked to each agent and the agents linked to each disease. Agents are chemical such as formaldehyde, or biological such as grain dust. Haz-Map links jobs and hazardous job tasks with occupational diseases and their symptoms. In Haz-Map, chronic occupational diseases are linked to both jobs and industries, while acute diseases and infectious diseases are linked only to jobs. Cancers are not linked to jobs, industries or findings. The information in Haz-Map comes from textbooks, journal articles, the Documentation of the Threshold Limit Values (published by ACGIH), and electronic databases such as NLM's Hazardous Substances Data Bank (HSDB). Haz-Map staff classifies, summarizes, and regularly updates the information found in the database.

Comparison of web annotation systems
type: Resource
type: NamedIndividual
has db xref: nif-0000-02741
IAO_0000115: Wikipedia offers a comparison of web annotation systems. Many of these systems require software to be installed to enable some or all of the features. This fact is only noted in footnotes if the software that is required is additional software provided by a third party.

Histology of Nervous Tissue Laboratory Course
type: Resource
type: NamedIndividual
has db xref: nif-0000-21192
synonym: Histology of Nervous Tissue Laboratories 9 and 10
abbrev: Histology of Nervous Tissue
IAO_0000115: A website for a neuroscience lab class from the University of South Carolina that contains images of different parts of the nervous system and allows students to identify each part and answer questions about it. You should be able to (a) recognize nervous tissue in routine histological sections; (b) distinguish peripheral nerves from dense CT and smooth muscle; (c) recognize the morphological differences between myelinated and unmyelinated nerves at both the light microscopic and electron microscopic levels; (d) recognize nerve cell bodies and their component parts; (e) identify and differentiate dendrites and axons; (f) understand and identify various types of neuroglia, including Schwann cells; (g) understand and identify the structural relationship of the Schwann cell cytoplasm and plasma membrane enveloping axons; (h) understand the general features of nerve synapses. You should be able to draw nerves, cell bodies, Nodes of Ranvier, synapses etc. as they would appear under both the electron and light microscopes.

MetaMorph Microscopy Automation and Image Analysis Software
type: Resource
type: NamedIndividual
has db xref: SciRes_000136
synonym: MetaMorph image analysis software
synonym: MetaMorph version 7.8.0.0
synonym: Molecular Devices Metamorph Premier Software
abbrev: MetaMorph
IAO_0000115: Software tool for automated microscope acquisition, device control, and image analysis. Used for integrating dissimilar fluorescent microscope hardware and peripherals into a single custom workstation, while providing all the tools needed to perform analysis of acquired images. Offers user friendly application modules for analysis such as cell signaling, cell counting, and protein expression.

HistoWeb: Nervous System
type: Resource
type: NamedIndividual
has db xref: nif-0000-21194
synonym: HistoWeb Nervous System
synonym: KU HistoWeb Nervous System
synonym: University of Kansas Nervous System
abbrev: HistoWeb Nervous
abbrev: KU Nervous
abbrev: KU Nervous System
IAO_0000115: Histology atlas of different parts of the nervous system that corresponds with the laboratory exercises of the Cell & Tissue Biology course of the School of Medicine of the University of Kansas. Succinct explanations of the tissues to guide the first-year medical student in the use of their microscope is provided and subsequently serves as a permanent histology resource for all medical students and physicians. Sections of the brain that are included are: * Spinal Cord * Central Canal * White Matter * Gray Matter * Dorsal Root Ganglion * Cerebellum * Cerebrum * Astrocytes * Nerve * Node of Ranvier * Pacinian Corpuscle

Human Mortality Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-21197
synonym: The Human Mortality Database
abbrev: HMD
IAO_0000115: A database providing detailed mortality and population data to those interested in the history of human longevity. For each country, the database includes calculated death rates and life tables by age, time, and sex, along with all of the raw data (vital statistics, census counts, population estimates) used in computing these quantities. Data are presented in a variety of formats with regard to age groups and time periods. The main goal of the database is to document the longevity revolution of the modern era and to facilitate research into its causes and consequences. New data series is continually added to this collection. However, the database is limited by design to populations where death registration and census data are virtually complete, since this type of information is required for the uniform method used to reconstruct historical data series. As a result, the countries and areas included are relatively wealthy and for the most part highly industrialized. The database replaces an earlier NIA-funded project, known as the Berkeley Mortality Database. * Dates of Study: 1751-present * Study Features: Longitudinal, International * Sample Size: 37 countries or areas

SBARS
type: Resource
type: NamedIndividual
has db xref: biotools:sbars
has db xref: OMICS_03432
synonym: S.B.A.R.S
synonym: S.B.A.R.S - Spectral-Based Approach for Repeats Search
synonym: S.B.A.R.S.
synonym: Spectral-Based Approach for Repeats Search
IAO_0000115: Bioinformatics tool for searching different types of long repeats in sequences comparable by size with chromosomes.

DPARSF
type: Resource
type: NamedIndividual
has db xref: nlx_155735
synonym: Data Processing Assistant for Resting-State fMRI
IAO_0000115: A MATLAB toolbox forpipeline data analysis of resting-state fMRI that is based on Statistical Parametric Mapping (SPM) and a plug-in software within DPABI. After the user arranges the Digital Imaging and Communications in Medicine (DICOM) files and click a few buttons to set parameters, DPARSF will then give all the preprocessed (slice timing, realign, normalize, smooth) data and results for functional connectivity, regional homogeneity, amplitude of low-frequency fluctuation (ALFF), fractional ALFF, degree centrality, voxel-mirrored homotopic connectivity (VMHC) results. DPARSF can also create a report for excluding subjects with excessive head motion and generate a set of pictures for easily checking the effect of normalization. In addition, users can also use DPARSF to extract time courses from regions of interest. DPARSF basic edition is very easy to use while DPARSF advanced edition (alias: DPARSFA) is much more flexible and powerful. DPARSFA can parallel the computation for each subject, and can be used to reorient images interactively or define regions of interest interactively. Users can skip or combine the processing steps in DPARSF advanced edition freely.

Human Proteomics Initiative
type: Resource
type: NamedIndividual
has db xref: nif-0000-21199
synonym: Human Proteome Initiative
synonym: UniProtKB/Swiss-Prot Human Proteome Initiative
abbrev: HPI
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 03, 2011. IT HAS BEEN REPLACED BY A NEW UniProtKB/Swiss-Prot ANNOTATION PROGRAM CALLED UniProt Chordata protein annotation program. The Human Proteome Initiative (HPI) aims to annotate all known human protein sequences, as well as their orthologous sequences in other mammals, according to the quality standards of UniProtKB/Swiss-Prot. In addition to accurate sequences, we strive to provide, for each protein, a wealth of information that includes the description of its function, domain structure, subcellular location, similarities to other proteins, etc. Although as complete as currently possible, the human protein set they provide is still imperfect, it will have to be reviewed and updated with future research results. They will also create entries for newly discovered human proteins, increase the number of splice variants, explore the full range of post-translational modifications (PTMs) and continue to build a comprehensive view of protein variation in the human population. The availability of the human genome sequence has enabled the exploration and exploitation of the human genome and proteome to begin. Research has now focused on the annotation of the genome and in particular of the proteome. With expert annotation extracted from the literature by biologists as the foundation, it has been possible to expand into the areas of data mining and automatic annotation. With further development and integration of pattern recognition methods and the application of alignments clustering, proteome analysis can now be provided in a meaningful way. These various approaches have been integrated to attach, extract and combine as much relevant information as possible to the proteome. This resource should be valuable to users from both research and industry. We maintain a file containing all human UniProtKB/Swiss-Prot entries. This file is updated at every biweekly release of UniProt and can be downloaded by FTP downlo…

Hazardous Substances Data Bank
type: Resource
type: NamedIndividual
has db xref: nif-0000-21201
has db xref: r3d100011209
synonym: Hazardous Substances DataBank
synonym: HSDB - A TOXNET DATABASE
abbrev: HSDB
IAO_0000115: A toxicology database that focuses on the toxicology of potentially hazardous chemicals. It provides information on human exposure, industrial hygiene, emergency handling procedures, environmental fate, regulatory requirements, nanomaterials, and related areas. The information in HSDB has been assessed by a Scientific Review Panel.

Neighbourhood Approximation Forest
type: Resource
type: NamedIndividual
has db xref: SciRes_000135
synonym: Neighbourhood Approximation Forests
abbrev: NAF
IAO_0000115: General purpose machine learning tool that is useful for supervised classification and regression problems as well as more generic problems such as patch-based segmentation.

IconBAZAAR
type: Resource
type: NamedIndividual
has db xref: nif-0000-21212
IAO_0000115: This website contains animated 3D molecular models for amino acids, carbohydrates, and drugs. The amino acids listed are: -Alanine -Arginine -Asparagine -Aspartate -Cysteine -Glutamine -Glutamate -Glycine -Histidine -Isoleucine -Leucine -Lysine -Methionine -Phenylalanine -Proline -Serine -Threonine -Tryptophan -Tyrosine -Valine The categories of drugs included are: -Analgesics -Mood Elevators -Antacids -Psychedelics -Aphrodisiacs -Depressants -Stimulants -Intoxicants The carbohydrates listed are: -Fructose -Glucosamine -Glucose -Glyceraldehyde -Glycerol -Lactose -Maltose -Mannitol -Ribose -Ribulose -Sorbitol -Sucrose

International Committee on Taxonomy of Viruses
type: Resource
type: NamedIndividual
has db xref: nif-0000-21213
synonym: Universal Virus Database
synonym: Virus Taxonomy Knowledgebase
synonym: Virus Taxonomy: A community Knowledgebase Supporting Virus Research
abbrev: ICTV
IAO_0000115: International Committee on Taxonomy of Viruses (ICTV) is charged by the Virology Division of the International Union of Microbiological Societies (IUMS) with developing, refining, and maintaining the official, universal taxonomy of all viruses. The goal is to classify and name all known viruses into a single taxonomy that reflects their evolutionary relationships. It provides a variety of resources in support of that goal including online and downloadable versions of current and historical releases of the virus taxonomy.

IDbases
type: Resource
type: NamedIndividual
has db xref: nif-0000-21214
IAO_0000115: IDbases are locus-specific databases for immunodeficiency-causing mutations. Our aim is to establish database for every immunodeficiency or provide links to those maintained elsewhere. IDbases contain in addition to gene mutation, also information about clinical presentation. Information has been collected from literature as well as received directly from researchers. It would be most glad if those analyzing mutations would send their information by using the interactive web submission available in each database. A number of articles have been published related to IDbases. IDbases are curated and distributed with proprietary MUTbase software suite.

Images from the Clendening Library
type: Resource
type: NamedIndividual
has db xref: nif-0000-21217
IAO_0000115: Database of images from medical and natural history texts, most of which were printed before 1800. They are organized by theme: diagnostics, human body, imaging, instruments, physician-patient culture, portraits, public health, reproduction, reproduction instruments, therapeutics. The Clendening History of Medicine Library and Museum is the rare books and manuscripts library of the University of Kansas Medical Center. We actively collect rare books as well as current works in the history of medicine, nursing, and the allied professions. The Library also supports the biomedical ethics and medical humanities curriculum by collecting contemporary secondary works in these areas. Under the auspices of its Museum, the Library also owns hundreds of medical artifacts.

UniProt
type: Resource
type: NamedIndividual
has db xref: nif-0000-00377
has db xref: r3d100010357
has db xref: SCR_018750
synonym: The Universal Protein Resource
synonym: UNIPROT Universal Protein Resource
synonym: Universal Protein Resource
IAO_0000115: Collection of data of protein sequence and functional information. Resource for protein sequence and annotation data. Consortium for preservation of the UniProt databases: UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc), UniProt Proteomes. Collaboration between European Bioinformatics Institute (EMBL-EBI), SIB Swiss Institute of Bioinformatics and Protein Information Resource. Swiss-Prot is a curated subset of UniProtKB.

Neuroscience Course - Atlas Images
type: Resource
type: NamedIndividual
has db xref: nif-0000-00117
synonym: Neuroscience Course Atlas Images
IAO_0000115: Online educational resource for human brain and spinal cord anatomy through images. Each image is annotated with major structures and coarse dissections.

Clinical and Laboratory Standards Institute
type: Resource
type: NamedIndividual
has db xref: OMICS_01777
abbrev: CLSI
IAO_0000115: A not-for-profit membership organization that brings together the global laboratory community to foster excellence in laboratory medicine by facilitating the development of clinical laboratory testing standards based on input from and consensus among industry, government, and health care professionals. CLSI is setting the standard for quality in clinical laboratory testing around the world.

JGI Genome Portal
type: Resource
type: NamedIndividual
has db xref: biotools:jgi_genome_portal
has db xref: nif-0000-21230
has db xref: nlx_69965
has db xref: OMICS_01654
synonym: DOE Joint Genome Institute Genome Portal
IAO_0000115: Portal providing access to all JGI genomic databases and analytical tools, sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms. The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web.

Cancer Genomics Consortium
type: Resource
type: NamedIndividual
has db xref: OMICS_01776
synonym: Cancer Cytogenomics Microarray Consortium
synonym: CCMC
abbrev: CGC
IAO_0000115: Consortium promoting communication and collaboration among cancer cytogenomics laboratories, who are interested in applying microarray technologies to cancer diagnosis and cancer research. Their oals are to (1) establish platform-neutral and cancer specific microarray designs for diagnostic purposes, (2) share cancer microarray data between participating institutions for education purposes, (3) create a public cancer array database, and (4) carry out multicenter cancer genome translational research. Collaboration amongst the different laboratories and researchers will not only provide validation for the microarray design(s) but ultimately provide more comprehensive molecular information and more accurate interpretation to better serve cancer patients and further cancer research. The CGC was officially incorporated in June 2010 as a not-for-profit organization.

University of Amsterdam; Amsterdam; Netherlands
type: Organization
type: NamedIndividual
has db xref: nlx_19684
synonym: Universiteit van Amsterdam
synonym: University of Amsterdam
abbrev: UvA
IAO_0000115: Public research university in the Netherlands that offers programs in humanities, social and behavioural sciences, economics and business, science, law, medicine, and dentistry.

Concierge
type: Resource
type: NamedIndividual
has db xref: nif-0000-00379
synonym: Concierge Project
synonym: Concierge: Personal Database Software for Digital Research Resources
synonym: Concierge: Personal Database Software for Managing Digital Research Resources
synonym: The Concierge Project: Personal Database Software for Digital Research Resources
IAO_0000115: A data management tool which stores, classifies and manages digital resources such as publications, experimental data, presentation files, etc, together with its metadata. A key feature of the software is a high level of extensibility. By installing optional plug-ins, users can customize and extend the usability of the software based on their needs. It has a function of sharing data with open digital archives based on the XooNIps system, such as neuroinformatics platforms in operation and publicly available at J-Node (http://www.neuroinf.jp). The Concierge Project is a part of neuroinformatics research by Laboratory for Neuroinformatics in RIKEN Brain Science Institute. Concierge's primary goal is to encourage research resource sharing in neuroscience communities. A key feature of the software is its pluggable configuration. Based on the basic functions, various applications can be developed as plug-ins. It has already developed several application plug-ins specific to neuroscience research, e.g. literature manager, electronic laboratory notebook, etc.

BEAT
type: Resource
type: NamedIndividual
has db xref: OMICS_03425
synonym: BEAT - BS-Seq Epimutation Analysis Toolkit
synonym: BS-Seq Epimutation Analysis Toolkit
IAO_0000115: Software that implements all bioinformatics steps required for the quantitative, high-resolution analysis of DNA methylation patterns from bisulfite sequencing data.

GeneNetwork
type: Resource
type: NamedIndividual
has db xref: nif-0000-00380
synonym: GeneNetwork / WebQTL
synonym: GeneNetwork and WebQTL
synonym: GeneNetwork WebQTL
synonym: The GeneNetwork / WebQTL
synonym: www.genenetwork.org
abbrev: WebQTL
IAO_0000115: Web platform that provides access to data and tools to study complex networks of genes, molecules, and higher order gene function and phenotypes. Sequence data (SNPs) and transcriptome data sets (expression genetic or eQTL data sets). Quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. Used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Users are welcome to enter their own private data.

Honey Bee Brain EST Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-00118
synonym: Honeybee EST Project
abbrev: Bee-ESTdb
IAO_0000115: A database integrating data from the bee brain EST sequencing project with data from sequencing and gene research projects from other organisms, primarily the fruit fly Drosophila melanogaster. The goal of Bee-ESTdb is to provide updated information on the genes of the honey bee, currently using annotation primarily from flies to suggest cellular roles, biological functions, and evolutionary relationships. The site allows searches by sequence ID, EST annotations, Gene Ontology terms, Contig ID and using BLAST. Very nice resource for those interested in comparative genomics of brain. A normalized unidirectional cDNA library was made in the laboratory of Prof. Bento Soares, University of Iowa. The library was subsequently subtracted. Over 20,000 cDNA clones were partially sequenced from the normalized and subtracted libraries at the Keck Center, resulting in 15,311 vector-trimmed, high-quality, sequences with an average read length of 494 bp. and average base-quality of 41. These sequences were assembled into 8966 putatively unique sequences, which were tested for similarity to sequences in the public databases with a variety of BLAST searches. The Clemson University Genomics Institute is the distributor of these public domain cDNA clones. For information on how to purchase an individual clone or the entire collection, please contact www.genome.clemson.edu/orders/ or generobi (at) life.uiuc.edu.

GLIRT
type: Resource
type: NamedIndividual
has db xref: nlx_155763
synonym: Groupwise and Longitudinal Image Registration Toolbox
IAO_0000115: Software for both groupwise registration and longitudinal registration, which are the necessary steps for many brain-related applications. Specifically, groupwise registration is important for unbiased analysis of a large set of MR brain images. Therefore, in this software package, they have included two of their recently-developed groupwise registration algorithms: 1) Improved unbiased groupwise registration guided with the sharp group-mean image, and 2) Hierarchical feature-based groupwise registration with implicit template (Groupwise-HAMMER for short). On the other hand, they also included their recently-developed groupwise longitudinal registration algorithm that aligns not only the longitudinal image sequence for each subject, but also align all longitudinal image sequences of all subjects to the common space simultaneously.

MINC
type: Resource
type: NamedIndividual
has db xref: nlx_155794
synonym: Medical Imaging NetCDF
synonym: MINC - Medical Image NetCDF
IAO_0000115: A medical imaging data format and an associated set of tools and libraries including a 3 level API for medical image analysis with a particular focus on the needs of research. There are also a number of tools including Registration and Non-Uniformity correction.

DOMINO: Domain peptide interactions
type: Resource
type: NamedIndividual
has db xref: nif-0000-02759
has db xref: OMICS_01907
has db xref: r3d100010684
synonym: DOMINO
IAO_0000115: Open-access database comprising more than 3900 annotated experiments describing interactions mediated by protein-interaction domains. The curation effort aims at covering the interactions mediated by the following domains (SH3, SH2, 14-3-3, PDZ, PTB, WW, EVH, VHS, FHA, EH, FF, BRCT, Bromo, Chromo, GYF). The interactions deposited in DOMINO are annotated according to the PSI MI standard and can be easily analyzed in the context of the global protein interaction network as downloaded from major interaction databases like MINT, INTACT, DIP, MIPS/MPACT. It can be searched with a versatile search tool and the interaction networks can be visualized with a convenient graphic display applet that explicitly identifies the domains/sites involved in the interactions.

Visible Mouse Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-00119
synonym: The Visible Mouse Project
IAO_0000115: Educational resource to introduce users to the anatomy, physiology, histology, and pathology of the laboratory mouse, with an emphasis on the Genetically Engineered Mouse (GEM). It provides access to histological images, scanned at high resolution and browsable through Zoomify, movie loops and animations derived from MRI, correlated MRI and histology. It has CNS data but is focused on the whole body, e.g., physiological data is available for the heart in the form of wave patterns, histology, CNS, pathology, magnetic resonance imaging, neoplasms; animation, virtual histology, mouse, correlated imaging, necropsy, whole mouse. It may be useful to neuroscientists by relating brain anatomy to the rest of the body. There is a movie illustrating necropsy of the mouse. A link to a compendium of histological slices of brain neoplasms is provided under the Image Archive link. There is a CNS link under construction for anatomical system, which presumably will include detailed CT imaging. This site still appears to be under construction.

R Tutorial - An R Introduction to Statistics
type: Resource
type: NamedIndividual
has db xref: OMICS_01762
synonym: R Tutorial (An R Introduction to Statistics)
abbrev: R Tutorial
IAO_0000115: Couple of introductory tutorials on basic R concepts that provides an introduction to the R programming language, and illustrates its use by solving elementary statistics textbook exercises. Beyond the basics, they also cover topics of GPU computing in R. An R Tutorial eBook is also available.

R Tutorial
type: Resource
type: NamedIndividual
has db xref: OMICS_01761
IAO_0000115: Online educational resource that provides introductory-level material for new R users who have basic experience with programming.

Online Information Center for Immunohistochemistry
type: Resource
type: NamedIndividual
has db xref: nif-0000-00120
synonym: IHC World
IAO_0000115: This site provides access to a very wide variety of histological protocols either directly or through links. An entire section is devoted to neuroscience, including neurohistology and cell culture protocols.protocol, experimental technique.

Group Level Imputation of Statistic Maps
type: Resource
type: NamedIndividual
has db xref: nlx_155768
IAO_0000115: A software toolkit that performs multiple imputation for group level, single sample t-tests. Whole brain group level statistic maps from fMRI rarely cover the entire brain as a result of missing data. Missingness between subjects in fMRI datasets can result from susceptibility artifacts, bounding box (acquisition parameters), and small differences in post-normalized morphology. The toolkit consists of several interactive command line scripts that guide the user to map the spatial distribution of missing data across contrast images, calculate spatial neighborhood averages that help impute values, perform conventional and multiple imputed t-statistics, save the results to brain maps, and create result tables. The toolkit contains an instruction manual (pdf), two Matlab scripts and one R-Statistics script, which depend on functions defined in the popular SPM toolbox and functions defined in the MICE package for (R).

NeuroSpin MEG
type: Resource
type: NamedIndividual
has db xref: SciRes_000132
synonym: Neuro Spin MEG
IAO_0000115: A magnetoencephalography facility hosted at NeuroSpin (CEA Saclay, France) equipped with a 306-channel MEG system from Elekta Neuromag, EEG and EGI systems, and an Eyelink 1000 eye-tracker from SR research. A large set of MEG data analysis tools are being used in the lab including mne-python, fieldtrip, brainstorm, spm, adjust and in-house techniques are also being developed.

DOMINE: Database of Protein Interactions
type: Resource
type: NamedIndividual
has db xref: biotools:domine
has db xref: nif-0000-02758
has db xref: OMICS_01906
synonym: Database of Protein Domain Interactions
abbrev: DOMINE
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13,2026. Database of known and predicted protein domain (domain-domain) interactions containing interactions inferred from PDB entries, and those that are predicted by 8 different computational approaches using Pfam domain definitions. DOMINE contains a total of 26,219 domain-domain interactions (among 5,410 domains) out of which 6,634 are inferred from PDB entries, and 21,620 are predicted by at least one computational approach. Of the 21,620 computational predictions, 2,989 interactions are high-confidence predictions (HCPs), 2,537 interactions are medium-confidence predictions (MCPs), and the remaining 16,094 are low-confidence predictions (LCPs). (May 2014)

University of Angers; Angers; France
type: Organization
type: NamedIndividual
has db xref: nlx_153965
synonym: Universite d'Angers
synonym: University of Angers
abbrev: UA
IAO_0000115: Public institution of higher learning in western France that offers programs four major areas: law, economics and business; arts, letters and languages; human and social sciences; and sciences, technology and health.

Avian Brain Circuitry Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-00386
abbrev: ABCD
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 21, 2017. Database developed for storing, retrieving and cross-referencing neuroscience information about the connectivity of the avian brain. It contains entries about the new and old terminology of the areas and their hierarchy and data on connections between brain regions, as well as a functional keyword system linked to brain regions and connections.

Neuroanatomy Atlas
type: Resource
type: NamedIndividual
has db xref: nif-0000-00121
IAO_0000115: Annotated magnetic resonance brain images, both slices and surface views, normalized to Talairach space, along with annotations and a nice tutorial on image normalization. A viewer for MRI images (MRicro) is available and is described in a separate entry. Series of coronal, axial and sagittal brain slices along with some rendered volumes with major brain structures delineated. Slices are presented as static series with partial overlap of slices, so they are not suitable for 3d reconstruction. This neuroanatomy atlas shows regions on normalized MRI scans. Normalization is the process of warping a brain to match a standard size, orientation and shape of other brains. You can normalize MRI scans using programs like AIR, FLIRT or SPM. Once normalized, the overall shape of your MRI scan will approximately match those in this atlas. However, normalization preserves the unique sulcal features of each brain, so there will be some variation between your image and the images shown in this atlas. There is a great deal of individual variability even after normalization, so any atlas is only a rough guide to the shape and location of structures in an individuals brain. As I have noted before, secondary and tertiary sulci are not found in all individuals (Ono et al. 1990, Atlas of Cerebral Sulci). Another benefit of normalizing brains is it makes it easy to complete an accurate "scalp stripping" with brain extracting software (my MRIcro software implements Steve Smith's BET for this task). You can then create a useful volume rendering of the cortical surface. Typically, it is much easier to identify cortical sulci and gyri by looking at a rendered image of the brain's surface. This atlas shows you how to recognize these landmarks on a rendered MRI scan.

MRIcron
type: Resource
type: NamedIndividual
has db xref: biotools:MRIcron
has db xref: nif-0000-00122
synonym: mricron - magnetic resonance image conversion viewing and analysis
IAO_0000115: Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron.

Inter-Group Registration Toolbox
type: Resource
type: NamedIndividual
has db xref: nlx_155777
abbrev: InterGroupReg
IAO_0000115: Software package that provides solutions for registering two groups of images, which are the necessary steps for many brain-related applications.

UPR Conrado F. Asenjo Library
type: Resource
type: NamedIndividual
has db xref: nlx_156601
IAO_0000115: The most comprehensive health sciences collection in Puerto Rico.

GenomeSmasher
type: Resource
type: NamedIndividual
has db xref: OMICS_00251
IAO_0000115: Software repository for tools used to create diploid FASTA files with containing snps, indels, duplications, deletions, and translocations. They can be used to create artificial genomes for next-gen sequencing simulations.

Rhetorical Document Structure Group HCLS IG W3C
type: Resource
type: NamedIndividual
has db xref: nif-0000-02764
abbrev: Rhetorical Document Structure Group
IAO_0000115: This group aims to define a "rhetorical structure" for scientific papers, to use in authoring or mark-up tools. They are trying to come to a definition of such a format; have an intermediary proposal of their own and are beginning to make an overview of existing publisher's proposals. Objectives *O1: Study and develop a model -- set of elements -- (a core model plus additional domain-specific modules), that capture the rhetorical aspects of scientific publications at different granular levels. *O2: In the long run, integrate the developed model in different environments to improve the authoring, retrieving and browsing user experience. *O3: Make a mocked up annotated document collection using this element set for each use case. *O4: Disseminate these models and document systems to the rest of the W3C and the community at large.

UPR Confocal Microscope Facility
type: Resource
type: NamedIndividual
has db xref: nlx_156600
IAO_0000115: Core facility that provides the following services: Classic confocal imaging experiments.

DOSY Toolbox
type: Resource
type: NamedIndividual
has db xref: OMICS_03393
synonym: The DOSY Toolbox
synonym: The DOSY Toolbox processing PFG-NMR diffusion data
IAO_0000115: Software toolbox for processing PFG NMR diffusion data that aims to incorporate many of the important processing schemes. It has a graphical user interface to make it easy to access a variety of different processing schemes (and a command mode for more advanced options). It is written in MATLAB, but can also be obtained as free standing compiled version that does not require a MATLAB installation. The MATLAB version runs on any platform, and the compiled version is presently available for Windows, Linux, and Mac.

Marine Biological Laboratory
type: Organization
type: NamedIndividual
has db xref: grid.144532.5
has db xref: ISNI: 000000012169920X
has db xref: nif-0000-00389
has db xref: Wikidata: Q500632
synonym: Marine Biological Laboratory in Woods Hole
abbrev: MBL
IAO_0000115: Private non-profit laboratory at the University of Chicago that works on scientific discovery of biodiversity, understanding the environment and exploring the human condition through education and research.

PaleoVu
type: Resource
type: NamedIndividual
has db xref: SciRes_000130
IAO_0000115: A complete browse and visualization tool for all types of paleoclimate and paleoecological data (Version 1.0 for Windows 3.1 and the Macintosh). Point and click to create queries, list site information, display or plot variables and data, or export the data for further processing and analysis. Note: PaleoVu is no longer maintained or supported. Data content is not being updated, and compatibility problems may exist with newer operating systems. PaleoVu is still suitable as a teaching tool, but our internet-based browsing tools are the most up to date source for paleoclimatic data.

MUMA
type: Resource
type: NamedIndividual
has db xref: OMICS_03370
synonym: Metabolomic Univariate and Multivariate Analysis
synonym: Metabolomics Univariate and Multivariate Analysis (MUMA)
IAO_0000115: Software that provides guidelines for the whole process of metabolomic data interpretation, from data pre-processing, to dataset exploration and visualization, to identification of potentially interesting metabolites. Guidelines outline the following processes: preprocessing of high-throughput data (normalization and scalings); principal component analysis with help tool for choosing best-separating principal components and automatic testing for outliers; automatic univariate analysis for parametric and non-parametric data, with generation of specific reports (volcano and box plots); partial least square discriminant analysis (PLS-DA); orthogonal partial least square discriminant analysis (OPLS-DA); Statistical Total Correlation Spectroscopy (STOCSY); and Ratio Analysis Nuclear Magnetic Resonance (NMR) Spectroscopy (RANSY).

Database of Rice Transcription Factors
type: Resource
type: NamedIndividual
has db xref: nif-0000-02771
has db xref: OMICS_00554
abbrev: DRTF
IAO_0000115: Database collection of known and predicted transcription factors of Oryza sativa L. ssp. indica and Oryza sativa L. ssp. japonica. DRTF currently contains 2,025 putative transcription factors (TF) gene models in indica and 2,384 in japonica, distributed in 63 families. THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13,2026.

VennDiagram
type: Resource
type: NamedIndividual
has db xref: OMICS_05570
synonym: VennDiagram: Generate high-resolution Venn and Euler plots
IAO_0000115: Software providing a set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.

Neocortical Microcircuit Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-00124
abbrev: NMDB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 26, 2011. Neurons are characterized in terms of their morphological, physiological and gene expression profiles. Synaptic connections are characterized in terms of their physiological and anatomical profiles. Neuron morphology profiles are obtained from detailed morphometric breakdown of 3D reconstructed neurons (m-Profiles), neuron physiology profiles are obtained from detailed measurement of the electrophysiological responses to a series of stimulus protocols (e-Profiles), and neuron gene expression profiles are obtained from single cell RT-PCR data (g-Profiles) and in the near future from gene-chips. Synaptic connections are characterized by the identity of the pre and postsynaptic neurons (sn-Profile), the anatomy of synaptic connections as characterized by the axonal and dendritic location of light microscopically identified putative synapses (sm-Profile), and the physiology of synaptic connections as characterized by a profile of electrophysiological parameters obtained from a series of stimulation protocols applied to the presynaptic neuron (se-Profile).

Nervous Tissue Color Images
type: Resource
type: NamedIndividual
has db xref: nif-0000-21281
synonym: UD Nervous Tissue Color Images
synonym: University of Delaware Nervous Tissue Color Images
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13,2026. An image collection of tissue from the central nervous system and peripheral nervous system.

Quick-R
type: Resource
type: NamedIndividual
has db xref: OMICS_01760
synonym: Quick-R - accessing the power of R
IAO_0000115: Training material created for both current R users, and experienced users of other statistical packages (e.g., SAS, SPSS, Stata) who would like to transition to R to help you quickly access this language in your work. The book inspired by this site takes the material here and significantly expands upon it.

Ligand-Gated Ion Channel Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-00037
has db xref: r3d100010796
synonym: LGIC Database
abbrev: LGICdb
IAO_0000115: Database providing access to information about transmembrane proteins that exist under different conformations, with three primary subfamilies: the cys-loop superfamily, the ATP gated channels superfamily, and the glutamate activated cationic channels superfamily. Due to the lack of evolutionary relationship, these three superfamilies are treated separately. It currently contains 554 entries of ligand-activated ion channel subunits. In this database one may find: the nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Additionally, the atomic coordinates of subunits, or portion of subunits, are provided when available. Redundancy is kept to a minimum, i.e. one entry per gene. Each entry in the database has been manually constructed and checked by a researcher of the field in order to reduce the inaccuracies to a minimum. NOTE: This database is not actively maintained anymore. People should not consider it as an up-to-date trustable resource. For any new work, they should consider using alternative sources, such as UniProt, Ensembl, Protein Databank etc.

MCML and CONV
type: Resource
type: NamedIndividual
has db xref: nlx_155791
synonym: Monte Carlo for Multi-Layered media
abbrev: CONV
abbrev: MCML
abbrev: MCML & CONV
IAO_0000115: MCML is a Monte Carlo simulation program for Multi-layered Turbid Media with an infinitely narrow photon beam as the light source. The simulation is specified by an input text file called, for example, sample.mci, which can be modified by any simple text editor. The output is another text file called, for example, sample.mco. (The names are arbitrary.) CONV is a convolution program which uses the MCML output file to convolve for photon beams of any size in a Gaussian or flat field shape. CONV can provide a variety of output formats (reflectance, transmission, iso-fluence contours, etc.), which are compatible with standard graphics applications.

MEGSIM
type: Resource
type: NamedIndividual
has db xref: nlx_155793
IAO_0000115: Realistic simulated MEG datasets ranging from basic sensory to oscillatory sets that mimic functional connectivity; as well as basic visual, auditory, and somatosensory empirical sets. The simulated sets were created for the purpose of testing analysis algorithms across the different MEG systems when the truth is known. MEG baseline recordings were obtained from 5 healthy participants, using three MEG systems: VSM/CTF Omega, Elekta Neuromag Vectorview, 4-D Magnes 3600. Simulated signals were embedded within the CTF and Neuromag 306 baseline recordings (4-D to be added). Participant MRIs are available. Averaged simulation files are available as netcdf files. Neuromag 306 averaged simulations are also available in fif format. Also available: single trials of data where the simulated signal is jittered about a mean value, continuous fif files where the simulated signal is marked by a trigger, and simulations with oscillations added to mimic functional connectivity.

UPR Department of Environmental Health Core Laboratory
type: Resource
type: NamedIndividual
has db xref: nlx_156602
IAO_0000115: Laboratory that provides physical space for equipment and research by faculty at the University of Puerto Rico.

MIRIAD
type: Resource
type: NamedIndividual
has db xref: nlx_155795
synonym: Minimal Interval Resonance Imaging in Alzheimer's Disease
synonym: Minimal Interval Resonance Imaging in Alzheimer's Disease - public dataset
synonym: MIRIAD database
synonym: MIRIAD dataset
synonym: MIRIAD XNAT database
IAO_0000115: A database of volumetric MRI brain-scans of 46 Alzheimer's sufferers and 23 healthy elderly people. Many scans were collected of each participant at intervals from 2 weeks to 2 years, the study was designed to investigate the feasibility of using MRI as an outcome measure for clinical trials of Alzheimer's treatments. It includes a total of 708 scans and should be of particular interest for work on longitudinal biomarkers and image analysis.

NIH Toolbox - Assessment of Neurological and Behavioral Function
type: Resource
type: NamedIndividual
has db xref: nif-0000-00393
synonym: NIH Toolbox - Assessment of Neurological Behavioral Function
synonym: NIH Toolbox for Assessment of Neurological and Behavioral Function
synonym: NIH Toolbox for the Assessment of Neurological and Behavioral Function
abbrev: NIH Toolbox
IAO_0000115: An integrated set of tools for measuring cognitive, emotional, motor and sensory function. These tools are being validated for use in diverse cultures, ethnic and geographic groups, ages (3-85 years) and study types. The toolbox is expected to provide a more complete picture of neurological and behavioral health in large-scale longitudinal studies, epidemiological studies, and clinical trials; and to facilitate cross-study comparisons. Moreover, the toolbox will: * be minimally burdensome to subjects and investigators, * utilize state-of-the art psychometric approaches and technology, including computer-assisted evaluation, and * be dynamic and adaptable to changes in measurement and technology. * be available in English and Spanish Many clinical studies collect data on aspects of neurological and behavioral function. However, the neurological and behavioral tests currently available to researchers lack uniformity and often require specialized training to administer. These limitations make it difficult to compile data across the full range of normal neurological function, and to compare data across studies. The toolbox is royalty-free and is expected to be available online by summer 2012.

MRI Defacer
type: Resource
type: NamedIndividual
has db xref: nlx_155798
synonym: mri deface
abbrev: mri_deface
IAO_0000115: Tool to remove facial features from an MRI structural image for the purpose of de-identification.

MS lesion segmentation challenge 2008
type: Resource
type: NamedIndividual
has db xref: nlx_155799
synonym: 2008 MICCAI MS Lesion Segmentation Challenge
abbrev: MS Lesion Segmentation 08
IAO_0000115: Training material for the MS lesion segmentation challenge 2008 to compare different algorithms to segment the MS lesions from brain MRI scans. Data used for the workshop is composed of 54 brain MRI images and represents a range of patients and pathology which was acquired from Children's Hospital Boston and University of North Carolian. Data has initially been randomized into three groups: 20 training MRI images, 24 testing images for the qualifying and 8 for the onsite contest at the 2008 workshop. The downloadable online database consists now of the training images (including reference segmentations) and all the 32 combined testing images (without segmentations). The naming has not been changed in comparison to the workshop compeition in order to allow easy comparison between the workshop papers and the online database papers. One dataset has been removed (UNC_test1_Case02) due to considerable motion present only in its T2 image (without motion artifacts in T1 and FLAIR). Such a dataset unfairly penalizes methods that use T2 images versus methods that don't use the T2 image. Currently all cases have been segmented by expert raters at each institution. They have significant intersite variablility in segmentation. MS lesion MRI image data for this competition was acquired seperately by Children's Hospital Boston and University of North Carolina. UNC cases were acquired on Siemens 3T Allegra MRI scanner with slice thickness of 1mm and in-plane resolution of 0.5mm. To ease the segmentation process all data has been rigidly registered to a common reference frame and resliced to isotrophic voxel spacing using b-spline based interpolation. Pre-processed data is stored in NRRD format containing an ASCII readable header and a separate uncompressed raw image data file. This format is ITK compatible. If you want to join the competition, you can download data set from links here, and submit your segmentation results at http://www.ia.unc.edu/MSseg after registering your team.…

EBI Genomes
type: Resource
type: NamedIndividual
has db xref: nif-0000-02778
synonym: ENA Genomes Server
synonym: Genomes Pages - At the EBI
IAO_0000115: The EBI genomes pages give access to a large number of complete genomes including bacteria, archaea, viruses, phages, plasmids, viroids and eukaryotes. Methods using whole genome shotgun data are used to gain a large amount of genome coverage for an organism. WGS data for a growing number of organisms are being submitted to DDBJ/EMBL/GenBank. Genome entries have been listed in their appropriate category which may be browsed using the website navigation tool bar on the left. While organelles are all listed in a separate category, any from Eukaryota with chromosome entries are also listed in the Eukaryota page. Within each page, entries are grouped and sorted at the species level with links to the taxonomy page for that species separating each group. Within each species, entries whose source organism has been categorized further are grouped and numbered accordingly. Links are made to: * taxonomy * complete EMBL flatfile * CON files * lists of CON segments * Project * Proteomes pages * FASTA file of Proteins * list of Proteins

ANOVA
type: Resource
type: NamedIndividual
has db xref: SciRes_000129
synonym: Analysis of Variance
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2023. Matlab code for two-factor (location and year) analysis-of-variance model for the calculation of climate anomalies, in which the reference interval is specified as the full length of the dataset. This scheme avoids the affects of shorter (e.g. 1961-1990) reference intervals on the temporal evolution of the spatial standard deviation of climate anomalies. Data files provided.

ABCDE Format
type: Resource
type: NamedIndividual
has db xref: nif-0000-02794
synonym: ABCDE Format - Publishing Semantic Conference Papers
abbrev: ABCDE
IAO_0000115: Proposed format for papers to be machine-readable for computers and wikis. The goal is to make mining, integration, and consumption of published information by semantic browsers and wikis easier.

Measure Projection Toolbox
type: Resource
type: NamedIndividual
has db xref: nlx_155809
synonym: Measure Projection Toolbox (MPT)
abbrev: MPT
IAO_0000115: This toolbox is an EEGLAB plugin for performing Measure Projection Analysis. Measure Projection Analysis (MPA) is a novel probabilistic multi-subject inference method that overcomes EEG Independent Component (IC) clustering issues by abandoning the notion of distinct IC clusters. Instead, it searches voxel by voxel for brain regions having event-related IC process dynamics that exhibit statistically significant consistency across subjects and/or sessions as quantified by the values of various EEG measures. Local-mean EEG measure values are then assigned to all such locations based on a probabilistic model of IC localization error and inter-subject anatomical and functional differences.

EchoBASE
type: Resource
type: NamedIndividual
has db xref: biotools:echobase
has db xref: nif-0000-02781
has db xref: r3d100011646
synonym: EchoBASE: an integrated post-genomic database for Escherichia coli
IAO_0000115: A database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655. It has been created to integrate information from post-genomic experiments into a single resource with the aim of providing functional predictions for the 1500 or so gene products for which we have no knowledge of their physiological function. While EchoBASE provides a basic annotation of the genome, taken from other databases, its novelty is in the curation of post-genomic experiments and their linkage to genes of unknown function. Experiments published on E. coli are curated to one of two levels. Papers dealing with the determination of function of a single gene are briefly described, while larger dataset are actually included in the database and can be searched and manipulated. This includes data for proteomics studies, protein-protein interaction studies, microarray data, functional genomic approaches (looking at multiple deletion strains for novel phenotypes) and a wide range of predictions that come out of in silico bioinformatic approaches. The aim of the database is to provide hypothesis for the functions of uncharacterized gene products that may be used by the E. coli research community to further our knowledge of this model bacterium.

VS-Lite
type: Resource
type: NamedIndividual
has db xref: SciRes_000128
synonym: Vaganov-Shashkin-Lite
synonym: Vaganov-Shashkin-Lite Model of Tree-Ring Width
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2023. A simple, efficient, process-based forward model of tree-ring growth, requires as inputs only latitude and monthly temperature and precipitation.

Confocal Microscopy Image Gallery - Rat Brain Tissue Sections
type: Resource
type: NamedIndividual
has db xref: nif-0000-21299
synonym: Olympus Rat Brain Tissue Sections
IAO_0000115: An image gallery of the rat brain labeled via immunofluorescence in coronal, horizontal, and sagittal thick sections using laser scanning confocal microscopy.

EcoCyc
type: Resource
type: NamedIndividual
has db xref: nif-0000-02783
has db xref: OMICS_01645
has db xref: r3d100011277
synonym: EcoCyc REF
IAO_0000115: Database for the bacterium Escherichia coli K-12 MG1655, the EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways. The long-term goal of the project is to describe the molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level understanding of E. coli. EcoCyc is an electronic reference source for E. coli biologists, and for biologists who work with related microorganisms.

PROW
type: Resource
type: NamedIndividual
has db xref: nif-0000-21340
synonym: Protein Reviews On the Web
synonym: Protein Reviews on the Web
synonym: PROW - Protein Reviews on the Web
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. It offers short, structured reviews of proteins and protein families, especially leukocyte surface membrane molecules. Index of information available from PROW includes CD molecule, Alternate names, Current Guides, Past Guides, Entrez Gene and Assigning workshop. Current guides: expanded format including Summary Sentence and Abstract Past guides: older guides with excellent information, some data may be dated

object-oriented Transcription Factors Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-21303
synonym: ooTFD
IAO_0000115: ooTFD (object-oriented Transcription Factors Database) is a successor to TFD, the original Transcription Factors Database. This database is aimed at capturing information regarding the polypeptide interactions which comprise and define the properties of transcription factors. ooTFD contains information about transcription factor binding sites, as well as composite relationships within transcription factors, which frequently occur as multisubunit proteins that form a complex interface to cellular processes outside the transcription machinery through protein-protein interactions. ooTFD contains information represented in TFD but also allows the representation of containment, composite, and interaction relationships between transcription factor polypeptides. It is designed to represent information about all transcription factors, both eukaryotic and prokaryotic, basal as well as regulatory factors, and multiprotein complexes as well as monomers.

Tree of Life
type: Resource
type: NamedIndividual
has db xref: OMICS_01725
synonym: The Tree of Life
IAO_0000115: Blog by evolutionary biologist and UC Davis professor Jonathan Eisen. Topics of his posts include microbiology, phylogenomics, product reviews, and a variety of miscellaneous topics.

EcoGene
type: Resource
type: NamedIndividual
has db xref: nif-0000-02784
has db xref: r3d100010546
synonym: EcoGene Database of Escherichia coli Sequence and Function
abbrev: ECK
abbrev: ECOGENE
abbrev: ECOGENE G
IAO_0000115: Database that contains updated information about the Escherichia coli K-12 genome and proteome sequences, including extensive gene bibliographies. Users are able to download customized tables, perform Boolean query comparisons, generate sets of paired DNA sequences, and download any E. coli K-12 genomic DNA sub-sequence. BLAST functions, microarray data, an alphabetical index of genes, and gene overlap queries are also available. The Database Table Downloads Page provides a full list of EG numbers cross-referenced to the new cross-database ECK numbers and other common accession numbers, as well as gene names and synonyms. Monthly release archival downloads are available, but the live, daily updated version of EcoGene is the default mysql database for download queries.

Mindboggle
type: Resource
type: NamedIndividual
has db xref: nlx_155813
IAO_0000115: Mindboggle (http://mindboggle.info) is open source software for analyzing the shapes of brain structures from human MRI data. The following publication in PLoS Computational Biology documents and evaluates the software: Klein A, Ghosh SS, Bao FS, Giard J, Hame Y, Stavsky E, Lee N, Rossa B, Reuter M, Neto EC, Keshavan A. (2017) Mindboggling morphometry of human brains. PLoS Computational Biology 13(3): e1005350. doi:10.1371/journal.pcbi.1005350

Mindboggle-101 atlases
type: Resource
type: NamedIndividual
has db xref: nlx_155814
synonym: Mindboggle-101 manually labeled brains
abbrev: Mindboggle-101
IAO_0000115: Complete set of free, publicly accessible, downloadable atlases, templates, and individual manually labeled brain image data, the largest collection of publicly available, manually labeled human brains in the world! http://journal.frontiersin.org/article/10.3389/fnins.2012.00171/full

flowBeads
type: Resource
type: NamedIndividual
has db xref: OMICS_05592
synonym: flowBeads: Analysis of flow bead data
IAO_0000115: Software package for the analysis of flow cytometry bead data. It extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalization.

ModelGUI
type: Resource
type: NamedIndividual
has db xref: nlx_155816
abbrev: mgui
IAO_0000115: An open source Java-based project intended to provide a graphic user interface (GUI) for interactions between scientists (or enthusiasts) and their data. In its current (beta) form, mgui offers the following functionality: * Cross-platform functionality (with a Java Runtime installation, runs on Linux, Windows, Mac, or Solaris) * 2D rendering of data based upon Java2D, and 3D rendering based upon Java3D * The ability to organize complex datasets into intuitive mgui projects * A processing pipeline interface which allows users to process their datasets with any available Java or native software tools * An extensible I/O framework accommodating a variety of standard and non-standard file formats * Database connectivity using JDBC * Graph visualization based upon the JUNG library * An intuitive Swing-based GUI for managing, querying, and visualizing data * Various CAD-type tools for editing and creating geometry * A computational modelling framework

Multi-Modal MRI Reproducibility Resource
type: Resource
type: NamedIndividual
has db xref: nlx_155818
IAO_0000115: Scan-rescan imaging sessions on 21 healthy volunteers (no history of neurological disease) intended to be a resource for statisticians and imaging scientists to be able to quantify the reproducibility of their imaging methods using data available from a generic 1 hour session at 3T. Imaging modalities include MPRAGE, FLAIR, DTI, resting state fMRI, B0 and B1 field maps, ASL, VASO, quantitative T1 mapping, quantitative T2 mapping, and magnetization transfer imaging. All data have been converted to NIFTI format. Please cite: Bennett. A. Landman, Alan J. Huang, Aliya Gifford, Deepti S. Vikram, Issel Anne L. Lim, Jonathan A.D. Farrell, John A. Bogovic, Jun Hua, Min Chen, Samson Jarso, Seth A. Smith, Suresh Joel, Susumu Mori, James J. Pekar, Peter B. Barker, Jerry L. Prince, and Peter C.M. van Zijl. ?Multi-Parametric Neuroimaging Reproducibility: A 3T Resource Study?, NeuroImage. (2010) NIHMS/PMC:252138 doi:10.1016/j.neuroimage.2010.11.047

Neuron Registry Annotated Corpus
type: Resource
type: NamedIndividual
has db xref: nlx_155862
abbrev: NeuronRegistryCorpus
IAO_0000115: Annotated document corpus, containing PubMed identifiers and text spans of documents reviewed for consideration for the Neuron Registry by Kyle H. Ambert, PhD.

University of Antwerp; Antwerp; Belgium
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100007660
has db xref: grid.5284.b
has db xref: ISNI:0000 0001 0790 3681
has db xref: nlx_44049
has db xref: Wikidata:Q175241
synonym: UAntwerp
synonym: Universiteit Antwerpen
synonym: University of Antwerp
IAO_0000115: Public university in Antwerp, Belgium that offers programs in economics, engineering, arts, design sciences, and medicine and health.

MultiTracer
type: Resource
type: NamedIndividual
has db xref: nlx_155819
synonym: MultiTracer version 2
IAO_0000115: A Java application that allows images to be displayed in three dimensions. The tool allows anatomic structures to be traced and the tracings to be saved in a format that facilitates review and revision. It supports NIfTI-1.1 format float, double and signed and unsigned byte, short, and integer formats and provides legacy support for Analyze 7.5 8 and 16 bit images. It provides image display, editing, delineation of structure boundaries, export of traced contours and generation of masked volumes. Images are displayed in 3 orthogonal views. Time series can be displayed as averaged or contrast images and time courses can be visualized graphically. Version 2 provides enhancements to the original MultiTracer feature set.

Multicomponent T2 estimation with stimulated echo correction
type: Resource
type: NamedIndividual
has db xref: nlx_155820
IAO_0000115: Software tool designed to assist users in the estimation of multiple relaxation components from MRI T2 weighted spin-echo data such as that produced by a Carr-Purcell-Meiboom-Gill (CPMG) sequence. This problem is important to study myelin content in white matter diseases such as multiple sclerosis. Stimulated echoes arising from non-ideal flip angles are accounted for using the Extended Phase Graph (EPG) algorithm. The distribution is modelled as a small number of discrete components and a Bayesian estimation algorithm is provided to determine the weights and locations of the components as well as the actual flip angle. This algorithm outperforms iterative gradient descent based approaches.

NCANDA: Data Integration Component
type: Resource
type: NamedIndividual
has db xref: nlx_155821
synonym: National Consortium on Alcohol and NeuroDevelopment in Adolescence: Data Integration Component
abbrev: NCANDA-Datacore
IAO_0000115: Manuals, training materials, and computational tools developed by the National Consortium on Alcohol and NeuroDevelopment in Adolescence (NCANDA) Data Component. The NCANDA consortium consists of an Administrative Component at UC San Diego, the Data Integration Component at SRI International, and five data collection sites, Duke University, Oregon Health & Sciences University, SRI International, University of Pittsburgh, and UC San Diego. Each collection site will collect data from about 150 adolescents, each of them seen for one baseline and three annual follow-up visits.

UNC Joint Vector Laboratories
type: Resource
type: NamedIndividual
has db xref: SciRes_000117
has db xref: SciRes_000124
synonym: UNC Gene Therapy Center Joint Vector Laboratories
synonym: UNC Gene Therapy Center Vector Core
synonym: University of North Carolina Vector Core
abbrev: UNC Vector Core
IAO_0000115: Core facility to access a comprehensive range of resources and services for gene transfer research including vector production services for research, preclinical and clinical materials. Services include: * Adeno-associated Virus (AAV) Custom Production; * AAV In-Stock Aliquots: Reporters, Deisseroth, Boyden, Roth, Uchida, Shah; * Lentivirus Custom Production

EDAS - EST-Derived Alternative Splicing Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02786
has db xref: OMICS_01885
synonym: EDAS: EST Derived Alternative Splicing Database
synonym: EST Derived Alternative Splicing Database
abbrev: EDAS
IAO_0000115: Databases of alternatively spliced genes with data on the alignment of proteins, mRNAs, and EST. It contains information on all exons and introns observed, as well as elementary alternatives formed from them. The database makes it possible to filter the output data by changing the cut-off threshold by the significance level. It contains splicing information on human, mouse, dog (not yet functional) and rat (not yet functional). For each database, users can search by keyword or by overall gene expression. They can also view genes based on chromosomal arrangement or other position in genome (exon, intron, acceptor site, donor site), functionality, position, conservation, and EST coverage. Also offered is an online Fisher test.

NFT
type: Resource
type: NamedIndividual
has db xref: nlx_155823
synonym: Neuroelectromagnetic Forward Head Modeling Toolbox
synonym: Neuroelectromagnetic Forward Modeling Toolbox
synonym: NFT: Neuroelectromag Forward Modeling
IAO_0000115: A MATLAB Toolbox for generating realistic head models from available data (MRI and/or electrode locations), for computing numerical solutions for the forward problem of electromagnetic source imaging and for single dipole source localization. The NFT includes tools for segmenting scalp, skull, cerebrospinal fluid (CSF) and brain tissues from T1-weighted magnetic resonance (MR) images. The Boundary Element Method (BEM) and Finite Element Method (FEM) are used for the numerical solution of the forward problem. When a subject MR image is not available a template head model can be warped to measured electrode locations to obtain an individualized head model. Toolbox functions may be called either from a graphic user interface compatible with EEGLAB or from the MATLAB command line.

A modular structure for scientific articles in an electronic environment
type: Resource
type: NamedIndividual
has db xref: nif-0000-02787
synonym: Modular Physics Paper
IAO_0000115: This thesis proposes a modular form for Physics papers: by investigating a collection of papers, a more fine-grained structure for science papers and an extensive relationships taxonomy is proposed. Examples of modular articles are included.

University of Applied Sciences; Mecklenburg-Vorpommern; Germany
type: Organization
type: NamedIndividual
has db xref: nlx_156704
synonym: Fachhochschule Stralsund
synonym: FH Stralsund
synonym: University of Applied Sciences
synonym: University of Applied Sciences of Stralsund
synonym: University of Applied Sciences Stralsund
IAO_0000115: Public university in Germany for vocational training in the applied sciences.

Net Station EEG Software
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_155825
synonym: Netstation
abbrev: Net Station
IAO_0000115: A complete software package for working with electroencephalography (EEG) and event-related potential (ERP) data. You can acquire, review, analyze, and now ?see? your participant with synchronized video. Net Station also offers specialized tools and workflow options for both clinical and research applications, allows you to save different combinations of view settings (called workspaces) and helps with your reporting requirements by letting you set up and print custom cover pages. For more specialized work, Net Station also provides an optional electrical source estimation module (GeoSource) and an optional sensor location digitizer (Geodesic Photogrammetry System).

Network Based Statistic Toolbox
type: Resource
type: NamedIndividual
has db xref: nlx_155826
synonym: Network-Based Statistic (NBS)
abbrev: NBS
IAO_0000115: Matlab toolbox for testing hypotheses about the human connectome. NBS has been widely used to identify connections and networks comprising the connectome that are associated with an experimental effect or a between-group difference. User provides a series of connectivity matrices from different cohorts, or from the same subject during different experimental conditions. Connectivity matrices are inferred from neuroimaging data using other packages that, for example, count the number of tractography streamlines that interconnect each pair of regions (diffusion-MRI), or measure the extent of inter-regional correlation in BOLD response (fMRI). User specifies hypothesis to be tested at every connection with the general linear model. Features include: graphical user interface; NBSview, a basic network viewer modeled on SPMresults; exchange blocks for repeated measures; options to measure network size with intensity or extent; false discovery rate (FDR) option. Developed by Zalesky, Fornito, Cocchi and Bullmore.

NeuroScope
type: Resource
type: NamedIndividual
has db xref: nlx_155828
IAO_0000115: An advanced viewer for electrophysiological and behavioral data: it can display local field potentials (EEG), neuronal spikes, behavioral events, as well as the position of the animal in the environment. It also features limited editing capabilities.

eggNOG
type: Resource
type: NamedIndividual
has db xref: nif-0000-02789
has db xref: OMICS_01689
synonym: eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups)
synonym: eggNOG: evolutionary genealogy of genes: Non-supervised Orthologous Groups
synonym: evolutionary genealogy of genes: Non-supervised Orthologous Groups
IAO_0000115: A database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories). eggNOG's database currently counts 1.7 million orthologous groups in 3686 species, covering over 7.7 million proteins (built from 9.6 million proteins). (Jan 30, 2014)

Numerical Fibre Generator
type: Resource
type: NamedIndividual
has db xref: nlx_155832
synonym: Numerical Fibre Generator (NFG)
abbrev: NFG
IAO_0000115: A collection of tools that generate numerical fiber structures with the complexity of human white matter and simulate Diffusion-Weighted MR images that would arise from them. Its primary use is to enable the testing of tracking algorithms

NRDR
type: Resource
type: NamedIndividual
has db xref: OMICS_01702
synonym: Non-coding RNA Databases Resource
synonym: NRDR: Non-coding RNA Databases Resource
IAO_0000115: Searchable portal for public non-coding RNA databases. The databases are classified by RNA family, information source, information content, and available search mechanisms.

University of Arizona; Arizona; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100007899
has db xref: grid.134563.6
has db xref: ISNI:0000 0001 2168 186X
has db xref: nlx_13022
has db xref: Wikidata:Q503419
synonym: U of A
synonym: University of Arizona
synonym: UofA
abbrev: UA
IAO_0000115: Public research university in Tucson, Arizona that offers undergraduate and graduate degree programs in psychology, audiology, speech pathology, and medicine.

PSTNet | MRI Simulator
type: Resource
type: NamedIndividual
has db xref: nlx_155834
synonym: Psychology Software Tools MRI Simulator
abbrev: MRI Simulator
IAO_0000115: MRI Simulator that provides a realistic approximation of an actual MRI scanner to allow habituation and training of participants in an environment less daunting than a real scanner. Special populations such as children, the elderly, and psychiatric patients, are often prone to claustrophobia and anxiety in the bore of a magnet, and consequently have a much higher rate of terminating the experiment or scan session before its completion. Some centers that have dealt with these populations estimate a 50%-80% failure rate. With the use of the MRI Simulator this failure rate can often be reduced below 5%, improving cost effectiveness.

HIBAL
type: Resource
type: NamedIndividual
has db xref: SciRes_000127
synonym: HIBAL Hydrologic Isotopic Balance Model for Paleolake Systems
synonym: Hydrologic Isotopic Balance
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2023. FORTRAN code for a simple hydrologic-isotopic-balance model for application to paleolake d18O records. Inputs to the model include discharge, on-lake precipitation, evaporation, and the d18O values of these fluid fluxes. Benson and Paillet (2002)

Pharmabase - an open content cheminformatics resource linking physiology with pharmacology
type: Resource
type: NamedIndividual
has db xref: nif-0000-21324
abbrev: Pharmabase
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 25, 2015. Open content cheminformatics database linking physiology with pharmacology, it targets the action and use of pharmacological compounds in modifying protein function, while revealing molecular relationships and linking out to related databases and sites. Pharmabase has been developed as a research tool, a resource for students, and an ongoing interactive forum on the use of pharmacological compounds in cellular research. It has several navigational routes, including a graphics browser (shows graphics of cell types and pathways) and membrane transport, which also illustrates the diversity of mechanisms that are covered. Users have access to detailed compound records with interactive features, and a form to send comments to the editor. Investigators are encouraged to alert the editors to mistakes, omissions or new compound information available from their reading and research.

Public Health Image Library
type: Resource
type: NamedIndividual
has db xref: nif-0000-21325
synonym: Public Health Image Library (PHIL)
abbrev: PHIL
IAO_0000115: Database of CDC's pictures organized into hierarchical categories of people, places, and science, presented as single images, image sets, and multimedia files. Much of the information critical to the communication of public health messages is pictorial rather than text-based. Created by a Working Group at the Centers for Disease Control and Prevention (CDC), the PHIL offers an organized, universal electronic gateway to CDC's pictures. Public health professionals, the media, laboratory scientists, educators, students, and the worldwide public are welcome to use this material for reference, teaching, presentation, and public health messages.

YLoc
type: Resource
type: NamedIndividual
has db xref: OMICS_01638
synonym: Yloc - Interpretable Subcellular Localization Prediction
IAO_0000115: An interpretable web server for predicting subcellular localization. In addition to the predicted location, YLoc gives a reasoning why this prediction was made and which biological properties of the protein sequence lead to this prediction. Moreover, a confidence estimate helps users to rate predictions as trustworthy. YLoc+ is able to predict the location of multiple-targeted proteins with high accuracy. The YLoc webserver is also accessible via SOAP.

AutoQuant
type: Resource
type: NamedIndividual
has db xref: SciRes_000125
synonym: AutoQuant X3
IAO_0000115: Software package of 2D and 3D restoration algorithms.Advanced image deconvolution and 3D visualization software for Life Science Researchers.

CAMERA - Collection of annotation related methods for mass spectrometry data
type: Resource
type: NamedIndividual
has db xref: biotools:camera
has db xref: OMICS_03366
abbrev: CAMERA
IAO_0000115: A Bioconductor package integrating algorithms to extract compound spectra, annotate isotope and adduct peaks, and propose the accurate compound mass even in highly complex data.

cortex
type: Resource
type: NamedIndividual
has db xref: biotools:cortex
has db xref: nlx_155842
synonym: Sample Size Estimates for Well-Powered Cross-Sectional Cortical Thickness Studies
IAO_0000115: Software package with functions that will help researchers plan how many subjects per group need to be included in an MRI-based cortical thickness study to ensure a thickness difference is detected. The package requires cortical thickness mapping and co-registration to be carried out using Freesurfer. The power analyses are implemented in the R software package., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Primate Cortical Connectivity Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-21332
IAO_0000115: Bibliography for primate cortical connectivity. The page displays the articles by their year of publication and links to PubMed.

EID: Exon-Intron Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02793
has db xref: OMICS_01886
synonym: Exon-Intron Database
synonym: The Exon-Intron Database
abbrev: EID
IAO_0000115: Data sets of protein-coding intron-containing genes that contain gene information from humans, mice, rats, and other eukaryotes, as well as genes from species whose genomes have not been completely sequenced. This is a comprehensive and convenient dataset of sequences for computational biologists who study exon-intron gene structures and pre-mRNA splicing. The database is derived from GenBank release 112, and it contains protein-coding genes that harbor introns, along with extensive descriptions of each gene and its DNA and protein sequences, as well as splice motif information. They have created subdatabases of genes whose intron positions have been experimentally determined. The collection also contains data on untranslated regions of gene sequences and intron-less genes. For species with entirely sequenced genomes, species-specific databases have been generated. A novel Mammalian Orthologous Intron Database (MOID) has been introduced which includes the full set of introns that come from orthologous genes that have the same positions relative to the reading frames.

iBEAT
type: Resource
type: NamedIndividual
has db xref: nlx_155851
synonym: iBEAT: Infant Brain Extraction and Analysis Toolbox
synonym: Infant Brain Extraction and Analysis Toolbox
synonym: LIBRA
IAO_0000115: A toolbox with graphical user interfaces for processing infant brain MR images. Longitudinal (or single-time-point) multimodality (including T1, T2, and FA) (or single-modality) data can be processed using the toolbox. Main functions of the software (step by step) include image preprocessing, brain extraction, tissue segmentation and brain labeling. Linux operating system (64 bit) is required. A workstation or server with memory >8G is recommended for processing many images simutaneously. The graphical user interfaces and overall framework of the software are implemented in MATLAB. The image processing functions are implemented with the combination of C/C++, MATLAB, Perl and Shell languages. Parallelization technologies are used in the software to speed up image processing.

Liquid Publications: Scientific Publications meet the Web
type: Resource
type: NamedIndividual
has db xref: nif-0000-02800
synonym: Liquid Publications
abbrev: LiquidPub
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 08, 2014. Project proposing a "liquid" format for science papers that consists of a set of research objects, connected by links. The immediate targets are the scientific research communities including publishers that, in a liquid world, will need to develop novel services and business models. Results and additional reading material (case studies, surveys, and the like) will be made available. The project also is creating an open source development effort and a platform to manage liquid publications and their evaluation. Their current main effort is developing the Liquid Journal and Liquid Conference use cases.

WoLF PSORT
type: Resource
type: NamedIndividual
has db xref: OMICS_01637
synonym: WoLF PSORT - Protein Subcellular Localization prediction
IAO_0000115: Data analysis service for protein subcellular localization prediction.

Entrez Gene
type: Resource
type: NamedIndividual
has db xref: biotools:entrez_gene
has db xref: nif-0000-02801
has db xref: OMICS_01651
has db xref: r3d100010650
synonym: Gene - Gene and mapped phenotypes
synonym: Gene - Gene mapped phenotypes
synonym: Gene Database
synonym: GeneID
synonym: NCBI Gene
abbrev: NCBI Genen NCBI Entrez
abbrev: NCBI_Gene
IAO_0000115: Database for genomes that have been completely sequenced, have active research community to contribute gene-specific information, or that are scheduled for intense sequence analysis. Includes nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases. All entries follow NCBI's format for data collections. Content of Entrez Gene represents result of curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases, and from many other databases available from NCBI. Records are assigned unique, stable and tracked integers as identifiers. Content is updated as new information becomes available.

NCBI Genome
type: Resource
type: NamedIndividual
has db xref: nif-0000-02802
has db xref: r3d100010785
synonym: Entrez Genome
synonym: Entrez Genomes
synonym: Genome
synonym: Genome Database
synonym: Genome: Information by genome sequence
synonym: NCBI
IAO_0000115: Database that organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations in six major organism groups: Archaea, Bacteria, Eukaryotes, Viruses, Viroids, and Plasmids. Genomes of over 1,200 organisms can be found in this database, representing both completely sequenced organisms and those for which sequencing is in progress. Users can browse by organism, and view genome maps and protein clusters. Links to other prokaryotic and archaeal genome projects, as well as BLAST tools and access to the rest of the NCBI online resources are available.

M3
type: Resource
type: NamedIndividual
has db xref: nlx_155877
synonym: Multi-modal imaging and multi-level characteristic with multi-classifier
IAO_0000115: A brain imaging classification tool, which can help researchers to discriminate patients from normal controls. The M3 includes three steps: feature selection, maximum uncertainty linear discriminant analysis (MLDA)-based classification and multi-classifier. A leave-one-out cross-validation (LOOCV) is further used to estimate the performance of the M3. Finally, the most discriminative features are identified.

Mason
type: Resource
type: NamedIndividual
has db xref: OMICS_00252
synonym: Mason2
IAO_0000115: Collection of software tools for simulating biological sequences, including simulations of genome fragment sampling, random genomic sequences, methylation levels, and NGS reads.

ECO
type: Resource
type: NamedIndividual
has db xref: nlx_155860
synonym: Evidence Codes Ontology
synonym: Evidence Ontology
synonym: evidenceontology
synonym: The Evidence Ontology
IAO_0000115: A controlled vocabulary that describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. Researchers can use these types of evidence to support assertions about research subjects that result from scientific research, such as scientific conclusions, gene annotations, or other statements of fact. ECO comprises two high-level classes, evidence and assertion method, where evidence is defined as a type of information that is used to support an assertion, and assertion method is defined as a means by which a statement is made about an entity. Together evidence and assertion method can be combined to describe both the support for an assertion and whether that assertion was made by a human being or a computer. However, ECO can not be used to make the assertion itself; for that, one would use another ontology, free text description, or other means. ECO was originally created around the year 2000 to support gene product annotation by the Gene Ontology. Today ECO is used by many groups concerned with provenance in scientific research. ECO is used in AmiGO 2

Group ICA Of EEG Toolbox
type: Resource
type: NamedIndividual
has db xref: nlx_155861
synonym: Group ICA Of EEG Toolbox (EEGIFT)
abbrev: EEGIFT
IAO_0000115: Implements multiple algorithms for independent component analysis and blind source separation of group (and single subject) EEG data. This MATLAB toolbox is compatible with MATLAB 6.5 and higher.

QualitySNPng
type: Resource
type: NamedIndividual
has db xref: biotools:qualitysnpng
has db xref: OMICS_00070
IAO_0000115: Software for the detection and visualization of single nucleotide polymorphisms (SNPs) from next generation sequencing data that uses a haplotype-based strategy.

4D-PARSeR Pathological Anatomy Regression via Segmentation and Registration
type: Resource
type: NamedIndividual
has db xref: nlx_155870
synonym: 4D-PARSeR (Pathological Anatomy Regression via Segmentation and Registration)
synonym: 4D-Pathological Anatomy Regression via Segmentation and Registration
abbrev: 4D-PARSeR
IAO_0000115: A tool for analyzing 4D images with pathology. Originally developed for processing longitudinal images of patients with traumatic brain injury, the tool contains new image analysis algorithms that combine registration and segmentation in a coherent framework, accounting for extreme changes due to extensive tissue damage.

Automatic Segmentation Tool Adapter
type: Resource
type: NamedIndividual
has db xref: nlx_155871
IAO_0000115: An open source learning-based software that automatically learns how to transfer the output of a host segmentation tool closer to the user's manual segmentation using the image data and manual segmentation provided by the user. The motivation of this project is to bridge the gap between the segmentation tool developer and the tool users such that the existing segmentation tools can more effectively serve the community. More and more automatic segmentation tools are publicly available to today's researchers. However, when applied by their end-users, these segmentation tools usually can not achieve the performance that the tool developer reported. Discrepancies between the tool developer and its users in manual segmentation protocols and imaging modalities are the main reasons for such inconsistency.

DTI-TEMPLATE-RHESUS-MACAQUES
type: Resource
type: NamedIndividual
has db xref: nlx_155872
IAO_0000115: A population-specific DTI template for young adolescent Rhesus Macaque (Macaca mulatta) monkeys using 271 high-quality scans. Using such a large number of animals in generating a template allows it to account for variability in the species. Their DTI template is based on the largest number of animals ever used in generating a computational brain template. It is anticipated that their DTI template will help facilitate voxel-based and tract specific WM analyses in non-human primate species, which in turn may increase our understanding of brain function, development, and evolution.

LONI Provenance Editor
type: Resource
type: NamedIndividual
has db xref: nlx_155876
IAO_0000115: A self-contained, platform-independent application that automatically extracts the provenance information from an image header (such as a DICOM image) and generates a data provenance XML file with that information.

MNI N3
type: Resource
type: NamedIndividual
has db xref: nlx_155878
synonym: MNI N3 Software Package
synonym: MNI_N3
synonym: MNI_N3 Software Package
synonym: N3 - MINC B0 nonuniformity correction
synonym: Non-parametric Non-uniform intensity Normalization
abbrev: N3
IAO_0000115: The perl script nu_correct implements a novel approach to correcting for intensity non-uniformity in MR data that achieves high performance without requiring supervision. By making relatively few assumptions about the data, the method can be applied at an early stage in an automated data analysis, before a tissue intensity or geometric model is available. Described as Non-parametric Non-uniform intensity Normalization (N3), the method is independent of pulse sequence and insensitive to pathological data that might otherwise violate model assumptions. To eliminate the dependence of the field estimate on anatomy, an iterative approach is employed to estimate both the multiplicative bias field and the distribution of the true tissue intensities. Preprocessing of MR data using N3 has been shown to substantially improve the accuracy of anatomical analysis techniques such as tissue classification and cortical surface extraction.

EPDnew
type: Resource
type: NamedIndividual
has db xref: nif-0000-02806
synonym: Eukaryotic Promoter Database
synonym: Eukaryotic Promoter Database new
abbrev: EPD
abbrev: HT-EPD
IAO_0000115: EPDnew databases are the result of merging Eukaryotic Promoter Database, EPD, promoters within house analysis of promoter specific high throughput data for selected organisms only. EPDnew is a set of species specific databases of experimentally validated promoters.

MRI Digital Projection System
type: Resource
type: NamedIndividual
has db xref: nlx_155879
synonym: Hyperion MRI Digital Projection System
abbrev: Hyperion
IAO_0000115: MRI Digital Projection System that uses Digital Light Processing (DLP) technology providing microsecond pixel rise times, outstanding contrast with all-digital fiber optic control that allows you to project crystal clear, sharp images. Includes: * High resolution (1024x768) DLP Projector with RF filtered enclosure, custom lens assembly, digital video (DVI) over fiber, high flow fans, internal thermal sensor * Control room device to perform DVI to Fiber conversion, remotely power down the projector, and allow use of projector remote control from control room * 30 meter fiber optic cable that runs between the projector and projector control station * Heavy duty, magnet compatible, projector stand (assembly required) * Heavy duty, magnet compatible mirror stand with mirror (assembly required) * High resolution, lenticular pitch rear projection screen for high quality image reproduction * Optional VGA to DVI converter (native DVI video cards on Windows or Macintosh recommended)

ENZYME
type: Resource
type: NamedIndividual
has db xref: nif-0000-02803
synonym: Enzyme nomenclature database
IAO_0000115: A repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided. These include * EC number * Recommended name * Alternative names (if any) * Catalytic activity * Cofactors (if any) * Pointers to the Swiss-Prot protein sequence entry(ies) that correspond to the enzyme (if any) * Pointers to human disease(s) associated with a deficiency of the enzyme (if any) We believe that the ENZYME database can be useful to anybody working with enzymes and that it can be of help in the development of computer programs involved with the manipulation of metabolic pathways. Available services include downloading ENZYME by FTP as well as report forms for a new ENZYME entry or for an error/update in an existing entry.

NIDB - Neuroinformatics Database
type: Resource
type: NamedIndividual
has db xref: nlx_155882
synonym: Neuroinformatics Database
abbrev: NIDB
IAO_0000115: Neuroimaging database designed to allow simple importing, searching, and sharing of imaging data. NIDB also provides automated pipelining with importing of results back into NIDB which can be searched along with imaging meta data.

NIPY
type: Resource
type: NamedIndividual
has db xref: nlx_155883
synonym: NIPY Structural and Functional Analysis
IAO_0000115: A complete Python environment for the analysis of structural and functional neuroimaging data. It currently has a full system for general linear modeling of functional magnetic resonance imaging (fMRI).

NIRAL Utilities
type: Resource
type: NamedIndividual
has db xref: nlx_155884
IAO_0000115: Open-source utilities that are C++ based command line applications that allow image analysis and processing using ITK or VTK libraries. Specifically the following utilities are contained thus far: * ImageMath - the swiss army knife image modification * ImageStat - compute stats on images * IntensityRescaler - rescale/normalize intensities using a prior brain tissue segmentation * convertITKformats - convert 3D images in all ITK formats (NRRD, NIFTI, GIPL, Meta etc) * DWI_NiftiNrrdConversion - convert DWI and DTI from/to NRRD and NIFTI, works with UNC DTI tools and FSL * CropTools - crops 3D and 4D images * PolydataMerge - Merges VTK polydata files * PolydataTransform - Transforms polydata files * TransformDeformationField - concatenates or average deformation fields (H-fields or displacement fields) * DTIAtlasBuilder - Creates a DTI average from multiple DTI images

NIRx NIRS Neuroimaging
type: Organization
type: NamedIndividual
has db xref: nlx_155886
synonym: NIRx Optical Neuroimaging
IAO_0000115: Commercial technology solutions for NIRS neuroscience imaging applications.

NIRx2nirs: A NIRx to .nirs data converter
type: Resource
type: NamedIndividual
has db xref: nlx_155887
abbrev: NIRx2nirs
IAO_0000115: A matlab script which takes near-infrared spectroscopy data recorded by NIRx system(s) and converts it to a .nirs file format for use with the HOMER2 NIRS processing pacakge.

realSFS
type: Resource
type: NamedIndividual
has db xref: OMICS_00071
IAO_0000115: Software program used to estimate allele frequency and SNP calling., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

NITRC Enhanced Services
type: Resource
type: NamedIndividual
has db xref: nlx_155890
IAO_0000115: Support and community integration for the enhanced NITRC services of the Image Repository (IR) and the Computational Environment (CE). The NITRC Computational Environment, an on-demand, cloud based computational virtual machine pre-installed with popular NITRC neuroimaging tools built using NeuroDebian. NITRC Image Repository is built upon XNAT and supports both NIfTI and DICOM images. The NITRC-IR offers 3,733 Subjects, and 3,743 Imaging Sessions searchable across seven projects to promote re-use and integration of valuable NIH-funded data.

NITRC GForge Extensions
type: Resource
type: NamedIndividual
has db xref: nlx_155891
IAO_0000115: Software repository of custom extensions to the GForge collaborative environment.

NPTK
type: Resource
type: NamedIndividual
has db xref: nlx_155893
IAO_0000115: Non-rigid registration / distortion correction tools for enhanced functional localization through the registration of EPI fMRI to high-resolution anatomical MRI.

NeuroImaging Analysis Kit (NIAK)
type: Resource
type: NamedIndividual
has db xref: nlx_155894
synonym: Neuroimaging Analysis Kit for Matlab and Octave
abbrev: NIAK
IAO_0000115: Software library of modules and pipelines for fMRI processing with Octave or Matlab(r) that can run in parallel either locally or in a supercomputing environment. Linux OS and MINC file format are supported. NIAK currently includes a preprocessing, a region growing and a connectome pipelines. NIAK features powerful pipeline management capabilities, including parallel computing, generation of detailed logs and automatic handling of pipeline failures or updates.

NiBabel
type: Resource
type: NamedIndividual
has db xref: nlx_155896
synonym: NIPY File IO
IAO_0000115: A Python package for reading and writing a variety of medical and neuroimaging file formats. This includes: ANALYZE (plain, SPM99, SPM2), NIfTI1, as well as MINC. NiBabel is the successor of PyNIfTI.

NiftyRec
type: Resource
type: NamedIndividual
has db xref: nlx_155898
synonym: NiftyRec Open Source Tomography Toolbox
synonym: NiftyRec Tomography Toolbox
IAO_0000115: Software toolbox that includes reconstruction tools for emission and transmission imaging modalities, including Single Photon Emission Computed Tomography (SPECT), Positron Emission Tomography (PET), cone-beam X-Ray CT and parallel-beam X-Ray CT. At the core of NiftyRec are efficient, GPU accelerated, projection, back-projection and iterative reconstruction algorithms. The easy to use Matlab and Python interfaces of NiftyRec enable fast prototyping and development of reconstruction algorithms. NiftyRec includes standard iterative reconstruction algorithms such as Maximum Likelihood Expectation Maximisation (MLEM), Ordered Subsets Expectation Maximisation (OSEM) and One Step Late Maximum A Posteriori Expectation Maximisation (OSL-MAPEM), for multiple imaging modalities.

pymzML
type: Resource
type: NamedIndividual
has db xref: biotools:pymzml
has db xref: OMICS_03355
IAO_0000115: Python module to parse mzML data in Python based on cElementTree. It is an extension to Python that offers (i) an easy access to mass spectrometry (MS) data that allows the rapid development of tools, (ii) a very fast parser for mzML data and (iii) a set of functions to compare or handle spectra., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

AQnowledge Bookmarklet
type: Resource
type: NamedIndividual
has db xref: nlx_156032
synonym: AQnowledge Semantic Bookmarklet
synonym: AQnowledge Semantic Bookmarklet (Life Science)
abbrev: AQnowledgeBM
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Bookmarklet suitable for all main browsers, that, when invoked, highlights concepts of scientific significance in text and offers links to many open information resources about any concept highlighted.

Nipype
type: Resource
type: NamedIndividual
has db xref: nlx_155901
synonym: NIPY Pipeline and Interfaces
synonym: Nipype: Neuroimaging in Python Pipeline and Interfaces
IAO_0000115: A package for writing fMRI analysis pipelines and interfacing with external analysis packages (SPM, FSL, AFNI). Current neuroimaging software offer users an incredible opportunity to analyze their data in different ways, with different underlying assumptions. However, this has resulted in a heterogeneous collection of specialized applications without transparent interoperability or a uniform operating interface. Nipype, an open-source, community-developed initiative under the umbrella of Nipy, is a Python project that solves these issues by providing a uniform interface to existing neuroimaging software and by facilitating interaction between these packages within a single workflow. Nipype provides an environment that encourages interactive exploration of algorithms from different packages (e.g., SPM, FSL), eases the design of workflows within and between packages, and reduces the learning curve necessary to use different packages. Nipype is creating a collaborative platform for neuroimaging software development in a high-level language and addressing limitations of existing pipeline systems.

Nirfast
type: Resource
type: NamedIndividual
has db xref: nlx_155902
abbrev: NIRFAST
IAO_0000115: Software package for modeling Near-Infrared light transport in tissue and image reconstruction. This includes: Standard single wavelength absorption and reduced scatter, Multi-wavelength spectrally constrained models and Fluorescence models.

Nitime
type: Resource
type: NamedIndividual
has db xref: nlx_155903
synonym: Nitime: time-series analysis for neuroscience
abbrev: NiTime
IAO_0000115: Software library for time-series analysis of data from neuroscience experiments. It contains a core of numerical algorithms for time-series analysis both in the time and spectral domains, a set of container objects to represent time-series, and auxiliary objects that expose a high level interface to the numerical machinery and make common analysis tasks easy to express with compact and semantically clear code.

Non-Rigid Image Registration Evaluation Project
type: Resource
type: NamedIndividual
has db xref: nlx_155904
synonym: Non-Rigid Image Registration Evaluation Project (NIREP)
abbrev: NIREP
IAO_0000115: Project to develop software tools and provide shared image validation databases for rigorous testing of non-rigid image registration algorithms. NIREP will extend the scope of prior validation projects by developing evaluation criteria and metrics using large image populations, using richly annotated image databases, using computer simulated data, and increasing the number and types of evaluation criteria. The goal of this project is to establish, maintain, and endorse a standardized set of relevant benchmarks and metrics for performance evaluation of nonrigid image registration algorithms. Furthermore, these standards will be incorporated into an exportable computer program to automatically evaluate the registration accuracy of nonrigid image registration algorithms.

Normative Independent Component Analysis
type: Resource
type: NamedIndividual
has db xref: nlx_155906
abbrev: NICA
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Software program, executable under any Windows32 OS, performs Group BSS (Blind Source Separation) analysis comparing two groups of individuals and it performs NICA (Normative ICA) analysis where individuals are compared individually to a (normative) group. All analysis is performed in the frequency domain, that is, for all frequencies. The program also performs all these analysis for qEEG, that is, at the electrode level, without any BSS. The program does all computations, saves and displays results. The rationale and methods used in this program are explained in all details in the following paper: Congedo M, John ER, De Ridder D, Prichep L (2010) Group Independent Component Analysis of Resting-State EEG in Large Normative Samples International Journal of Psychophysiology 78, 89-99.

OEI | fMRI compatible olfactometer
type: Resource
type: NamedIndividual
has db xref: nlx_155907
abbrev: OEI fMRI compatible olfactometer
IAO_0000115: A computerized, odor delivery device that can be used for basic research applications including mapping olfactory centers, cognitive / learning research, neuro-marketing among other uses. Additional products including tests for odor threshold, odor identification, odor discrimination and odor memory.

RUbioSeq
type: Resource
type: NamedIndividual
has db xref: biotools:rubioseq
has db xref: OMICS_00072
synonym: RUbioSeq+
IAO_0000115: Stand-alone and multiplatform application for the integrated analysis of NGS data. It implements pipelines for the analysis of single nucleotide and copy-number variation and bisulfite-seq and ChIP-seq experiments.

ORS Visual SI
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_155908
synonym: Object Research Systems Visual SI
IAO_0000115: Software with advanced visualization techniques and state-of-the-art volume rendering provide unparalleled insight into the details and properties of neurological data acquired by CT, micro-CT, MRI, PET, SPECT, microscopy and other modalities. With data fusion tools, intramodality and multimodality registration of MR/CT or PET/CT is easily accomplished, while semi-automatic VOI delineation on fused datasets can improve analysis. Standard formats, such as DICOM, RAW, JPEG, NIFTI, Analyze are supported and 3D/4D sequences can be played. Other features include MPR, oblique, CPR, volume clipping, and surface visualization of cortex, skull, and scalp models. Also standard are easy-to-use tools for voxel-based delineation of features and the measurement of properties, including areas, volumes, counts, and intensity profiles. Present your findings by creating annotated animations or high-resolution images for posters. An SDK is also available to create plug-ins that provide new workflows or functionalities.

OpenMEEG
type: Resource
type: NamedIndividual
has db xref: nlx_155910
IAO_0000115: A C++ package for low-frequency bio-electromagnetism solving forward problems in the field of EEG and MEG with very high accuracy.

PANDA
type: Resource
type: NamedIndividual
has db xref: nlx_155911
synonym: PANDA (Pipeline for Analyzing braiN Diffusion imAges)
synonym: panda-tool
synonym: PANDA: a pipeline tool for diffusion MRI
synonym: PANDA: Pipeline for Analyzing braiN Diffusion imAges
synonym: Pipeline for Analyzing braiN Diffusion imAges
IAO_0000115: Software matlab toolbox for pipeline processing of diffusion MRI images. For each subject, PANDA can provide outputs in 2 types: i) diffusion parameter data that is ready for statistical analysis; ii) brain anatomical networks constructed by using diffusion tractography. Particularly, there are 3 types of resultant diffusion parameter data: WM atlas-level, voxel-level and TBSS-level. The brain network generated by PANDA has various edge definitions, e.g. fiber number, length, or FA-weighted. The key advantages of PANDA are as follows: # fully-automatic processing from raw DICOM/NIFTI to final outputs; # Supporting both sequential and parallel computation. The parallel environment can be a single desktop with multiple-cores or a computing cluster with a SGE system; # A very friendly GUI (graphical user interface).

PBSIM
type: Resource
type: NamedIndividual
has db xref: OMICS_00253
synonym: PacBio reads simulator
IAO_0000115: Software that simulates PacBio reads by using either a model-based or sampling-based simulation.

PESTICA fMRI Physio Detection/Correction
type: Resource
type: NamedIndividual
has db xref: nlx_155912
synonym: Physiologic EStimation by Temporal ICA
abbrev: PESTICA
IAO_0000115: Software tool to detect physiologic signals from the data itself as well as an adaptive physiologic noise removal tool (Impulse Response Function or IRF-RETROICOR) that zooms in on noise with only 6 regressors, getting all the noise that 5th order RETROICOR gets. These tools will allow you to correct your data for physiologic noise with what you currently have. These signals are equivalent to a parallel monitored pulse signal and a respiratory chest-bellows signal. Do you have 3D+time EPI data (BOLD or perfusion) but no usable physio signals for pulse and respiration? Are you concerned about the effect of physio noise on your data but don't know what to do but regress data-derived signals that mix unknown functional signal with possible physio noise signal? Are you concerned about the number of regressors you're incorporating once you add 5th order RETROICOR (20 more regressors!)? This is for you.

PHYCAA+: adaptive physiological noise correction for BOLD fMRI
type: Resource
type: NamedIndividual
has db xref: nlx_155913
abbrev: PHYCAA+
IAO_0000115: Software algorithm that automatically estimates and removes physiological noise in BOLD fMRI data, including the effects of heartbeat and respiration. This algorithm (1) masks out high-variance CSF and vascular tracts that may otherwise confound analyses, and (2) regresses out noise timeseries in grey matter tissue, using an adaptive multivariate component decomposition (Canonical Autocorrelations Analysis). PHYCAA+ is an efficient, automated procedure that does NOT require external measures of physiology, nor does it require the user to manually identify noise components. Based on the peer-reviewed article: Churchill & Strother (2013). PHYCAA+: An Optimized, Adaptive Procedure for Measuring and Controlling Physiological Noise in BOLD fMRI. NeuroImage 82: 306-325

University of Arkansas; Arkansas; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100007756
has db xref: grid.411017.2
has db xref: ISNI:0000 0001 2151 0999
has db xref: nlx_90713
has db xref: Wikidata:Q1070333
synonym: UArkansas
synonym: University of Arkansas
abbrev: UA
abbrev: UARK
IAO_0000115: Public, co educational research university in Fayetteville, Arkansas.

ParaView
type: Resource
type: NamedIndividual
has db xref: nlx_155917
IAO_0000115: Open source, multi platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView's batch processing capabilities. ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of terascale as well as on laptops for smaller data.

Parkinson’s Disease Biomarkers Program Data Management Resource (PDBP DMR)
type: Resource
type: NamedIndividual
has db xref: nlx_155919
synonym: Parkinson's Disease Biomarkers Program
synonym: Parkinson’s Disease Biomarkers Program Data Management Resource
synonym: PDBP DMR
synonym: PDBP: Parkinsons Disease Biomarkers Program
abbrev: PDBP
IAO_0000115: Common data management resource and web portal to promote discovery of Parkinson's Disease diagnostic and progression biomarker candidates for early detection and measurement of disease progression. PDBP will serve as multi-faceted platform for integrating existing biomarker efforts, standardizing data collection and management across these efforts, accelerating discovery of new biomarkers, and fostering and expanding collaborative opportunities for all stakeholders.

PennCNV
type: Resource
type: NamedIndividual
has db xref: nlx_155921
has db xref: OMICS_00729
synonym: PennCNV: copy number variation detection
IAO_0000115: A free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays. PennCNV implements a hidden Markov model (HMM) that integrates multiple sources of information to infer CNV calls for individual genotyped samples. It differs form segmentation-based algorithm in that it considered SNP allelic ratio distribution as well as other factors, in addition to signal intensity alone. In addition, PennCNV can optionally utilize family information to generate family-based CNV calls by several different algorithms. Furthermore, PennCNV can generate CNV calls given a specific set of candidate CNV regions, through a validation-calling algorithm.

pIRS
type: Resource
type: NamedIndividual
has db xref: OMICS_00254
synonym: pIRS (profile based Illumina pair-end Reads Simulator)
synonym: profile based Illumina pair-end Reads Simulator
IAO_0000115: Software for de novo data simulation. It uses empirical distribution to reproduce Illumina pair-end reads with real distribution of substitution sequencing errors, quality values and GC%-depth bias.

PeptideShaker
type: Resource
type: NamedIndividual
has db xref: OMICS_03347
IAO_0000115: Software providing a search engine independent platform for visualization of peptide and protein identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics data.

Presentation
type: Resource
type: NamedIndividual
has db xref: nlx_155925
synonym: Presentation 19.0
IAO_0000115: Stimulus delivery and experiment control program. Stimuli include auditory, 2D and 3D visual, and multimodal and experimental data include fMRI, ERP, MEG, psychophysics, eye movements, single neuron recording, and reaction time measures.

University of Arkansas for Medical Sciences; Arkansas; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100008519
has db xref: grid.241054.6
has db xref: ISNI:0000 0004 4687 1637
has db xref: nlx_152181
has db xref: Wikidata:Q941298
synonym: University of Arkansas for Medical Sciences
abbrev: UAMS
IAO_0000115: Division of medical sciences at a public research university in Arkansas. It focuses on education, research, and clinical programs with a specific goal to implement translational research in care.

Arrowsmith
type: Resource
type: NamedIndividual
has db xref: nif-0000-00126
synonym: Arrowsmith Project
IAO_0000115: Portal for documenting the Arrowsmith project and developing text mining tools for scientific, and specifically neuroscience, literature. It also contains a search functions that identifies similar concepts between two articles.

PySurfer
type: Resource
type: NamedIndividual
has db xref: nlx_155930
IAO_0000115: Software Python tool for visualization and interaction with cortical surface representations of neuroimaging data from Freesurfer. It extends Mayavi powerful visualization engine with interface for working with MRI and MEG data. PySurfer offers command-line interface designed to broadly replicate Freesurfer program as well as Python library for writing scripts to explore complex datasets., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Pythagorean Displacement and Motion Regressors
type: Resource
type: NamedIndividual
has db xref: nlx_155931
IAO_0000115: Matlab script that uses the Pythagorean Theorem to calculate head motion and position, while preserving degrees of freedom. The motion parameters output by SPM (rp*.txt) estimate head position relative to the first volume in 3D translation and 3D rotation, which are often entered as a nuisance regressor during individual-level statistics. Regressing the total displacement and relative position can potentially explain more variance in voxel-level BOLD signals that is related to head movement during an fMRI experiment.

MBF BioScience | Stereo Investigator
type: Resource
type: NamedIndividual
has db xref: SciRes_000114
has db xref: SCR_018948
has db xref: SCR_024705
synonym: Stereo Investigator system
IAO_0000115: Stereo Investigator system includes microscope, computer, and Stereo Investigator software. Software works with Brightfield, Multi-Channel Fluorescence, Confocal, and Structured Illumination Microscopes. System used to provide estimates of number, length, area, and volume of cells or biological structures in tissue specimen in areas of neuroscience including neurodegenerative diseases, neuropathy, memory, and behavior, pulmonary research, spinal cord research, and toxicology.

Quantitative Diffusion Tools
type: Resource
type: NamedIndividual
has db xref: nlx_155933
IAO_0000115: Slicer3 modules for quantitative diffusion analysis. Modules include tools for clustering fiber tracts, summarizing measures over tract clusters, etc.

R-package for adaptive DWI analysis
type: Resource
type: NamedIndividual
has db xref: nlx_155934
IAO_0000115: The package dti provides methods for structural adaptive smoothing of diffusion weighted data in the context of the diffusion tensor model. Through its edge preserving properties they reduce data noise without compromizing significant structures.

ShotGun
type: Resource
type: NamedIndividual
has db xref: biotools:abcd
has db xref: OMICS_00255
synonym: ShotGun: a Flexible Short Read Simulator to Facilitate Sequencing-based Study Designs
IAO_0000115: Software for short read simulating in order to facilitate sequencing-based study designs.

R-package for adaptive fMRI analysis
type: Resource
type: NamedIndividual
has db xref: nlx_155935
IAO_0000115: The package fmri provides fMRI analysis with R using structural adaptive smoothing methods. They allow smoothing especially at low SNR avoiding the apparent blurring of non-adapative smoothing and thus without reducing the effective spatial resolution.

Ear Lab
type: Resource
type: NamedIndividual
has db xref: nif-0000-00404
synonym: the ear lab
abbrev: Earlab
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Computationally oriented experimental laboratory interested in the encoding of auditory information in the cerebral cortex and brainstem, and in the mechanisms of tinnitus and the effect of various drugs (Lidocaine, steroids, anti-oxidants) in relieving noise trauma induced tinnitus. The ferret (Mustela putorius) and the rat serve as their system model. Through chronic implants, they obtain electrophysiological data from awake behaving animals in order to investigate the response properties and functional organization of the auditory system, both in health and after noise trauma that induces tinnitus in rats. Projects: * Response Modulation to Ongoing Broadband Sounds in Primary Auditory Cortex * Neuronal Response Characteristics in the Inferior Colliculus of the Awake Ferret and Rat * Spectro-Temporal Representation of Feature Onsets in Primary Auditory Cortex * Targeting the changes in inferior colliculus induced by tinnitus

REX
type: Resource
type: NamedIndividual
has db xref: nlx_155937
IAO_0000115: A stand-alone MATLAB-based toolkit for the rapid and flexible exploration of Region of Interest (ROI) response waveforms and other signals from across large fMRI datasets. An alpha-release is currently available for use with an example dataset and tutorial.

RFT FDR
type: Resource
type: NamedIndividual
has db xref: nlx_155938
synonym: RFT-FDR
abbrev: RFT_FDR
IAO_0000115: So far there is a lack for Random Field Theory (RFT) -based multiple comparison correction for surfaces generated in Freesurfer software package. This set of Matlab-based functions can be used for that purpose. They are based on Worsley?s SurfStat toolbox. You also need to have installed Freesurfer software package and included the Freesurfer?s matlab subdirectory in the Matlab?s search path. In addition, this tool implements the RFT-FDR hierarchical correction that can be used for optimizing the amount of smoothing in cortical thickness analyses (Neuroimage 52, 158-171).

ROBEX
type: Resource
type: NamedIndividual
has db xref: nlx_155939
synonym: Robust Brain Extraction
synonym: Robust Brain Extraction (ROBEX)
IAO_0000115: An automatic whole-brain extraction tool for T1-weighted MRI data (commonly known as skull stripping). Whole-brain segmentation is often the first component in neuroimage pipelines and therefore, its robustness is critical for the overall performance of the system. Many methods have been proposed in the literature, but they often: * work well on certain datasets but fail on others. * require case-specific parameter tuning ROBEX aims for robust skull-stripping across datasets with no parameter settings. It fits a triangular mesh, constrained by a shape model, to the probabilistic output of a supervised brain boundary classifier. Because the shape model cannot perfectly accommodate unseen cases, a small free deformation is subsequently allowed. The deformation is optimized using graph cuts.

RT Image
type: Resource
type: NamedIndividual
has db xref: nlx_155940
abbrev: RT_Image
IAO_0000115: Software application to visualize, segment, and quantify three-dimensional images. Multiple datasets may be loaded, displayed, fused, processed, and quantitatively analyzed simultaneously. Data may be imported from any DICOM-compatible three dimensional imaging modality. Regions-of-interest may be defined using a number of manual, semi-automatic, and automated tools to segment three-dimensional pixel volumes. They may also be imported from and exported to DICOM structure sets. This software has been applied to preclinical and clinical computed tomography (CT), positron emission tomography (PET), single photon emission computed tomography (SPECT), magnetic resonance imaging (MRI), and optical imaging data.

Resource Ontology Discussion Group
type: Resource
type: NamedIndividual
has db xref: nlx_155943
IAO_0000115: Project to discuss, debate, develop and deploy ontological practices for the fMRI community.

Xbase
type: Resource
type: NamedIndividual
has db xref: nif-0000-21423
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Database aimed at helping laboratory-based bacteriologists make best use of bacterial genome sequence data, with a particular emphasis on comparative genomics. The latest version, xBASE 2.0, now provides comprehensive coverage of all bacterial genomes and features an updated modularized backend and an improved user interface, which includes a taxonomy browser and a powerful full-text search facility. There are 2082 genomes in the database, 1062 complete and 1020 incomplete xSites: * coliBASE - a genome resource for the E. coli research community * campyDB - a genome resource for the Campylobacter research community * MycoDB - a genome resource for the Mycobacteria research community * RhizoDB - a genome resource for the Rhizobia research community * FtBASE - a genome resource for the Francisella research community * ClostriDB - a genome resource for the Clostridiales research community If you use xBASE in your work, please cite: xBASE2: a comprehensive resource for comparative bacterial genomics. Chaudhuri RR, Loman NJ, Snyder LA, Bailey CM, Stekel DJ, Pallen MJ. Nucleic Acids Res. 2008 Jan;36(Database issue):D543-6. Epub 2007 Nov 5.PMID: 17984072 This work is supported by the BBSRC, grant number BBE0111791, awarded to MJP and DJS.

Rodent Brain Extraction Tool
type: Resource
type: NamedIndividual
has db xref: nlx_155945
abbrev: rBET
IAO_0000115: A modified version of the Brain Extraction Tool (BET) that can process rodent brains.

Rodent Cortical Thickness Analysis
type: Resource
type: NamedIndividual
has db xref: nlx_155946
synonym: RodentThickness
IAO_0000115: An automatic cortical thickness measurement tool for rat brains. The pipeline consists of four steps: preprocessing to create binary mask and label map, thickness measurement which produces laplacian field and thickness map in order, run particle correspondence followed by statistical analysis resulting in mean thickness color map and t-test result. By running RodentThickness, you will need to fill in informations in a Graphical User Interface, and then compute. You can also run the tool in command line without using the GUI. Using the GUI, you will be able to save or load a dataset file or a configuration file. The tool needs these other tools to work, so be sure to have these installed on your computer: * ImageMath * measureThicknessFilter * GenParaMeshCLP * ParaToSPHARMMeshCLP * ShapeWorksRun * ShapeWorksGroom * SegPostProcessCLP * BinaryToDistanceMap * MeshPointsIntensitysampling

S-rep Fitting Statistics and Segmentation
type: Resource
type: NamedIndividual
has db xref: nlx_155948
IAO_0000115: Software to fit s-reps to segmented anatomic objects, to compute probability distributions on these s-reps, to train and to apply classifiers between two classes of anatomic objects, and to apply hypothesis testing to determine which geometric or physiological features vary significantly between two classes. Software for object segmentation from medical images may also be included. S-reps are skeletal models for anatomic objects especially suited for computing probability distributions from populations of these objects and for providing object-related coordinates for the interior of these objects. They allow classification and hypothesis testing using their geometric features and physiological features derived from medical images. They also allow the definition of shape spaces, probability-based geometric typicality functions, and appearance models used for segmentation or registration. A variety of successful applications to objects in neuroimages have already been performed.

SCIRun
type: Resource
type: NamedIndividual
has db xref: nlx_155949
IAO_0000115: A Problem Solving Environment (PSE) for modeling, simulation and visualization of scientific problems. SCIRun now includes the biomedical components formally released as BioPSE, as well as BioMesh3D. BioMesh3D is a free, easy to use program for generating quality meshes for the use in biological simulations. The most recent stable release is version 4.6.

SCRalyze
type: Resource
type: NamedIndividual
has db xref: nlx_155950
synonym: SCRalyze - A matlab environment for model-based psychophysiology
IAO_0000115: A powerful software for model-based analysis of peripheral psychophysiology (e.g. skin conductance, heart rate, pupil size etc.). General linear modelling and dynamic causal modelling of these signals provide for inference on neural states/processes. SCRalyze includes flexible data import and display, statistical inference and results display and export. Easy programming of add-ons for new data formats, signal channels, and models.

SfN Brain Briefings
type: Resource
type: NamedIndividual
has db xref: nif-0000-00437
synonym: Society for Neuroscience: Brain Briefings
abbrev: Brain Briefings
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 09, 2013. Brain Briefings is a newsletter series explaining how basic neuroscience discoveries lead to clinical applications. Brain Briefings is published during the academic year and prepared for a lay audience.

SOCK
type: Resource
type: NamedIndividual
has db xref: nlx_155951
synonym: Spatially Organized Component Klassifikator
IAO_0000115: A software toolbox that can automatically identify many of the artifact components that are often present in independent component analysis (ICA) of functional MRI (fMRI). The method: * Does not require temporal information about the fMRI paradigm. * Does not require the user to train the algorithm. * Requires only the EPI images (additional acquisition of anatomical images is not required). * Is able to identify a high proportion of artifact-related ICs without removing components that are likely to be of neuronal origin. * Can be applied to resting-state fMRI. * Is automated, requiring minimal or no human intervention.

SPHARM-MAT
type: Resource
type: NamedIndividual
has db xref: nlx_155952
IAO_0000115: A matlab-based 3D shape modeling and analysis toolkit, and is designed to aid statistical shape analysis for identifying morphometric changes in 3D structures of interest related to different conditions. SPHARM-MAT is implemented based on a powerful 3D Fourier surface representation method called SPHARM, which creates parametric surface models using spherical harmonics.

SPHARM-PDM Toolbox
type: Resource
type: NamedIndividual
has db xref: nlx_155953
synonym: SPHARM-PDM UNC Toolbox
synonym: UNC SPHARM-PDM
IAO_0000115: Software tool that computes point-based models using a parametric boundary description for the computing of Shape analysis. The point-based models computed with the SPHARM-PDM tool can be used in combination with the also UNC designed statistical tool shapeAnalysisMANCOVA to perform quantitative morphological assessment of structural changes at speci?c locations. Shape analysis has become of increasing interest to the medical community due to its potential to precisely locate morphological changes between healthy and pathological structures.

Authorea
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_156033
abbrev: Au
IAO_0000115: Online word processor for scientific and scholarly papers. Write, share, cite, comment, export, and track changes of articles in one place.

X-linked Adrenoleukodystrophy Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-21424
IAO_0000115: X-ALD database initiated July 1999 by Hugo W. Moser, M.D. and Stephan Kemp, Ph.D. The primary aims of the database are: to catalogue and facilitate the analysis of X-ALD mutations; to provide background information on X-ALD; to provide links to X-ALD patient organizations; and to help with contacting and finding (local) X-ALD health care professionals. The purpose of the X-linked adrenoleukodystrophy database is to provide general educational information about X-ALD.

XplorMed
type: Resource
type: NamedIndividual
has db xref: nif-0000-21425
synonym: Xploring Medline abstracts
synonym: XplorMed: eXploring Medline abstracts
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Server that allows you to explore a set of abstracts derived from a MEDLINE search. The system gives you the main associations between the words in groups of abstracts. Then, you can select a subset of your abstracts based on selected groups of related words and iterate your analysis on them. The only input needed is a set of abstracts (in one of the currently accepted input formats) or a definition of how to obtain them. XplorMed is recommended for cases in which you do not know exactly what are you expecting to find. Your interests may be modified by the results obtained, or you may want to inquire new questions as the analysis develops. Also, the results may suggest you additional words that should be used to expand your query in MEDLINE (e.g., unexpected abbreviations of a protein name, or synonyms of a disease).

Gibbs Motif Sampler
type: Resource
type: NamedIndividual
has db xref: biotools:gibbs_motif_sampler
has db xref: OMICS_00496
synonym: The Gibbs Motif Sampler
IAO_0000115: Software to identify motifs, conserved regions, in DNA or protein sequences.

SRI24 Atlas: Normal Adult Brain Anatomy
type: Resource
type: NamedIndividual
has db xref: nlx_155957
synonym: SRI24 Multi-Channel Atlas of Normal Adult Human Brain Structure
synonym: sri24-atlas - MRI-based brain atlas of normal adult human brain anatomy
abbrev: SRI24
abbrev: SRI24 Atlas
abbrev: sri24-atlas
IAO_0000115: An MRI-based atlas of normal adult human brain anatomy, generated by template-free nonrigid registration from images of 24 normal control subjects. The atlas comprises T1, T2, and PD weighted structural MRI, tissue probability maps (GM, WM, CSF), maximum-likelihood tissue segmentation, DTI-based measures (FA, MD, longitudinal and transversal diffusivity), and two labels maps of cortical regions and subcortical structures. The atlas is provided at 1mm isotropic image resolution in Analyze, NIFTI, and Nrrd format. We are also providing an experimental packaging for use with SPM8.

Seg3D
type: Resource
type: NamedIndividual
has db xref: nlx_155959
IAO_0000115: A free volume processing segmenting tool that combines a flexible manual interface with powerful image processing and segmentation algorithms. Users can explore and label image volumes using slice windows and 3D volume rendering.

ShapeComplexAtlas
type: Resource
type: NamedIndividual
has db xref: nlx_155960
IAO_0000115: A Matlab demo for constructing a neuro-anatomical shape complex atlas from 3D MRI brain structures, based on the paper Ting Chen, Anand Rangarajan, Stephan J. Eisenschenk and Baba C. Vemuri, Construction of a Neuroanatomical Shape Complex Atlas from 3D MRI Brain Structures. In NeuroImage, Volume 60, Page 1778-1787, 2012

Signed Differential Mapping
type: Resource
type: NamedIndividual
has db xref: nlx_155962
abbrev: SDM
IAO_0000115: Statistical method and software for conducting image- and coordinate-based meta-analysis of neuroimaging studies investigating differences in brain activity (e.g. BOLD response in fMRI, metabolism in PET) or structure (e.g. gray matter volume in VBM, voxel-based or TBSS white matter fractional anisotropy in DTI, etcetera).

Sleuth
type: Resource
type: NamedIndividual
has db xref: nlx_155963
synonym: Sleuth Version 2.4
IAO_0000115: Software application that searches the BrainMap Database for papers of interest, reads their corresponding meta-data, and plots their results as coordinates on a standard glass brain in Talairach space.

Bamboo DiRT
type: Resource
type: NamedIndividual
has db xref: nlx_156034
synonym: Bamboo Digital Research Tools
synonym: Bamboo Dirt registry of digital research tools for scholarly use
IAO_0000115: Registry of digital research tools for scholarly use that makes it easy for digital humanists and others conducting digital research to find and compare resources ranging from content management systems to music OCR, statistical analysis packages to mindmapping software., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Slice:Drop
type: Resource
type: NamedIndividual
has db xref: nlx_155964
IAO_0000115: A viewer for medical imaging data that supports a variety of scientific file formats out-of-the-box (see https://github.com/xtk/X/wiki/X:Fileformats for a complete list). We think that the best way to render your files is without any necessary conversions. Just drop'em on a website and they are ready to render. Just drag'n'drop some medical imaging files on this website or try one of the four examples in the right corner. Then, play with the panels on the left and click, drag and rotate the 3d content. Slice:Drop uses WebGL and HTML5 Canvas to render the data in 2D and 3D. We use our own open-source toolkit to perform the rendering, called XTK ( http://goxtk.com ).

Altmetric Badges
type: Resource
type: NamedIndividual
has db xref: nlx_156029
synonym: Altmetric.com embeds
synonym: The Altmetric Badges
IAO_0000115: A single line of code to add your article pages to include the Altmetric score and donut graphic on your own site with minimal technical effort. Choose from an array of different badge styles, including the colourful and iconic Altmetric donut. Implement article level metrics into your pages in minutes. Their pricing is based on the number of journals you want covered, with significant discounts for larger portfolios. You can try out the badges for free and without any commitment - however, your visitors will only see a subset of activity for each article when they click through. See the technical documentation for details.

Slicer3 Example Modules
type: Resource
type: NamedIndividual
has db xref: nlx_155965
IAO_0000115: Example Slicer3 plugins that can be built against a Slicer3 build or a Slicer3 installation. Note: these are for 3D Slicer version 3. There is now a version 4 of 3D Slicer available. Information about extensions for version 4 can be found at the following links: http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/SlicerApplication/ExtensionsManager http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/BuildTestPackageDistributeExtensions

Zebrafish Information Network (ZFIN)
type: Resource
type: NamedIndividual
has db xref: biotools:zfin
has db xref: nif-0000-21427
has db xref: OMICS_01666
has db xref: r3d100010421
has db xref: SCR_017504
synonym: The Zebrafish Model Organism Database
synonym: Zebra Model Organism Database
synonym: Zebrafish Database
synonym: ZebraFish Information Network
synonym: ZFIN
IAO_0000115: Model organism database that serves as central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. Data represented are derived from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations. Data formats include text, images and graphical representations.Serves as primary community database resource for laboratory use of zebrafish. Developed and supports integrated zebrafish genetic, genomic, developmental and physiological information and link this information extensively to corresponding data in other model organism and human databases.

Source Information Flow Toolbox
type: Resource
type: NamedIndividual
has db xref: nlx_155967
abbrev: SIFT
IAO_0000115: A GUI-enabled EEGLAB plugin for modeling and visualizing dynamical interactions between electrophysiological signals (EEG, ECoG, MEG, etc), preferably after transforming signals into the source domain. The toolbox consists of four modules: (1) Data Preprocessing, (2) Model Fitting and Connectivity Estimation, (3) Statistical Analysis, (4) Visualization, with a fifth Group Analysis module in development. Module 2 currently includes several adaptive multivariate autoregressive modeling (AMVAR) algorithms, including segmentation AMVAR and Kalman filtering. This subsequently allows the user to validate the model and estimate (in the time-frequency domain) a wide range of multivariate Granger-causal and coherence measures published to date. Module 3 includes routines for parametric and non-parametric significance testing. Module 4 contains routines for interactive visualization of dynamical interactions across time, frequency and anatomical source location.

Spanish Resting State Network
type: Resource
type: NamedIndividual
has db xref: nlx_155968
abbrev: SRSN
IAO_0000115: Forum (Spanish) for sharing information and knowledge on this network, a collaboration between different research groups in Spain and national and international centres. (Foro para compartir datos y conocimiento sobre esta red. Se constituye el Spanish Resting State Network como una colaboracion entre distintos grupos de investigacion de Espa������a y centros nacionales e internacionales.)

Spatial Analysis 3D
type: Resource
type: NamedIndividual
has db xref: nlx_155969
abbrev: SA3D
IAO_0000115: A user-friendly, graphical user interface (GUI) that allows statistical and visual manipulations of real and simulated three-dimensional spatial point patterns. The analyses use files containing sets of X, Y, Z coordinates. These point patterns are frequently coordinates of cells of specific cell classes within in volumes of tissue derived from microscopy analyses. The analyses are scale independent so spatial analyses of coordinates from larger and smaller scale distributions are possible. The software can also generate sample sets of X, Y, Z coordinates for program exploration and modeling purposes.

University of Arkansas System; Arkansas; USA
type: Organization
type: NamedIndividual
has db xref: nlx_152182
synonym: UA System
synonym: University of Arkansas System
IAO_0000115: The public university system in Arkansas, USA that includes 4-year institutions, 2-year colleges, and affiliated units for agriculture, public service and criminal justice programs.

University of Aveiro; Aveiro; Portugal
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100007689
has db xref: grid.7311.4
has db xref: ISNI:123236065
has db xref: nlx_151934
has db xref: Wikidata:Q29671
synonym: Universidade de Aveiro
synonym: University of Aveiro
abbrev: UA
IAO_0000115: Public research university and polytechnic education center in Aveiro, Portugal. It offers undergraduate, graduate and post-graduate degree programs in applied mathematics, physics, chemistry, telecommunications, robotics, bioinformatics, sea sciences, materials, design, business administration and industrial engineering.

University of Central Arkansas; Arkansas; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100010073
has db xref: grid.266128.9
has db xref: ISNI:0000 0001 2161 1001
has db xref: nlx_64240
has db xref: Wikidata:Q1782724
synonym: University of Central Arkansas
abbrev: UCA
IAO_0000115: Public research university in Conway, Arkansas that offers degree programs in nursing, education, physical therapy, business, performing arts, and psychology.

Wessim
type: Resource
type: NamedIndividual
has db xref: OMICS_00259
IAO_0000115: Software simulator for a targeted resequencing generally known as exome sequencing. Wessim generates a set of artificial DNA fragments for next generation sequencing (NGS) read simulation.

Stereoscopic Atlas of Intrinsic Brain Networks
type: Resource
type: NamedIndividual
has db xref: nlx_155970
synonym: Stereoscopic Atlas of Intrinsic Brain Networks (SAIBN)
abbrev: SAIBN
IAO_0000115: A 3D stereoscopic (anaglyph method) full brain functional connectivity atlas created using a parcellation atlas published by Craddock et al. (2012). Using 3D Slicer 3.6.3 and the two hundred Region of Interest (ROI) version of the Craddock atlas, 200 grayscale surface models were created using a z-stat threshold > 2.3, and each surface model was processed with a surface decimation algorithm, smoothed with the Taubin algorithm and without surface normals. For improved visualization of the functional connectivity networks and their relative anatomical position, the surface model of five subcortical anatomical structures (corpus callosum, bilateral caudate, pallidum, putamen, thalamus, amygdala and hippocampus) were included in SAIBN. These surfaces were created with 3D Slicer using the segmentation computed with Freesurfer v. 5.1. The viewer should use red-cyan glasses to see the 3D stereoscopic effect using 3D Slicer (version 3.6.3, http://www.slicer.org/pages/Special:SlicerDownloads).

UNC Infant 0-1-2 Atlases
type: Resource
type: NamedIndividual
has db xref: nlx_155971
synonym: UNC 0-1-2 Infant Atlases
IAO_0000115: 3 atlases dedicated for neonates, 1-year-olds, and 2-year-olds. Each atlas comprises a set of 3D images made up of the intensity model, tissue probability maps, and anatomical parcellation map. These atlases are constructed with the help of state-of-the-art infant MR segmentation and groupwise registration methods, on a set of longitudinal images acquired from 95 normal infants (56 males and 39 females) at neonate, 1-year-old, and 2-year-old.

UNC Primate Brain Atlas
type: Resource
type: NamedIndividual
has db xref: nlx_155972
IAO_0000115: Symmetric atlas of the primate brain created using 18 cases of rhesus macaques aged 16-34 months. It includes the T1-weighted image (with and without skull), and also tissue segmentation probability maps (white matter, gray matter, CSF, rest), subcortical structures segmentation (amygdala, caudate, hippocampus, pallidus, putamen), and a lobar parcellation map. You can find more details about the creation of this atlas in the following paper : M. Styner, R. Knickmeyer, S. Joshi, C. Coe, S. J. Short, and J. Gilmore. Automatic brain segmentation in rhesus monkeys. In Proc SPIE Vol 6512, Medical Imaging, 2007, pp. 65122 L1-8

XCEDE Schema
type: Resource
type: NamedIndividual
has db xref: nlx_155974
synonym: XML-Based Clinical Experiment Data Exchange Schema
abbrev: XCEDE
IAO_0000115: Data management software that provides an extensive metadata hierarchy for describing and documenting research and clinical studies. The schema organizes information into five general hierarchical levels: a complete project, studies within a project, subjects involved in the studies, visits for each of the subjects, the full description of the subject's participation during each visit.

peak nii
type: Resource
type: NamedIndividual
has db xref: nlx_155975
synonym: peak_nii: Statistical image clustering peak detection and data extraction
abbrev: peak_nii
IAO_0000115: Software toolbox for statistical image clustering, peak detection and data extraction developed to allow the user to have flexibility of clustering their data. Based on your threshold, it will cluster your data and find the peaks within each cluster. Additionally, it has been combined with a data extraction tool that allows one to extract the data from all the scans of the analysis from all the clusters, along with several other extraction options, with a single command.

pydicom
type: Resource
type: NamedIndividual
has db xref: nlx_155976
IAO_0000115: Software Python package for working with DICOM files, made for inspecting and modifying DICOM data in an easy pythonic way. The modifications can be written again to a new file. As a pure python package, it should run anywhere python runs without any other requirements.

pyxnat
type: Resource
type: NamedIndividual
has db xref: nlx_155977
synonym: pyxnat: XNAT in Python
IAO_0000115: Software Python library that relies on the REST API provided by the XNAT platform since its 1.4 version. XNAT is an extensible database for neuroimaging data. The main objective is to ease communications with an XNAT server to plug-in external tools or python scripts to process the data.

University of Barcelona; Barcelona; Spain
type: Organization
type: NamedIndividual
has db xref: nlx_21784
synonym: Universitat de Barcelona
synonym: University of Barcelona
abbrev: UB
IAO_0000115: Public university in Barcelona, Spain that offers degree programs in social sciences, engineering, and arts and humanities.

Mouse HapMap Imputation Genotype Resource
type: Resource
type: NamedIndividual
has db xref: nif-0000-21752
abbrev: Mouse HapMap
IAO_0000115: Genetic maps for 94 inbred strains of mouse and imputed genotypes using the NIEHS / Perlegen resequencing resource. Combining with the 13,094 Wellcome Trust SNPs (Single-nucleotide polymorphisms), a set of 132,285 SNPs was compiled and is available for download. Using the mouse HapMap resource, it is possible to accurately impute the genotypes of the 94 strains at the 8 million SNPs discovered by the NIEHS/Perlegen mouse resequencing project. They imputed the genotypes at the NIEHS/Perlegen SNPs from the mouse HapMap SNPs and an additional set of 7,570 gap-filling SNPs provided by NIEHS/Perlegen. Since each NIEHS/Perlegen SNP probe has different quality, they classified roughly half of the SNPs as "high-quality" SNPs, which do not have missing genotype at any of the 15 resequenced strains. The imputed genotypes are available for the high-quality SNPs, which has estimated error rate of 0.27% for high-confidence imputed genotypes. In addition, the imputed genotypes for all 8 million SNPs are also available for download. Their estimated error rate is 0.37% for high-confidence imputed genotypes.

scikit-learn
type: Resource
type: NamedIndividual
has db xref: nlx_155979
synonym: scikit-learn: machine learning in Python
IAO_0000115: scikit-learn: machine learning in Python

shapeAnalysisMANCOVA - SPHARM tools
type: Resource
type: NamedIndividual
has db xref: nlx_155980
abbrev: shapeAnalysisMANCOVA
IAO_0000115: shapeAnalysisMANCOVA offers statistical shape analysis based on a parametric boundary description (SPHARM) as the point-based model computing method. The point-based models will be analyzed with the methods here proposed using multivariate analysis of covariance (MANCOVA). Here, the number of variates being tested is the dimensionality of our observations. Each point of these observations is a three dimensional displacement vector from the mean. The number of contrasts is the number of equations involved in the null-hypothesis. In order to encompass varying numbers of variates and contrasts, and to account for independent variables, a matrix computation is performed. This matrix represents the multidimensional aspects of the correlation significance and it can be transformed into a scalar measure by manipulation of its eigenvalues. Details of the methods can be found in its Insight Journal publication: http://hdl.handle.net/10380/3124

VMTK in 3D Slicer
type: Resource
type: NamedIndividual
has db xref: nlx_155981
synonym: Slicer4:VMTK
synonym: Vascular Modeling Toolkit in 3D Slicer
synonym: Vascular Modeling Toolkit in 3D Slicer 4
synonym: VMTK Extension for 3D Slicer 4.2+
synonym: VMTK in 3D Slicer 4
IAO_0000115: Provides series of modules which enable functions of Vascular Modeling Toolkit in 3D Slicer. Functionality includes vessel enhancement filtering, level set segmentation, centerline computation, network extraction and branch splitting.VMTK is available through the extension manager for 3D Slicer from version 4.6.2. Main difference to Slicer3 version is that now all VMTK modules come as one extension bundle. This should enhance the installation experience for users.

BioStar
type: Resource
type: NamedIndividual
has db xref: nlx_155982
has db xref: OMICS_01706
synonym: biostars.org
abbrev: Biostar
IAO_0000115: A question answer forum for scientists, focusing on methods in bioinformatics, computational genomics and biological data analysis. They welcome detailed and specific posts, written clearly and simply.

3D Interactive Chemical Shift Imaging
type: Resource
type: NamedIndividual
has db xref: nlx_155986
synonym: 3D Chemical Shift Imaging
abbrev: 3DiCSI
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13,2026. Software program for multi-dimensional CSI data visualization, spectral processing, localization, quantification and multi-variate analysis.

BRAINSSurfaceStats
type: Resource
type: NamedIndividual
has db xref: nlx_155987
IAO_0000115: Software tool for performing a per vertex statistical analysis across a population. The underlying statistical framework uses the R language.

Brain lesion segmentation tool using SVM
type: Resource
type: NamedIndividual
has db xref: nlx_155988
synonym: Brain lesion segmentation tool using Support Vector Machines
IAO_0000115: Segmentation tool that uses image analysis and machine learning techniques (Support Vector Machines). Image intensities from multiple MR acquisition protocols, after coregistration, are used to form a voxel-wise attribute vector which is used to perform the segmentation. Computer algorithms have started to complement expert-readings of MRI as they may improve throughput and consistency, in addition to providing more accurate quantitative measures of lesion type and volume. Computerized segmentation methods can also offer more precise measurements of longitudinal change of a lesion with disease progression or treatment response.

MBASED
type: Resource
type: NamedIndividual
has db xref: OMICS_05502
synonym: MBASED - Package containing functions for ASE analysis using Meta-analysis Based Allele-Specific Expression Detection
synonym: Meta-analysis Based Allele-Specific Expression Detection
IAO_0000115: Software package containing functions for allele-specific gene expression (ASE) analysis using meta-analysis based allele-specific expression detection.

Diffusion Tractography with Kalman Filter
type: Resource
type: NamedIndividual
has db xref: nlx_155990
synonym: Tractography with Unscented Kalman Filter
IAO_0000115: Software framework which uses an unscented Kalman filter for performing tractography. At each point on the fiber the most consistent direction is found as a mixture of previous estimates and of the local model. It is very easy to expand the framework and to implement new fiber representations for it. Currently it is possible to tract fibers using two different 1-, 2-, or 3-tensor methods. Both methods use a mixture of Gaussian tensors. One limits the diffusion ellipsoids to a cylindrical shape (the second and third eigenvalue are assumed to be identical) and the other one uses a full tensor representation. The project is written in C++. It could be used both as a Slicer3 module and as a standalone commandline application.

Fast Nonlocal Means for MRI denoising
type: Resource
type: NamedIndividual
has db xref: nlx_155991
IAO_0000115: A fast and robust software implementation of the popular Nonlocal Means for MRI-Rician denoising. It works by computing the non-local weights based on distances in a features space comprising the local mean value and gradients of the image. It can reach an acceleration factor of 20x over the original implementation, with an improved performance for medium-low SNR images. They use a bias correction step for Rician noise based on the well-known Conventional Approach. This software can be compiled either as a Slicer module or a stand-alone: http://www.nitrc.org/snapshots.php?group_id=518

FedBizOpps.gov: Federal Business Opportunities
type: Resource
type: NamedIndividual
has db xref: nif-0000-21756
synonym: FBO
IAO_0000115: The system is a web-based portal which allows vendors to review Federal Procurement Opportunities over 25,000. From the sites main navigation page, users can view opportunities and awards as well as view a variety of information and resources. FBO now contains Recovery and Reinvestment Act actions. Vendors / citizens may search, monitor, and retrieve opportunities. Government users may post, manage, and award opportunities when logged in using their password protected account.

Monte Carlo Simulation Software: tMCimg
type: Resource
type: NamedIndividual
has db xref: nlx_155993
synonym: Monte Carlo Photon Transport
abbrev: tMCimg
IAO_0000115: Software application that uses a Monte Carlo algorithm to model the transport of photons through 3D volumes with spatially varying optical properties. Both highly-scattering tissues (e.g. white matter) and weakly scattering tissues (e.g. cerebral spinal fluid) are supported. Using the anatomical information provided by MRI, X-ray CT, or ultrasound, accurate solutions to the photon migration forward problems are computed in times ranging from minutes to hours, depending on the optical properties and the computing resources available.

Web Interfaces for Multiscale Images
type: Resource
type: NamedIndividual
has db xref: nlx_156020
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Venue for discussing and defining standard web interfaces for sharing images, annotations, and analyses of multiscale biological images. The goal is to increase interoperability of code to share the burden of infrastructure, increase code reuse, and allow us to spend more time focused on scientific questions. Please visit our Wiki to start participating. Together we can develop a small group of interfaces which are easy to implement, extensible, and cover the major tasks of developing tools for multiscale data on the web.

STAPLE
type: Resource
type: NamedIndividual
has db xref: nlx_155994
synonym: Simultaneous Truth and Performance Level Estimation
synonym: STAPLE - Simultaneous Truth and Performance Level Estimation
IAO_0000115: An algorithm for the Simultaneous Truth and Performance Level Estimation, which estimates a reference standard and segmentation generator performance from a set of segmentations. It has been widely applied for the validation of image segmentation algorithms, and to compare the performance of different algorithms and experts. It has also found application in the identification of a consensus segmentation, by combination of the output of a group of segmentation algorithms, and for segmentation by registration and template fusion., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Segmentation Validation Engine
type: Resource
type: NamedIndividual
has db xref: nlx_155995
abbrev: SVE
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. An automated online framework for performing validation studies of skull-stripping methods. Registered users may download 40 T1 MRI volumes, skull-strip them with the algorithm of their choice, and upload their segmentation results to the SVE website. The server will then compare the 40 skull-stripped results against a set of manually generated brain masks. The server computes a series of measures for the uploaded data, including Jaccard and Dice measures. It also produces images for visualizing the spatial location of the segmentation errors relative to a common space. The results are archived on the server, and the measures are viewable by visitors to the site.

Spatial Statistical Parametric Mapping
type: Resource
type: NamedIndividual
has db xref: nlx_155996
abbrev: SSPM
IAO_0000115: Software package representing Spatial Statistical Parametric Mapping that includes two tools presently: MAGEE and FADTTS. MAGEE represents the Multiscale Adaptive Generalized Estimating Equation. It was developed specifically for analyzing multivariate neuroimaging data in 3-dimensional volume (or on 2-dimensional surface) from longitudinal neuroimaging studies. FADTTS represents Functional Analysis of Diffusion Tensor Tract Statistics. The aim of this tool is to implement a functional analysis pipeline, for delineating the structure of the variability of multiple diffusion properties along major white matter fiber bundles and their association with a set of covariates of interest, in various diffusion tensor imaging studies.

SpineSegmentation module for 3DSlicer
type: Resource
type: NamedIndividual
has db xref: nlx_155997
synonym: Spine Segmentation module for 3D Slicer
abbrev: Spine Segmentation Module in Slicer3
IAO_0000115: 3D Slicer module for automated segmentation of the spine. This is an implementation of a novel model-based segmentation algorithm. This work was presented at the NA-MIC Week in Salt Lake City, Jan 2010.

Stochastic Tractography System
type: Resource
type: NamedIndividual
has db xref: nlx_155998
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14, 2026. Software tools which can perform Stochastic Tractography and related analysis on DWMRI data. Stochastic Tractography applies a Bayesian approach towards the estimation of nerve fiber tracts from DWMRI images.

Subject Library
type: Resource
type: NamedIndividual
has db xref: nlx_155999
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A collection of software tools used for processing and organizing MRI data. The Dicom Importer allows you to to view, assemble, and organize dicom files. Subject Library is a filesystem-based search and reporting tool that can be configured to work with many different organization schemes. This package also contains a python library that can be used to write scripts for custom tasks.

TAPIR
type: Resource
type: NamedIndividual
has db xref: nlx_156001
synonym: Tools for Advanced Parameterized Image Registration
IAO_0000115: A set of command line tools allowing 2D and 3D image registration, mainly for medical imaging (although also relevant to other image registration problems).

ESIP Data Management Short Course for Scientists
type: Resource
type: NamedIndividual
has db xref: nlx_156043
synonym: ESIP Commons Data Management Short Course for Scientists
synonym: ESIP Data Management Training for Scientists
abbrev: Data Management Short Course for Scientists
IAO_0000115: ESIP Federation training courses to improve the understanding of scientific data management among scientists, emerging scientists, and data professionals. The ESIP Federation, in cooperation with NOAA, seeks to share the community's knowledge with scientists who increasingly need to be better data managers, as well as to support workforce development for new data management professionals.

TARQUIN
type: Resource
type: NamedIndividual
has db xref: nlx_156002
synonym: TARQUIN MRS analysis package
IAO_0000115: An analysis tool for automatically determining the quantities of molecules present in NMR spectroscopic data. The intended purpose of TARQUIN is to aid the characterisation of pathologies, in particular brain tumours, both non-invasively with in-vivo 1H MRS and ex-vivo with 1H HR-MAS. TARQUIN has the following features: * Free to use and modify under the GPL licence. * Based on a flexible time-domain fitting routine designed to give accurate rapid and automated quantitation for routine analysis. * Cross platform, works on Windows, Linux and OSX. * Comes packaged with a quantum mechanically based metabolite simulator to allow basis set construction optimised for the investigation of particular pathologies sequence parameters. * Includes both GUI and command line interface for one-off and batch analyses.

Soft Flow
type: Resource
type: NamedIndividual
has db xref: nlx_152464
synonym: Soft Flow inc.
IAO_0000115: Commercial company that develops and sells flow cytometry assay development software and analytical cytology tools.

Template Image Processing Library
type: Resource
type: NamedIndividual
has db xref: nlx_156003
abbrev: TIPL
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A lightweight C++ template library designed mainly for medical imaging processing. The design paradigm follows generic programming, and the purpose is to provide an easy-to-use and also ready-to-use library. The code is template-based, and only header files are needed to be included to the source code. This library provides the following functions: # DICOM (r), Analyze(r), Nifti (r/w), and MATLAB MAT V4 (r/w) # numerical: add, multiply, gradient. # interpolation: linear, gaussian radial basis # filters: mean, gaussian, laplacian, sobel, anisotropic diffusion # morphological processing: erosion, expansion, opening, closing # template-based Fourier transform # linear coregistration: rigid body, affine transform, least square fit, mutual information # nonlinear coregistration: The Large Deformation Diffeomorphic Metric Mapping (LDDMM)

TetraMetrix
type: Resource
type: NamedIndividual
has db xref: nlx_156004
IAO_0000115: An open-source software project for distributed Tetrahedral Mesh Modeling and Analysis (TMMA) of multidimensional data. Tetrahedra are 3D, space filling, geometric objects that can be used to form representations and partitions of objects like volumes and shapes obtained from biomedical images (e.g., 3D MRI brain images). Tetrahedra are a natural extension of lines (1D) and surface triangulations (2D) which enable finite element analysis of irregular shapes, and permit a greater range of morphometric characterization of multidimensional objects. A beta version of the program is available for download. Please see the very brief instructions on the "Docs" tab on the left.

TractoR: Tractography with R
type: Resource
type: NamedIndividual
has db xref: nlx_156005
synonym: Tractography with R
abbrev: TractoR
IAO_0000115: Software application that includes R packages for reading, writing and visualising magnetic resonance images stored in Analyze, NIfTI and DICOM file formats (DICOM support is read only). It also contains functions specifically designed for working with diffusion MRI and tractography, including a standard implementation of the neighbourhood tractography approach to white matter tract segmentation. A shell script is also provided to run experiments with TractoR without interacting with R.

Triangle BioSystems
type: Organization
type: NamedIndividual
has db xref: nlx_156006
synonym: Triangle BioSystems International
abbrev: TBSI
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A biomedical device company focused on developing and manufacturing neural hardware solutions for application in medical research using animals when bio-monitoring, recording and stimulation functions are needed. * Neural Recording Equipment * Neural Stimulation Equipment * Data Acquisition Hardware and Software

TumorSim
type: Resource
type: NamedIndividual
has db xref: nlx_156007
IAO_0000115: Simulation software that generates pathological ground truth from a healthy ground truth. The software requires an input directory that describes a healthy anatomy (anatomical probabilities, mesh, diffusion tensor image, etc) and then outputs simulation images.

TurtleSeg
type: Resource
type: NamedIndividual
has db xref: nlx_156008
synonym: TurtleSeg - Interactive 3D Image Segmentation Software
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. An interactive segmentation tool originally designed for 3D medical images. Accurate and automatic 3D medical image segmentation remains an elusive goal and manual intervention is often unavoidable. TurtleSeg implements techniques that allow the user to provide intuitive yet minimal interaction for guiding the 3D segmentation process.

UNC Human Brain Atlas
type: Resource
type: NamedIndividual
has db xref: nlx_156009
IAO_0000115: Human brain atlases for adult, pediatric and elderly populations, by iterative joint deformable registration of training datasets into a single unbiased average image. Atlases packages include T1-weighted images, tissue priors (WM,GM,CSF), lobar parcellation maps and subcortical structures. Current available atlases: * Adult atlas: Symmetric atlas generated from 50+ healthy adult subjects (20-59 year old). * UNC-MNI Pediatric 1-year-old atlas: Symmetric atlas generated from 104 1-year-old subjects, combining children at high familial risk of autism and controls. * Pediatric 4-year-old atlas: Symmetric atlas generated from 10 4-year-old healthy subjects. * Elderly atlas: Atlas generated from 27 healthy elderly subjects (60+ years old). Additional information and acknowledgment for their usage can be found by clicking on the release notes.

University of Athens; Athens; Greece
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100005187
has db xref: grid.5216.0
has db xref: ISNI:0000 0001 2155 0800
has db xref: nlx_94434
has db xref: Wikidata:Q547867
synonym: National and Kapodistrian University of Athens
synonym: University of Athens
abbrev: UoA
IAO_0000115: Public university in Athens, Greece that offers degree programs in health sciences, law and economics, and theology.

VR Worlds 2
type: Resource
type: NamedIndividual
has db xref: nlx_156011
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. NOTE: VR Worlds 2 is no longer available as a standalone software. Software application designed for the creation and execution of neurobehavioral studies. The VR Worlds 2 platform allows accurate, real-time data collection of the navigation and interactions within a simulated environment. You are free to design and perform custom or predefined experiments tailored to your personal research or clinical needs. Create complex environments with meaningful content using VR Worlds 2?s user-friendly, drag-and-drop interface. Include triggers to launch simple or intricate events, such as a conversation between characters or a customizable rating scale. VR Worlds 2 provides several realistic simulations to immerse your subjects in context appropriate environments, including: * Residential/Urban Area * Hotel Lobby * Medical Office * Grocery Store * Neighborhood for drug and alcohol cue extinction treatment (featured on GMA, motion capture process) * Casino for gambling addiction research (featured on Canadian Discovery Channel) * Driving simulation for mild cognitive impairment research * Phobia scenarios * Spatial navigation mazes

Vaa3D
type: Resource
type: NamedIndividual
has db xref: nlx_156012
synonym: 3D Visualization-Assisted Analysis
synonym: V3D
synonym: V3D-Neuron
synonym: Vaa3D and Vaa3D-Neuron
synonym: Vaa3D: A Swiss army knife for bioimage visualization & analysis
synonym: Vaa3D: A Swiss army knife for bioimage visualization and analysis
abbrev: Vaa3D-Neuron
IAO_0000115: A handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. Vaa3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D/4D/5D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. Vaa3D is very easy to be extended via a powerful plugin interface. For example, many ITK tools are being converted to Vaa3D Plugins. Vaa3D-Neuron is built upon Vaa3D to make 3D neuron reconstruction much easier. In a recent Nature Biotechnology paper (2010, 28(4), pp.348-353) about Vaa3D and Vaa3D-Neuron, an order of magnitude of performance improvement (both reconstruction accuracy and speed) was achieved compared to other tools.

ValMap: simple statistical mapping tool
type: Resource
type: NamedIndividual
has db xref: nlx_156013
abbrev: ValMap
IAO_0000115: A command line voxel-wise statistical analysis software program for images. Images can be gray matter density, jacobian images, etc. The linear model is implemented, i.e. designs that can be modeled as Y=AB, where Y is a vector or matrix of dependent variables, B is a vector or matrix of parameters to be estimated, and A is a design matrix. Why use valmap? # Do not need a Matlab license to run. # Can incorporate a spatially varying independent variable (e.g., you have a perfusion map as your dependent variable, and you want to co-vary for gray matter at each voxel, so use a gray matter map as an independent variable). # Can use spatially invariant independent variables (e.g., you can have a cognitive test score as the dependent variable, and use jacobian maps as the independent variable). # Can have multiple dependent variables and do multivariate analyses (e.g., want to know the overall effect of disease on perfusion and structure, so use perfusion maps and jacobian maps as dependent variables).

Etherpad
type: Resource
type: NamedIndividual
has db xref: nlx_156044
IAO_0000115: Web application for real-time collaborative editing. It provides customizable options, a documented API and the ability to convert to various data exchange formats.

discoSnp
type: Resource
type: NamedIndividual
has db xref: biotools:discosnp
has db xref: OMICS_00267
synonym: DiscoSnp++
synonym: discovering Single Nucleotide Polymorphism
synonym: discovering Single Nucleotide Polymorphism (discoSNP)
IAO_0000115: Software designed for discovering Single Nucleotide Polymorphism (SNP) from raw sets of reads obtained with Next Generation Sequencers (NGS).

WFU Biological Parametric Mapping Toolbox
type: Resource
type: NamedIndividual
has db xref: nlx_156016
synonym: BPM
synonym: BPM - Integrated Tool for Biological Parametric Mapping
synonym: BPM toolbox
synonym: WFU Biological Parametric Mapping
abbrev: WFU BPM
abbrev: WFU_BPM
IAO_0000115: Software toolbox that performs SPM analysis with voxel-wise imaging covariates. The BPM toolbox incorporates information obtained from other modalities as regressors in a voxel-wise analysis, thereby permitting investigation of more sophisticated hypotheses. The BPM toolbox has been developed in Matlab with a user-friendly interface for performing analyses, including voxel-wise multimodal correlation, ANCOVA, and multiple regression. It has a high degree of integration with the SPM (statistical parametric mapping) software relying on it for visualization and statistical inference. Furthermore, statistical inference for a correlation field, rather than a widely used T-field, has been implemented in the correlation analysis for more accurate results. Requirements: * SPM2 or SPM5 * MATLAB version 6.5 or higher

WFU Pipeline
type: Resource
type: NamedIndividual
has db xref: nlx_156017
synonym: WFU SPM5 Pipeline
abbrev: WFU_Pipeline
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14, 2026. A fully automated software application for the processing of fMRI data using SPM. It is fully automated from the point of data acquisition at the MRI scanner. It incorporates tools for automated data transfer, archiving, real-time SPM5 batch script generation with distributed grid processing, automated error-recovery procedures, full data-provenance, email notifications, optional conversion back to DICOM (Digital Imaging and Communications in Medicine), and picture archiving and communications systems (PACS) insertion. The architecture allows for an infinite number of easily definable analyses that are fully automated from the point of acquisition. Requirements: * MATLAB 7.3 or greater with the Image Processing Toolbox * SPM5

University of Auckland; Auckland; New Zealand
type: Organization
type: NamedIndividual
has db xref: nlx_28115
IAO_0000115: Public university in New Zealand that offers degrees in areas such as the arts, business, education, medical and health science, and law.

National Toxicology Program: Department of Health and Human Services
type: Resource
type: NamedIndividual
has db xref: nif-0000-21757
synonym: NTP
IAO_0000115: The NTP is an interagency program whose mission is to evaluate agents of public health concern by developing and applying tools of modern toxicology and molecular biology. The program maintains an objective, science-based approach in dealing with critical issues in toxicology and is committed to using the best science available to prioritize, design, conduct, and interpret its studies. To that end, the NTP is continually evolving to remain at the cutting edge of scientific research and to develop and apply new technologies. More than 80,000 chemicals are registered for use in the United States. Each year, an estimated 2,000 new ones are introduced for use in such everyday items as foods, personal care products, prescription drugs, household cleaners, and lawn care products. We do not know the effects of many of these chemicals on our health, yet we may be exposed to them while manufacturing, distributing, using, and disposing of them or when they become pollutants in our air, water, or soil. Relatively few chemicals are thought to pose a significant risk to human health. However, safeguarding public health depends on identifying both what the effects of these chemicals are and at what levels of exposure they may become hazardous to humansthat is, understanding their toxicology. The program was created as a cooperative effort to: 1. Coordinate toxicology testing programs within the federal government. 2. Strengthen the science base in toxicology. 3. Develop and validate improved testing methods. 4. Provide information about potentially toxic chemicals to health, regulatory, and research agencies, scientific and medical communities, and the public. The need for a program like the NTP arose because of increasing scientific, regulatory, and Congressional concerns about the human health effects of chemical agents in our environment. Many human diseases were thought to be directly or indirectly related to chemical exposures; therefore, it was thought that decreasing or el…

Working Memory Trainer
type: Resource
type: NamedIndividual
has db xref: nlx_156022
abbrev: WM Trainer
IAO_0000115: A stand-alone axecutable under all main Windows OS for training the working memory. The WM Trainer looks and behaves a little bit like a video-game and has been specifically conceived for children attending the primary school. However, it can be used purposefully by people of any age, including adult and elderly. This application features highest graphic quality, a powerful adaptive engine for the difficulty level, a database of users and statistical tools to evaluate the progress. Currently English, French and Italian are supported, but any language can be easily supported.

College on Problems of Drug Dependence
type: Resource
type: NamedIndividual
has db xref: nif-0000-21909
synonym: Committee on Problems of Drug Dependence
abbrev: CPDD
IAO_0000115: The College on Problems of Drug Dependence (CPDD) is an interdisciplinary research society whose members address problems of drug dependence in the broadest range of scientific disciplines, including chemistry, basic biology, pharmacology, behavioral science, clinical research, sociology, psychology, anthropology, and history. CPDD serves as an interface among governmental, industrial and academic communities maintaining liaisons with regulatory and research agencies as well as educational, treatment, and prevention facilities in the drug abuse field. It also functions as a collaborating center of the World Health Organization. The Annual Scientific Meeting: Since 1938, a major focus of the CPDD's activities has been its sponsorship of an annual scientific meeting. This conference serves as a forum bringing together basic scientists and clinical investigators from industry, academia, and government. Representatives of regulatory agencies, as well as scientists and professionals in a number of diverse disciplines interested in the biochemical, behavioral, and public health aspects of drug dependence participate. Special Conferences: Periodically, the College sponsors conferences focused on timely topics of interest to researchers, government, industry, and the public. In recent years, CPDD has organized meetings on Abuse Liability Assessment of CNS Drugs; Drug Formulation and Abuse Liability; Pre-Clinical Abuse Liability Testing; Women and Smoking: Understanding Socioeconomic Influences; and Risk Management and Post-Marketing Surveillance for CNS-Acting Drugs. Consultation Activities: The CPDD provides consulting expertise in the area of epidemiology, treatment, prevention, and all the basic and clinical sciences related to drug dependence, drug abuse, and their behavioral and medical consequences. Sponsorship of Drug and Alcohol Dependence: The CPDD sponsors the journal Drug and Alcohol Dependence, published by Elsevier. A principal goal of the journal is to provide…

vis: SPM Visualized Statistics toolbox
type: Resource
type: NamedIndividual
has db xref: nlx_156024
synonym: vis: visualized statistics toolbox
synonym: Visualized Statistics toolbox
synonym: Visualized Statistics toolbox (vis)
abbrev: vis
IAO_0000115: Simple, menu-driven software toolbox for SPM 5/8 for exploratory data analysis for functional or structural images (.img / .nii) provides the user with several options: # a histogram of all non-zero voxel values in a brain image; # a scatter plot, Q-Q plot, or Bland-Altman plots comparing two images; # a surface plot of all voxel values at a particular axial slice; # easy Region of Interst (ROI)-based extraction of voxel values. Note: the toolbox calls various SPM 5/8 functions. The Q-Q plot function requires the MATLAB stats toolbox.

Commons In A Box
type: Resource
type: NamedIndividual
has db xref: nlx_156036
abbrev: CBOX
IAO_0000115: A free, distributable, easy-to-install software package of customizable, WordPress-based commons spaces for communities. This software project aimed at turning the infrastructure that successfully powers the CUNY (City University of New York) Academic Commons takes the complexity out of creating a Commons site, helping organizations create a space where their members can discuss issues, collaborate on projects, and share their work. CBOX also provides: * Out-of-the-box functionality with an intuitive set-up that guides site administrators through each step of installation. * A powerful, responsive, highly customizable theme developed for community engagement, based on PressCrew's Infinity Theming Engine. * Responsive design for easy viewing on many devices, including tablets and smartphones. * Collaborative document creation and file sharing. * Reply-By-Email functionality for quick, on-the-go communication. * Compatibility with many other WordPress and BuddyPress themes and plug-ins. * Expansive wiki options. CBOX will be useful to any organization that is looking for a shared space in which to build an engaged community of users and developers. Download their code, peruse their documentation, check out their project demo website, and join their community to find others using CBOX.

ESTHER
type: Resource
type: NamedIndividual
has db xref: nif-0000-02817
has db xref: nif-0000-30526
has db xref: r3d100010542
has db xref: SCR_008479
synonym: ESTerases and alpha / beta-hydrolase Enzymes and Relatives
synonym: ESTerases and alpha/beta-Hydrolase Enzymes and Relatives
synonym: ESTHER Database
IAO_0000115: Database and tools for analysis of protein and nucleic acid sequences belonging to superfamily of alpha/beta hydrolases homologous to cholinesterases. Covers multiple species, including human, mouse caenorhabditis and drosophila., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

CKAN
type: Resource
type: NamedIndividual
has db xref: nlx_156038
synonym: ckan - The open source data portal software
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A complete out-of-the-box data management software solution that makes data accessible by providing tools to streamline publishing, sharing, finding and using data. CKAN is aimed at data publishers (national and regional governments, companies and organizations) wanting to make their data open and available. It uses its internal model to store metadata about the different records, and presents it on a web interface that allows users to browse and search this metadata. It also offers a powerful API that allows third-party applications and services to be built around it. CKAN is built with Python on the backend and Javascript on the frontend, and uses the Pylons web framework and SQLAlchemy as its ORM. Its database engine is PostgreSQL and its search is powered by SOLR. It has a modular architecture that allows extensions to be developed to provide additional features such as harvesting or data upload. CKAN is currently used by governments and user groups worldwide to power both official and community data portals.

DMPTool
type: Resource
type: NamedIndividual
has db xref: nlx_156039
synonym: Data Management Planning Tool
synonym: DMP Tool
IAO_0000115: Free web application which guides users through the process of creating a data management plan (DMP) for a range of funders (NSF, NIH, etc.) and connect users with data management planning resources. The DMPTool allows users to edit, save, share, print, and download their data management plans. Institutions can customize the tool and configure Shibboleth login. Several universities and organizations are developing the DMPTool to help researchers meet these new requirements. In specific, the DMPTool will help researchers: * Create ready-to-use data management plans for specific funding agencies * Meet requirements for data management plans * Get step-by-step instructions and guidance for data management plan * Learn about resources and services available at your institution to fulfill the data management requirements of their grants

eScholarship
type: Resource
type: NamedIndividual
has db xref: nlx_156042
synonym: CDL eScholarship
IAO_0000115: Provides comprehensive publication services for Univeristy of California affiliated departments, research units, publishing programs, and individual scholars who seek to publish original, open access journals, books, conference proceedings, and other scholarship. Content is delivered via research platform and is available to scholars worldwide.

Git2PROV
type: Resource
type: NamedIndividual
has db xref: nlx_156047
IAO_0000115: Service that exports your Git repository to the new W3C PROV standard. Your Git repositories are a goldmine of provenance information, tracking the evolution of your code or data and the activities of the people involved. This information could be linked to other similar provenance data by exporting it in the provenance interchange W3C recommendation PROV (http://www.w3.org/TR/prov-overview/).

GeneSeer
type: Resource
type: NamedIndividual
has db xref: nlx_156048
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Database to access gene information through common names and allows identification of homologs and paralogs for a given gene. This publicly available tool leverages public sequence data, gene metadata information, and other publicly available data to calculate and display orthologous and paralogous gene relationships for all genes from several species, including yeasts, insects, worms, vertebrates, mammals, and primates such as humans.

Human Gene Connectome Server
type: Resource
type: NamedIndividual
has db xref: biotools:hgcs
has db xref: nlx_156049
abbrev: HGCS
IAO_0000115: An interactive web server that enables researchers to prioritize any list of genes by their biological proximity to defined core genes (i.e. genes that are known to be associated with the phenotype), and to predict novel gene pathways.

Human Gene Connectome
type: Resource
type: NamedIndividual
has db xref: nlx_156050
abbrev: HGC
IAO_0000115: Data set containing a gene-specific connectome file for each human gene and computer programs for ranking lists of genes within a gene-specific connectome, clustering and plotting the genes by the functional genomic alignment (FGA) approach, and generating gene-specific connectomes. The programs were developed and tested on Mac and Linux systems. The external software required for running these programs is open-source and free of charge. The HGC is the set of all biologically plausible routes, distances, and degrees of separation between all pairs of human genes. A gene-specific connectome contains the set of all available human genes sorted on the basis of their predicted biological proximity to the specific gene of interest. The HGC is a powerful approach for human genotype-phenotype high-throughput studies, for which it can be used to rank any list of genes within a gene-specific connectome for an experimentally validated core gene. Functional genomic alignment (FGA) is equivalent to traditional multiple sequence alignment (MSA), except that it clusters genes in trees on the basis of the functional biological distance between them predicted by HGC, rather than on the basis of molecular evolutionary genetic distance. This method is therefore more suitable for disease and phenotypic studies.

OMERO
type: Resource
type: NamedIndividual
has db xref: nlx_156069
synonym: OME Remote Objects
synonym: OMERO - Open Microscopy Environment Remote Objects
synonym: Open Microscopy Environment Remote Objects
IAO_0000115: Client-server software for management, visualization, and analysis of biological microscopy images. OMERO handles images in a secure central repository where users can view, organize, analyze and share data from anywhere with internet access. Work with images from a desktop app (Windows, Mac or Linux), from the web or from 3rd party software.

GitHub
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_156051
IAO_0000115: A web-based hosting service for software development projects that use the Git revision control system offering powerful collaboration, code review, and code management. It offers both paid plans for private repositories, and free accounts for open source projects. Large or small, every repository comes with the same powerful tools. These tools are open to the community for public projects and secure for private projects. Features include: * Integrated issue tracking * Collaborative code review * Easily manage teams within organizations * Text entry with understated power * A growing list of programming languages and data formats * On the desktop and in your pocket - Android app and mobile web views let you keep track of your projects on the go.

GROTOAP
type: Resource
type: NamedIndividual
has db xref: nlx_156053
synonym: GROTOAP: GROTOAP: GROund Truth for Open Access Publications
synonym: GROTOAP: GROund Truth for Open Access Publications
IAO_0000115: Test set for training and performance evaluation of page segmentation and zone classification algorithms. Contains input articles in a digital form and corresponding ground truth files. The test set is based on articles obtained from DOAJ database published under CC-BY license. The whole test set is available under the same license.

ImpactStory
type: Resource
type: NamedIndividual
has db xref: nlx_156056
IAO_0000115: A web application which provides altmetrics to help researchers measure and share the impacts of their research outputs. After making a profile, scientists can track which of their publications are most popular through number of citations, frequency of PDF downloads, etc. Information from research outputs such as journal articles, blog posts, datasets, and software contribute to a user's impact, which is viewable in their profile.

JCB DataViewer
type: Resource
type: NamedIndividual
has db xref: nlx_156057
has db xref: r3d100010895
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A web-based, multi-dimensional image data-viewing application for original microscopy image datasets associated with articles published in The Journal of Cell Biology, a peer-reviewed journal published by The Rockefeller University Press. The JCB DataViewer can host multidimensional fluorescence microscopy images, 3D tomogram data, very large (gigapixel) images, and high content imaging screens. Images are presented in an interactive viewer, and the scores from high content screens are presented in interactive graphs with data points linked to the relevant images. The JCB DataViewer uses the Bio-Formats library to read over 120 different imaging file formats and convert them to the OME-TIFF image data standard. Image data are archived by the Journal and may be freely accessed by readers using the JCB DataViewer. Download of author-provided image data and associated metadata in OME-TIFF format is also possible with author permission, allowing for independent analysis of image data irrespective of acquisition or viewing software. Although the JCB DataViewer is designed to host and facilitate sharing and analysis of original microscopy image data, authors may also upload other types of original image data as supplements to their manuscripts, including histology and electron micrographs and digital scans of gels or blots.

Memento
type: Resource
type: NamedIndividual
has db xref: nlx_156058
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. An extension for Chrome to see a version of a resource as it existed at some date in the past, by entering that URI in your browser and by specifying the desired date in a browser plug-in. Or you can actually browse the Web of the past by selecting a date and clicking. Whatever you land upon will be versions of Web resources as they were around the selected date. (This will only work if previous versions are available somewhere on the Web.)

RVD
type: Resource
type: NamedIndividual
has db xref: OMICS_00073
IAO_0000115: Algorithm for single nucleotide variant detection using next-generation resequencing. It estimates the error rate at each base position in the reference sequence utilizing a command-line user interface through MATLAB.

OME-TIFF Format
type: Resource
type: NamedIndividual
has db xref: nlx_156061
synonym: OME-TIFF: Open Microscopy Environment Tagged Image File Format
synonym: Open Microscopy Environment Tagged Image File Format
abbrev: OME-TIFF
IAO_0000115: A standardized file format for multidimensional microscopy image data. OME-TIFF maximizes the respective strengths of OME-XML and TIFF. It takes advantage of the rich metadata defined in OME-XML while retaining the pixel structure in multi-page TIF format for compatibility with many image-processing applications. An OME-TIFF dataset has the following characteristics: * Image planes are stored within one multi-page TIFF file, or across multiple TIFF files. Any image organization is feasible. * A complete OME-XML metadata block describing the dataset is embedded in each TIFF file's header. Thus, even if some of the TIFF files in a dataset are misplaced, the metadata remains intact. * The OME-XML metadata block may contain anything allowed in a standard OME-XML file. * OME-TIFF uses the standard TIFF mechanism for storing one or more image planes in each of the constituent files, instead of encoding pixels as base64 chunks within the XML. Since TIFF is an image format, it makes sense to only use OME-TIFF as opposed to OME-XML, when there is at least one image plane.

GUDMAP Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_156063
abbrev: GUDMAP Ontology
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A high-resolution ontology has been developed by members of the GUDMAP consortium to describe the subcompartments of the developing murine genitourinary tract. This ontology incorporates what can be defined histologically and begins to encompass other structures and cell types already identified at the molecular level. The GUDMAP ontology encompasses Theiler stage (TS) 17-27 of development as well as the sexually mature adult. It has been written as a partonomic, text-based, hierarchical ontology that, for the embryological stages, has been developed as a high-resolution expansion of the existing Edinburgh Mouse Atlas Project (EMAP) ontology. It also includes group terms for well-characterized structural and/or functional units comprising several sub-structures, such as the nephron and juxtaglomerular complex. Each term has been assigned a unique identification number. Synonyms have been used to improve the success of query searching and maintain wherever possible existing EMAP terms relating to this organ system.

Bioassay Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_156065
abbrev: BAO
IAO_0000115: Ontology to describe and categorize chemical biology and drug screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis. BAO is an extensible, knowledge-based, highly expressive (currently SHOIQ(D)) description of biological assays making use of descriptive logic based features of the Web Ontology Language (OWL). BAO currently has over 700 classes and also makes use of several other ontologies. It describes several concepts related to biological screening, including Perturbagen, Format, Meta Target, Design, Detection Technology, and Endpoint. Perturbagens are perturbing agents that are screened in an assay; they are mostly small molecules. Assay Meta Target describes what is known about the biological system and / or its components interrogated in the assay (and influenced by the Perturbagen). Meta target can be directly described as a molecular entity (e.g. a purified protein or a protein complex), or indirectly by a biological process or event (e.g. phosphorylation). Format describes the biological or chemical features common to each test condition in the assay and includes biochemical, cell-based, organism-based, and variations thereof. The assay Design describes the assay methodology and implementation of how the perturbation of the biological system is translated into a detectable signal. Detection Technology relates to the physical method and technical details to detect and record a signal. Endpoints are the final HTS results as they are usually published (such as IC50, percent inhibition, etc). BAO has been designed to accommodate multiplexed assays. All main BAO components include multiple levels of sub-categories and specification classes, which are linked via object property relationships forming an expressive knowledge-based representation.

LINCS Connectivity Map
type: Resource
type: NamedIndividual
has db xref: nlx_156066
synonym: Connectivity Map
abbrev: CMap
IAO_0000115: A catalog of gene-expression data collected from human cells treated with chemical compounds and genetic reagents. Computational methods to reduce the number of necessary genomic measurements along with streamlined methodologies enable the current effort to significantly increase the size of the CMap database and along with it, our potential to connect human diseases with the genes that underlie them and the drugs that treat them. The NIH has funded a large expansion of the Connectivity Map dataset through the Library of Integrated Network-based Cellular Signatures (LINCS). The Broad Institute's LINCS center aims to create a first installment of data generation and analysis for the LINCS program. Through these data LINCS intends to accelerate the discovery process by systematically revealing connections between genes/compounds discovered in screens and molecular pathways that underlie disease states.

Stowers Original Data Repository
type: Resource
type: NamedIndividual
has db xref: nlx_156067
synonym: Stowers Institute Original Data Repository
abbrev: ODR
abbrev: Stowers ODR
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented January 13, 2022. Open access repository of original, unprocessed data underlying work published by Stowers researchers to allow the scientific community to validate and extend the findings made by Stowers researchers. For papers first submitted for publication after November 1, 2011, the Stowers Institute requires its members to deposit original data files into the Stowers Original Data Repository or to repositories maintained by third parties at the time of publication. Access to the Stowers Original Data Repository is free, but you will be asked to register before you can download data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

OpenDOAR
type: Resource
type: NamedIndividual
has db xref: nlx_156070
synonym: Directory of Open Access Repositories
synonym: The Directory of Open Access Repositories - OpenDOAR
IAO_0000115: A quality-controlled directory of academic open access repositories that provides a simple repository list, and lets you search for repositories or search repository contents. Additionally, tools and support to both repository administrators and service providers in sharing best practice and improving the quality of the repository infrastructure are provided. The current directory lists repositories and allows breakdown and selection by a variety of criteria which can also be viewed as statistical charts. The underlying database has been designed from the ground up to include in-depth information on each repository that can be used for search, analysis, or underpinning services like text-mining.

Open Journal Systems
type: Resource
type: NamedIndividual
has db xref: nlx_156071
abbrev: OJS
IAO_0000115: Open source software made freely available to journals worldwide for the purpose of making open access publishing a viable option for more journals, as open access can increase a journal's readership as well as its contribution to the public good on a global scale. OJS assists with every stage of the refereed publishing process, from submissions through to online publication and indexing. Through its management systems, its finely grained indexing of research, and the context it provides for research, OJS seeks to improve both the scholarly and public quality of refereed research. OJS Features # OJS is installed locally and locally controlled. # Editors configure requirements, sections, review process, etc. # Online submission and management of all content. # Subscription module with delayed open access options. # Comprehensive indexing of content part of global system. # Reading Tools for content, based on field and editors' choice. # Email notification and commenting ability for readers. # Complete context-sensitive online Help support.

Paper Rejection Repository
type: Resource
type: NamedIndividual
has db xref: nlx_156072
IAO_0000115: Repository of rejections of papers - letters and comments - that were ultimately accepted by a journal to educate others. Your rejection letters and comments are welcome. Some journals have begun including reviewers' comments with accepted papers to make the views of experts available to the reader. However, often the paper has been submitted to several journals and rejected before it is finally accepted. The rejection letters and comments are equally useful in helping to judge what kind of papers might be acceptable to a journal, and what kind of comments lead to rejections. Rather than hiding these low points in the trajectory of a scientific paper, this forum offers a place to publish these letters and comments to educate others.

PLoS Impact Explorer
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_156073
synonym: Altmetric PLoS Impact Explorer
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Service that mashes up alt-metrics data from Altmetric with articles from the Public Library of Science (PLoS) that allows you to check which articles are seeing the most buzz from social media sites, newspapers and in online reference managers. Browse articles with mentions in the past: 1d, 3d, 1w, 1m, 3m or all time.

RDFaCE
type: Resource
type: NamedIndividual
has db xref: nlx_156074
synonym: RDFa Content Editor
IAO_0000115: A Semantic content editor based on TinyMCE WYSIWYG editor. RDFaCE is created as a proof of concept for WYSIWYM (What You See Is What You Mean) concept. WYSIWYM aims to enable end-users to easily annotate their content using RDFa and Microdata markups. RDFaCE employs external NLP APIs to suggest namespaces, properties, URIs and to automatically annotate content.

Digital Commons Network
type: Resource
type: NamedIndividual
has db xref: nlx_156076
abbrev: DCN
IAO_0000115: Bibliographic database that brings together free, full-text scholarly articles from hundreds of universities and colleges worldwide. Curated by university librarians and their supporting institutions, the Network includes a growing collection of peer-reviewed journal articles, book chapters, dissertations, working papers, conference proceedings, and other original scholarly work. A central discipline wheel features ten color-coded disciplines: law, social and behavioral sciences, arts and humanities, life sciences, physical sciences and mathematics, education, engineering, medicine and health sciences, business, and architecture. The size of each color-coded area reflects the size of each discipline's collection relative to the rest of DCN. Users can click on any segment of any layer of the wheel, with the selected discipline, subdiscipline, or subject navigating users to their chosen commons area where they can then proceed to a list of full-text PDFs. To be clear, typing a couple of keywords into the Search Entire Network box, also located on the homepage, might be a more efficient method than mousing around on this graphical browsing element. If you would like to contribute your institution's research to the Digital Commons Network, Use the form provided, http://network.bepress.com/about/

University of Bari; Bari; Italy
type: Organization
type: NamedIndividual
has db xref: nlx_55378
IAO_0000115: Public university in Bari, Italy that offers a variety of degree programs including agricultural science, economics, education, and veterinary medicine.

FEATURE
type: Resource
type: NamedIndividual
has db xref: nif-0000-23304
IAO_0000115: A suite of automated tools that examine biological molecules and produces useful representations of the key biophysical and biochemical features of these structures that are critical for understanding function. The utility of this system extends from medical / pharmaceutical applications (model-based drug design, comparing pharmacological activities) to industrial applications (understanding structural stability, protein engineering). The FEATURE code is made available, without too much support, to any interested scientists. Audience: Researchers interested in identifying functional sites in protein structures. Long Term Goals and Related Uses: Enable improved functional site prediction.

RightField
type: Resource
type: NamedIndividual
has db xref: biotools:rightfield
has db xref: nlx_156077
IAO_0000115: An open-source tool for adding ontology term selection to Excel spreadsheets. It is used by a "Template Creator" to create semantically aware Excel spreadsheet templates. The Excel templates are then reused by Scientists to collect and annotate their data; without any need to understand, or even be aware of, RightField or the ontologies used. For each annotation field, RightField can specify a range of allowed terms from a chosen ontology (subclasses, individuals or combinations). The resulting spreadsheet presents these terms to the users as a simple drop-down list. This reduces the adoption barrier for using community ontologies as the annotation is made by the scientist that generated the data rather than a third party, and the annotation is collected at the time of data collection. RightField is a standalone Java application which uses Apache-POI for interacting with Microsoft documents. It enables users to import Excel spreadsheets, or generate new ones from scratch. Ontologies can either be imported from their local file systems, or from the BioPortal ontology repository. Individual cells, or whole columns or rows can be marked with the required ranges of ontology terms and an individual spreadsheet can be annotated with terms from multiple ontologies.

Scholarly Open Access
type: Resource
type: NamedIndividual
has db xref: nlx_156078
abbrev: Scholarly OA
IAO_0000115: Blog featuring critical analysis of scholarly open-access journals by Jeffrey Beale. Good tool to consult if you have suspicions that a journal is less than legit. Jeffrey Beall works as a librarian at Auraria Library, University of Colorado Denver, in Denver, Colorado.

SEEK
type: Resource
type: NamedIndividual
has db xref: biotools:seek
has db xref: nlx_156079
has db xref: OMICS_01012
synonym: SEEK for Science
synonym: SEEK Platform
IAO_0000115: An open-source, web-based platform and suite of software tools for for sharing heterogeneous scientific research datasets, models or simulations, processes and research outcomes - and collaborations between scientists. It preserves associations between them, along with information about the people and organizations involved. Underpinning SEEK is the ISA infrastructure, a standard format for describing how individual experiments are aggregated into wider studies and investigations. Within SEEK, ISA has been extended and is configurable to allow the structure to be used outside of Biology. SEEK is incorporating semantic technology allowing sophisticated queries over the data, yet without getting in the way of your users. Access to the RESTful API to access the data within SEEK is available.

ShareLaTeX
type: Resource
type: NamedIndividual
has db xref: nlx_156080
IAO_0000115: An collaborative tool which allows users to edit LaTeX documents in their browser. Multiple users can simultaneously access and edit the same LaTeX document and see the changes in real time. The latest version is available online, and the built in chat helps communicate with others while editing.

Arredondo ANT fNIRS dataset1
type: Resource
type: NamedIndividual
has db xref: nlx_156086
synonym: ANT fNIRS Data Set1
synonym: ANT fNIRS Data Set 1
synonym: ANT fNIRS Dataset1
synonym: Arredondo ANT fNIRS Data Set1
synonym: Arredondo ANT fNIRS Data Set 1
abbrev: AAF Data
abbrev: AAF Data1
abbrev: AF Data
abbrev: AF Data1
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented September 12, 2017. Dataset in Bilingual exposure optimizes left-hemisphere dominance for selective attention processes in the developing brain by Arredondo, Su, Satterfield, & Kovelman (XX) Does early bilingual exposure alter the representations of cognitive processes in the developing brain? Theories of bilingual development have suggested that bilingual language switching might improve children''s executive function and foster the maturation of prefrontal brain regions that support higher cognition. To test this hypothesis, we used functional Near Infrared Spectroscopy to measure brain activity in Spanish-English bilingual and English-monolingual children during a visuo-spatial executive function task of attentional control (N=27, ages 7-13). Prior findings suggest that while young children start with bilateral activation for the task, it becomes right-lateralized with age (Konrad et al., 2005). Indeed monolinguals showed bilateral frontal activation, however young bilinguals showed greater activation in left language areas relative to right hemisphere and relative to monolinguals. The findings suggest that bilingual experience optimizes attention mechanisms in the language hemisphere, and highlight the importance of early experiences for neurodevelopmental plasticity of higher cognition. These data are made available from Ioulia Kovelman''s Language and Literacy Lab at University of Michigan and may be exported through the NIF Data Federation. To cite these data please use this text Data were published by Arredondo et al. (XX) and made available via the NIF at XX

GlimmerHMM
type: Resource
type: NamedIndividual
has db xref: nlx_156092
synonym: GlimmerHMM - Eukaryotic Gene-Finding System
IAO_0000115: A gene finder based on a Generalized Hidden Markov Model (GHMM). Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models . Currently, GlimmerHMM's GHMM structure includes introns of each phase, intergenic regions, and four types of exons (initial, internal, final, and single).

National Center for Microscopy and Imaging Research
type: Resource
type: NamedIndividual
has db xref: nif-0000-22234
abbrev: NCMIR
IAO_0000115: Biomedical technology research center that develops computer-aided, advanced microscopy for the acquisition of structural and functional data in the dimensional range of 1 nm to 100 um, a range encompassing macromolecules, subcellular structures and cells. Novel specimen-staining methods, imaging instrumentsincluding intermediate high-voltage transmission electron microscopes (IVEMs) and high-speed, large-format laser-scanning light microscopesand computational capabilities are available for addressing mesoscale biological microscopy of proteins and macromolecular complexes in their cellular and tissue environments. These technologies are developed to bridge understanding of biological systems between the gross anatomical and molecular scales and to make these technologies broadly available to biomedical researchers. NCMIR provides expertise, infrastructure, technological development, and an environment in which new information about the 3D ultrastructure of tissues, cells, and macromolecular complexes may be accurately and easily obtained and analyzed. NCMIR fulfills its mission through technology development, collaboration, service, training, and dissemination. It aims to develop preparative methods and analytical approaches to 3D microscopy applicable to neurobiology and cell biology, incorporating equipment and implementing software that expand the analysis of 3D structure. The core research activities in the areas of specimen development, instrument development, and software infrastructures maximize the advantages of higher voltage electron microscopy and correlated light microscopies to make ambitious imaging studies across scales routine, and to facilitate the use of resources by biomedical researchers. NCMIR actively recruits outside users who will not only make use of these resources, but who also will drive technology development and receive training.

National Biomedical Computation Resource
type: Resource
type: NamedIndividual
has db xref: nif-0000-22270
synonym: NBCR - National Biomedical Computation Resource
abbrev: NBCR
IAO_0000115: Biomedical technology research center that conducts, catalyzes and enables multiscale biomedical research, focusing on four key activities: 1) integrating computational, data and visualization resources in a transparent, advanced grid environment to enable better access to distributed data, computational resources, instruments and people; 2) developing and deploying advanced computational tools for modeling and simulation, data analysis, query and integration, three-dimensional image processing and interactive visualization; 3) delivering and supporting advanced grid/cyberinfrastructure for biomedical researchers; and 4) training a cadre of new researchers to have an interdisciplinary, working knowledge of computational technology relevant to biomedical scientists. NBCR enables biomedical scientists to address the challenge of integrating detailed structural measurements from diverse scales of biological organization that range from molecules to organ systems in order to gain quantitative understanding of biological function and phenotypes. Predictive multi-scale models and their driving biological research problems together address issues in modeling of sub-cellular biophysics, building molecular modeling tools to accelerate discovery, and defining tools for patient-specific multi-scale modeling. NBCR furthers these driving problems by developing tools and models based on rapid advances in mathematics and information technology, incorporating them into NBCR pipelines or problem solving environments, and addressing the inevitable changes in the underlying cyber-infrastructure technologies and continually adapting codes over time. Their technology focus integrates both the biological applications and the underlying support software into reproducible science workflows that can function across a number of physical infrastructures.

Cancer Genomics Hub
type: Resource
type: NamedIndividual
has db xref: nlx_156095
has db xref: r3d100011174
abbrev: CGHub
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A secure repository for storing, cataloging, and accessing cancer genome sequences, alignments, and mutation information from the Cancer Genome Atlas (TCGA) consortium and related projects. CGHub gives scientific researchers the statistical power of large cancer genome datasets to attack the molecular complexity of cancer.

fMRI Research Center at Columbia
type: Resource
type: NamedIndividual
has db xref: nif-0000-00405
synonym: Program for Imaging & Cognitive Sciences
synonym: Program for Imaging and Cognitive Sciences
abbrev: PICS
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on 7/28/13. Core facility of Columbia Neuroscience with the goal of establishing a collaborative and multi-investigator neuroimaging environment that is focused on the investigation of the neurocircuitry of the brain that underlies cognition, perception and action, and also the development of clinical applications that enhance the goals of personalized medicine. Within this environment the specific current research interests of the Hirsch group include several related directions of investigation. The first is conscious and subconscious neural processes that mediate emotion and cognition in healthy individuals and in patients with psychiatric disorders. This direction also includes neurocircuitry that is characteristic of disorders of consciousness such as minimally conscious or vegetative states, self and visual awareness, and attention. Neurocircuitry of other complex cognitive processes such as decisions, inductive and deductive reasoning, language, truthfulness and top-down influences of expectation, reward, and regulation on early visual and mid-level perceptual and emotional systems. On-going projects targeted for clinical applications include benefits for neurosurgery such as the development of task batteries to map the cortical locations of essential functions such as language, motor, sensation, memory, emotion and sensory functions including visions, audition and the chemical senses. Computational innovations for labeling correspondence between brain structure and specific functional regions are under development to achieve the highest interpretive precision. Current projects include integration of EEG and fMRI techniques to localize seizuregenic cortex in relation to eloquent and functioning cortex for neurosurgical planning; integration of TMS and fMRI to discriminate essential and associative language-sensitive cortical areas; and integration of VEP, EEG and fMRI to inform assessments of visual disease sec…

MethylAid
type: Resource
type: NamedIndividual
has db xref: biotools:methylaid
has db xref: OMICS_05457
synonym: MethylAid - Visual and interactive quality control of large Illumina 450k data sets
synonym: MethylAid: Visual and interactive quality control of large Illumina 450k data sets
IAO_0000115: Software for visual and interactive quality control of large Illumina 450k data sets. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored.

NBRC
type: Resource
type: NamedIndividual
has db xref: nif-0000-22391
synonym: Biological Resource Center NITE
synonym: National Institute of Technology and Evaluation Biological Resource Center
synonym: NITE Biological Resource Center
IAO_0000115: Collection of microbial resources and perform taxonomic characterization of individual microorganisms such as bacteria including actinomycetes and archaea, yeasts, fungi, algaes, bacteriophages and DNA resources for academic research and industrial applications. NBRC is a member of WFCC, OECD Global BRC Network, ACM and JSCC. They are certified by quality management system ISO 9001. To provide attractive biological resources with useful information attached, they actively collect potentially useful biological resources (microorganisms and cloned genes) and distributes them to promote basic research as well as industrial applications. At the Biological Resource Center, they explore, isolate and identify microorganisms from various natural environments and at the same time accept scientifically and industrially useful microorganisms from researchers in academic and industrial sectors. The microbial DNA library constructed at the Biotechnology Development Center is also part of their collection. To improve and expand the collection, new methodologies for the isolation, identification and preservation of microorganisms and DNA will be investigated and developed so as to provide biological resources of higher quality. Their resources serve, for example, as the standard for determining antimicrobial activity, in aseptic tests as well as for the production of pharmaceutical substances and will be constantly reinforced for wider distribution to researchers in academia and industries. Please refer to the catalog shown at the NBRC website for details.

Grants.gov
type: Resource
type: NamedIndividual
has db xref: nif-0000-22393
IAO_0000115: A source to FIND and APPLY for federal grants. The U.S. Department of Health and Human Services is proud to be the managing partner for Grants.gov, an initiative that is having an unparalleled impact on the grant community. All discretionary grants offered by the 26 federal grant-making agencies can be found on Grants.gov. Grants.gov was established as a governmental resource named the E-Grants Initiative, part of the President's 2002 Fiscal Year Management Agenda to improve government services to the public. The concept has its origins in the Federal Financial Assistance Management Improvement Act of 1999, also known as Public Law 106-107. Public Law 106-107 has since sunset and is now known as the Grants Policy Committee (GPC). For more information on the Grants Policy Committee, click here. Today, Grants.gov is a central storehouse for information on over 1,000 grant programs and provides access to approximately $500 billion in annual awards. You may find information on *What is a Grant? *Who is Eligible for a Grant? *Program highlights and accomplishments *Grants.gov in the News (Articles, press releases, milestones and events) *Program Status (Detailed information about our relationship with partner federal agencies, financial contributions, grant opportunities, fiscal reports, planning strategies and statistics.)

The Brain from Top to Bottom
type: Resource
type: NamedIndividual
has db xref: nif-0000-00127
IAO_0000115: A interactive and highly effective educational resource and review for training in neuroscience and cognitive science. Supported by the Canadian institute of neurosciences, mental health and addiction; and Canadian institutes of health research.

ExomeDepth
type: Resource
type: NamedIndividual
has db xref: biotools:exomedepth
has db xref: OMICS_05443
IAO_0000115: Software that calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders.

libmgf
type: Resource
type: NamedIndividual
has db xref: BioTools:libmgf
has db xref: biotools:libmgf
has db xref: OMICS_03343
synonym: libmgf (formerly MGFp)
synonym: MGFp
IAO_0000115: A flex/bison-based C++ Mascot Generic Format (MGF) parser library.

ExplorEnz
type: Resource
type: NamedIndividual
has db xref: nif-0000-02827
synonym: ExplorEnz - The Enzyme Database
synonym: ExplorEnz Database
synonym: ExplorEnz- The Enzyme Database
IAO_0000115: Enzyme database developed as a way to access the data of the IUBMB Enzyme Nomenclature List. The data, which are stored in a MySQL database, preserve the formatting of chemical names according to IUPAC standards. A simple, easy to use, web-based query interface is provided (Search), along with an advanced search engine for more complex queries (Advanced Search). Forms are provided to submit suggestions for new enzyme entries or to report errors in existing entries. Downloads of the database are available via FTP as SQL or XML.

Center for Research in Biological Systems
type: Resource
type: NamedIndividual
has db xref: nif-0000-23293
synonym: CRBS
IAO_0000115: CRBS is a UCSD organized research unit (ORU) that exists to provide human resources, high technology equipment, and administrative services to researchers engaged in fundamental research on cell structure and function relationships in central nervous system processes, cardiovascular networking, and muscular contraction through multiple scales and modalities. CRBS scientists investigate these processes through invention, refinement, and deployment of sophisticated technologies, especially: - High-powered electron microscopes that reveal three-dimensional cell structures - State-of-the-art X-ray crystallography and magnetic resonance analysis that provide detail on protein structures at high-resolution - Laser-scanning and confocal light microscopes that reveal molecules tagged with fluorescent markers as they traffic within cells and pass transfer signals within and between cells - High performance computing and grid-based integration of distributed data CRBS facilitates an interdisciplinary infrastructure in which people from biology, medicine, chemistry, and physics can work with those from computer science and information technologies in collaborative research. Researchers share interests in the study of complex biological systems at many scales, from the structures of enzymes, proteins, and the body's chemical communications network at atomic and molecular levels, to an organism's physiology, strength, and support at cellular and tissue levels. The CRBS infrastructure integrates resources for high-performance computing, visualization, and database technologies, and the grid-integration of large amounts of archival storage data. The California Institute for Telecommunications and Information Technology (Cal-IT2) and the San Diego Supercomputer Center (SDSC) are collaborators in simulating the activity of biological systems, analyzing the results, and organizing the growing storehouse of biological information. CRBS is an entity evolving as research evolves. It for…

FrontalCortex.com
type: Resource
type: NamedIndividual
has db xref: nif-0000-22726
synonym: FrontalCortex
IAO_0000115: A free website for for neurologists, neurology residents, and medical students. Contains thousands of images, hundreds of multiple-choice review questions, dozens of educational videos, several user forums, and a couple of online courses. Created by a neurology resident, it is currently maintained by a neurologist and a neuropathologist, with contributions from people from around the world. FrontalCortex.com is a free resource for neurology education. The target audience is neurology residents and medical students. It features a bank of hundreds of boards-type review questions, all of which contain feedback and references to relevant articles or texts. It also has an image gallery with thousands of images, including EEGs, radiographs, illustrations, and over a thousand unique neuropathology images. Online courses in neuropathology and electrodiagnostic testing have been created on the site, and continue to be refined. These include dozens of educational videos. FrontalCortex.com was created by a neurology resident. That resident is now a neurologist, and the neurology program director at Marshall University, and continues to run the page, with the help of other physicians volunteering their time. All the content contributions are donated by volunteers, and are reviewed by physicians. Financial support for the page comes from advertisements on the page, and the occasional donation. No login is required, unless you want to contribute to the growing bank of educational resources, in which case you can create a free account. : :education, neurology, resident, neuropathology, board review, RITE exam : :

Volocity 3D Image Analysis Software
type: Resource
type: NamedIndividual
has db xref: SciRes_000112
abbrev: Volocity Imaging software
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. 3D image analysis software to visualize, analyze and validate 3D fluorescence images from a wide range of confocal microscopy, widefield and high content screening systems. It is fully integrated for a seamless user experience.

EyeSite
type: Resource
type: NamedIndividual
has db xref: nif-0000-02830
synonym: EyeSite Database
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. An information and modeling database for families of proteins that function in the eye. Homologues are collected from all species and clustered according to tissue type, function and sequence similarity. A principal feature of the site is structural annotations, which range from experimentally solved structures to close structural neighbors to distant structure predictions. Many pre-generated homology models are provided. Other features include domain architecture analysis and pre-generated sequence alignments, and the site is extensively linked to other bioinformatic resources on the web.

Office of Scientific and Technical Information
type: Organization
type: NamedIndividual
has db xref: grid.483387.3
has db xref: ISNI: 0000 0004 0405 4313
has db xref: nif-0000-22793
has db xref: Wikidata: Q2015776
synonym: OSTI
IAO_0000115: The Office of Scientific and Technical Information's mission is to advance science and sustain technological creativity by making R&D findings available and useful to Department of Energy (DOE) researchers and the public. At OSTI you can find research results and science information from the Manhattan Project to the present, download documents, view energy citations, discover patents and e-prints, read about ongoing research projects and amazing accomplishments, search science conference proceedings and software, and connect to U.S. and global science portals. You can do this by using special online tools, such as: * Key Resources * DOE Science Accelerator * Science.gov * WorldWideScience.org Strategies for accomplishing the OSTI mission: * Collaborate within DOE through the Scientific and Technical Information Program to develop and maintain efficient, state-of-the-art access and delivery of research results. * Partner with others to facilitate alliances for national and international cooperation and information exchange. * Develop, deliver, and maintain customized information products and services for a variety of constituencies. * Implement Department-wide STI policy and best business practices. * Preserve STI, in tangible copies or electronically, as appropriate. * Accelerate the diffusion of knowledge to advance science. OSTI develops and maintains search tools that use a special technology called federated search. KEY RESOURCES Research Documents/Information Information Bridge Find DOE R&D full-text documents and bibliographic citations. DOE R&D Accomplishments Find information about the outcomes of past DOE R&D. DOE patents Find patents resulting from DOE-sponsored research and development. E-print Network Find e-prints in basic and applied sciences . Energy Citations Database (ECD) Find bibliographic records and full-text where available. Adopt-A-Doc? is an on-demand service that provides individuals the option to sponsor the digitization of full-text DOE te…

Autophagy Database
type: Resource
type: NamedIndividual
has db xref: biotools:the_autophagy_database
has db xref: OMICS_03306
has db xref: r3d100012565
abbrev: Autophagy DB
abbrev: AutophagyDB
IAO_0000115: Database that provides basic, up-to-date information on relevant literature, and a list of autophagy-related proteins and their homologs in eukaryotes.

T3DB
type: Resource
type: NamedIndividual
has db xref: biotools:t3db
has db xref: nif-0000-22933
has db xref: OMICS_01592
has db xref: r3d100012189
synonym: Toxin
synonym: Toxin and Toxin Target Database
synonym: Toxin Toxin Target Database
synonym: Toxin Toxin-Target Database
synonym: Toxin-Target Database
IAO_0000115: Database that combines detailed toxin data with comprehensive toxin target information. The database currently houses 3,053 toxins described by 32,276 synonyms, including pollutants, pesticides, drugs, and food toxins, which are linked to 1,670 corresponding toxin target records. Altogether there are 37,084 toxin, toxin target associations. (March 2014) Each toxin record (ToxCard) contains over 50 data fields and holds information such as chemical properties and descriptors, toxicity values, molecular and cellular interactions, and medical information. This information has been extracted from over 5,454 sources sources, which include other databases, government documents, books, and scientific literature. The focus of the T3DB is on providing mechanisms of toxicity and target proteins for each toxin. This dual nature of the T3DB, in which toxin and toxin target records are interactively linked in both directions, makes it unique from existing databases. It is also fully searchable and supports extensive text, sequence, chemical structure, and relational query searches

RopeBWT2
type: Resource
type: NamedIndividual
has db xref: biotools:ropebwt2
has db xref: OMICS_05300
IAO_0000115: A software tool for constructing the FM-index for a collection of DNA sequences. It works by incrementally inserting one or multiple sequences into an existing pseudo-BWT position by position, starting from the end of the sequences. This algorithm can be largely considered a mixture of BCR and dynamic FM-index. Nonetheless, ropeBWT2 is unique in that it may implicitly sort the input into reverse lexicographical order (RLO) or reverse-complement lexicographical order (RCLO) while building the index.

e-Driver
type: Resource
type: NamedIndividual
has db xref: biotools:e-Driver
has db xref: OMICS_05288
IAO_0000115: Software tool to identify cancer driver genes based on linear annotations of biological regions such as protein domains.Uses information on three-dimensional structures of mutated proteins to identify specific structural features. Then algorithm analyzes whether these features are enriched in cancer somatic mutations and are candidate driver genes.

Connectome Wiki
type: Resource
type: NamedIndividual
has db xref: nif-0000-24441
synonym: Connectome Wiki: collaborative neuroanatomy knowledge database
synonym: ConnectomeWiki
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on December 6, 2012. Connectome Wiki is a knowledge base for macro- and mesoscale brain region and brain structural connectivity information across species. Employing modern semantic wiki technology, it serves as collaborative platform as well. What can I get? * Brain Regions: Plenty of information, including links to relevant literature and much more. * Brain Connections: Well established neuronal connections based mainly on neuronal tracer studies from the literature. * Abbreviations: Look up abbreviations and corresponding English and Latin names * Partition Schemes: Foundational and more partitions with their corresponding delineation criteria and protocols. * Species: Information about different species is available, using their binomial name as identifier. * External: Enhance the ConnectomeViewer with Volume-To-Ontology mappings. * Data Source: You can download the raw data in RDF or JSON. How can I contribute? If your research is in particular brain regions, or model organisms not yet registered, feel free to act as domain expert and add your knowledge. If you do any tracer studies, add findings with appropriate published papers. Incrementally building a mesoscale skeleton wiring diagram. Complete anything that is missing. See also PapersToAdd. Register your own partition scheme and link it semantically against known schemes. Adding brain region pages for your particular research organisms. Use ConnectomeWiki as knowledge backend for your application concerned with gross neuroanatomy. The goals of this wiki are: * A collaborative platform to collect, collate, manage and disseminate mesoscale nervous system region and connectivity information across various species * Authority for Brain Region Abbreviations * Representation of Brain Region Homologies * Interrelation of Brain Partition Schemes * Information source for the ConnectomeViewer application

Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis
type: Resource
type: NamedIndividual
has db xref: nif-0000-23292
has db xref: OMICS_01476
has db xref: SCR_011924
abbrev: CAMERA
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016; however, the URL provides links to associated projects and data. A suite of data query, download, upload, analysis and sharing tools serving the needs of the microbial ecology research community, and other scientists using metagenomics data.

Zeiss | AxioVision Imaging System
type: Resource
type: NamedIndividual
has db xref: SciRes_000111
has db xref: SCR_018376
synonym: AxioVision
synonym: AxioVision Imaging System
synonym: AxioVision- Microscope Software
IAO_0000115: Digital image processing system where microscope settings and processing steps may be adjusted in single user interface. Can acquire images from variety of cameras. Includes software package for capturing, archiving and preparing images for publication. Allows users to visualize and present images in several dimensions. Functionality of imaging toolbox expands constantly with wide range of different modules that are tailored to specific applications or microscope accessories.

FANTOM DB
type: Resource
type: NamedIndividual
has db xref: biotools:fantom
has db xref: nif-0000-02833
synonym: FANTOM
synonym: FANTOM1
synonym: FANTOM2
synonym: FANTOM3
synonym: FANTOM4
synonym: FANTOM: Functional Annotation of Mouse
synonym: Functional Annotation of Mouse
synonym: Functional Annotation of the Mammalian Genome
IAO_0000115: The FANTOM consortium is an international collaborative research project initiated and organized by the RIKEN Omics Science Center. In earlier FANTOM efforts we cloned and annotated 103,000 full-length cDNAs from mouse and distributed them to researchers throughout the world. FANTOM1-3 focused on identifying the transcribed components of mammalian cells. This work improved estimates of the total number of genes and their alternative transcript isoforms in both human and mouse, expanded gene families, and revealed that a large fraction of the transcriptome is non-coding. In addition, with the development of Cap Analysis of Gene Expression (CAGE) FANTOM3 could map a large fraction of transcription start sites and revise our models of promoter structure. This updated web resource provides the previous FANTOM results mapped to current genome builds and presents the results of FANTOM4. In FANTOM4 the focus has changed to understanding how these components work together in the context of a biological network. Using deepCAGE (deep sequencing with CAGE) we monitored the dynamics of transcription start site (TSS) usage during a time course of monocytic differentiation in the acute myeloid leukemia cell line THP-1. This allowed us to identify active promoters, monitor their relative expression and define relevant regions for carrying out transcription factor binding site predictions. Computational methods were then used to build a network model of gene expression in this leukemia and the transcription factors key to its regulation. This work gives the first picture of the wiring between genes involved in acute myeloid leukemia and provides a strategy for identifying key factors that determine cell fates. In addition to the network, FANTOM4 data was used in two additional analyses. The first identified a novel class of short RNAs associated with transcription start sites and the second focused on the role of repetitive element expression in the transcriptome. TOOLS *Genome Bro…

Cardiovascular Model Repository
type: Resource
type: NamedIndividual
has db xref: nif-0000-23301
IAO_0000115: Repository of geometric models collected from on-going and past research projects in the Cardiovascular Biomechanics Research Laboratory at Stanford University. The geometric models are mostly built from imaging data of healthy and diseased individuals. For each of the models, a short description is given with a reference. The geometric models are in VTK PolyData XML .vtp format. * Audience: Biomechanical and computational researchers interested in complex models of cardiovascular applications * Long Term Goals and Related Uses: Allow users to download geometric models for cardiovascular applications. These geometric models can be used for research purposes, such as meshing and scientific visualization. Users are welcome to contact the project administrator, join the project and contribute additional models.

Simtk.org
type: Resource
type: NamedIndividual
has db xref: DOI:10.17616/R3QJ4B
has db xref: DOI:10.18735
has db xref: nif-0000-23302
synonym: SimTK - the Simulation Toolkit
synonym: Simulation Toolkit
abbrev: SimTK
IAO_0000115: A National NIH Center for Biomedical Computing that focuses on physics-based simulation of biological structures and provides open access to high quality simulation tools, accurate models and the people behind them. It serves as a repository for models that are published (as well as the associated code) to create a living archive of simulation scholarship. Simtk.org is organized into projects. A project represents a research endeavor, a software package or a collection of documents and publications. Includes sharing of image files, media, references to publications and manuscripts, as well as executables and applications for download and source code. Simulation tools are free to download and space is available for developers to manage, share and disseminate code.

ConTrack
type: Resource
type: NamedIndividual
has db xref: nif-0000-23303
synonym: Connectivity Tracking
synonym: Connectivity Tracking (ConTrack)
IAO_0000115: An algorithm for identifying pathways that are known to exist between two regions within DTI data of anisotropic tissue, e.g., muscle, brain, spinal cord. The ConTrack algorithms use knowledge of DTI scanning physics and apriori information about tissue architecture to identify the location of connections between two regions within the DTI data. Assuming a course of connection or pathway between these two regions is known to exist within the measured tissue, ConTrack can be used to estimate properties of these connections in-vivo.

Neuromuscular Models Library
type: Resource
type: NamedIndividual
has db xref: nif-0000-23307
IAO_0000115: The goal of the neuromuscular models library is to provide a resource for students, researchers, and clinicians to access, use, test, and develop models. The majority of models in this library are for use with OpenSIM and/or SIMM. Users who contribute models to the database can set up a project page where they can track who is using the model and contact with them.

OpenSim
type: Resource
type: NamedIndividual
has db xref: nif-0000-23308
IAO_0000115: OpenSim is an open-source software system that lets users develop models of musculoskeletal structures and create dynamic simulations of movement. The software provides a platform on which the biomechanics community can build a library of simulations that can be exchanged, tested, analyzed, and improved through multi-institutional collaboration. The underlying software is written in ANSI C++, and the graphical user interface (GUI) is written in Java. OpenSim technology makes it possible to develop customized controllers, analyses, contact models, and muscle models among other things. These plugins can be shared without the need to alter or compile source code. Users can analyze existing models and simulations and develop new models and simulations from within the GUI.

Simbody(tm): SimTK Multibody Dynamics Toolset
type: Resource
type: NamedIndividual
has db xref: nif-0000-23309
synonym: Simbody
IAO_0000115: This project is a SimTK Core toolset providing general multibody dynamics capability, i.e., the capability to solve Newton's 2nd law F=ma in any set of coordinates. The techniques of rigid body mechanics are used to provide results in Order(n) time for any set of n coordinates. This can be used for internal coordinate modeling of molecules, or for coarse-grained models based on larger chunks. It is also useful for large-scale mechanical models, such as neuromuscular models of human gait. Simbody is provided as an open source, object-oriented C++ API and delivers high-performance, accuracy-controlled science/engineering-quality results. Binaries of this software are bundled with other SimTK Core modules.

sapFinder
type: Resource
type: NamedIndividual
has db xref: biotools:sapfinder
has db xref: OMICS_05285
synonym: sapFinder - A package for variant peptides detection and visualization in shotgun proteomics.
IAO_0000115: An R software package, for detection of the variant peptides based on tandem mass spectrometry (MS/MS)-based proteomics data. It automates (1) variation-associated database construction, (2) database searching, (3) post-processing, (4) HTML-based report generation in shotgun proteomics.

SimVascular
type: Resource
type: NamedIndividual
has db xref: BioTools:SimVascular
has db xref: biotools:SimVascular
has db xref: nif-0000-23311
synonym: SimVascular: Cardiovascular Modeling and Simulation
IAO_0000115: Open source software suite for cardiovascular simulation. It includes code for reading 3D images, segmenting structures, generating models and meshes, and modeling blood flow in deformable vessels. The suite also includes tools for physiologic boundary conditions, fluid structure interaction, and an accurate and efficient finite element Navier-Stokes solver. Commercial components have been used in the simulation process, and for these components, the project attempts to provide interfaces that allow substitution of open source components. The SimVascular project is derived from the ASPIRE2 software project and includes modified portions of PHASTA from RPI/SCOREC.

Knowledgebase for Addiction Related Genes
type: Resource
type: NamedIndividual
has db xref: nif-0000-00411
synonym: KARG: Knowledgebase for Addiction Related Genes
synonym: KARG: Knowledgebase for Addiction-Related Gene
synonym: Knowledgebase for Addiction-Related Gene
abbrev: KARG
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Database of data and knowledge linking genes and chromosome regions to addiction that were extracted from reviewing more than 1,000 peer-reviewed publications from between 1976 and 2006. This list of publications included review papers on addiction selected from results of PUBMED query "(addiction OR drug abuse) AND review" as well as research papers selected from PUBMED query "(addiction OR drug abuse) AND (gene OR microarray OR proteomics OR QTL OR population association OR genetic linkage)". The data spanned multiple technology platforms including classical hypothesis-testing of single genes, identification of significantly differentially expressed genes in microarray experiments, identification of significantly differentially expressed proteins in proteomics assays, identification of addiction-vulnerable chromosome regions in animal QTL studies, genetic linkage studies, population association studies, and OMIM annotations. From each publication they collected the genes, proteins, or chromosome regions linked to addiction, as well as metadata such as species, nature of the addictive substance, studied brain regions, technology platforms, and experimental parameters. In total, they collected 2,343 items of evidence linking 1,500 human genes to addiction. Among them 396 genes were supported by two or more items of evidence. The interface supports browsing of the genes by chromosome or pathways, advanced text search by gene ID, organism, type of addictive substance, technology platform, protein domain, and/or PUBMED ID, and sequence search by BLAST similarity. All data, database schema, and MySQL commands are freely available for download.

UMMC Center for Psychiatric Neuroscience Labs and Facilities
type: Resource
type: NamedIndividual
has db xref: SciEx_8930
synonym: CPN Research Resource Cores
synonym: UMMC Center for Psychiatric Neuroscience Labs & Facilities
synonym: UMMC Center for Psychiatric Neuroscience Research Resource Cores
synonym: UMMC CPN Research Resource Cores
synonym: University of Mississippi Medical Center Center for Psychiatric Neuroscience
abbrev: UMMC CPN Labs & Facilities
abbrev: UMMC CPN Labs and Facilities
IAO_0000115: Core facility that provides access to psychiatrically characterized post-mortem brain specimens, state-of-the-art equipment, cutting-edge technologies and the technical advice of highly trained faculty members who serve as Core Directors. The sophisticated imaging systems and biotechnologically advanced molecular core resources are provided on a shared-use basis to CPN and UMMC researchers. The CPN Research Resources Cores include the Human Brain Collection Core, Animal Core, Imaging Core, Molecular Biology Core, and Information Technologies Core.

PharmGKB
type: Resource
type: NamedIndividual
has db xref: nif-0000-00414
has db xref: OMICS_01586
has db xref: r3d100012325
synonym: Pharmacogenomics Knowledge Base
IAO_0000115: Database and central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB welcomes submissions of primary data from all research into genes and genetic variation and their effects on drug and disease phenotypes. PharmGKB collects, encodes, and disseminates knowledge about the impact of human genetic variations on drug response. They curate primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways. PharmGKB is part of the NIH Pharmacogenomics Research Network (PGRN), a nationwide collaborative research consortium. Its aim is to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs. A selected subset of data from PharmGKB is accessible via a SOAP interface. Downloaded data is available for individual research purposes only. Drugs with pharmacogenomic information in the context of FDA-approved drug labels are cataloged and drugs with mounting pharmacogenomic evidence are listed.

Synchronized Histological Image Viewing Architecture
type: Resource
type: NamedIndividual
has db xref: nif-0000-23318
synonym: Synchronized Histological Image View Arc
abbrev: SHIVA
IAO_0000115: A Java-based visualization and analysis application that can process 2D and 3D image files and provides convenient methods for users to overlay multiple datasets. * Simultaneous visualization of multiple image volumes. * Tools for labeling and masking of structures. * Framework for the Mouse Atlas Project.

SuperPred: Drug classification and target prediction
type: Resource
type: NamedIndividual
has db xref: biotools:superpred
has db xref: nif-0000-00415
abbrev: SuperPred
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 24,2025. Publicly available web-server to predict medical indication areas based on properties and similarity of chemical compounds. The web-server translates a user-defined molecule into a structural fingerprint that is compared to about 6300 drugs, which are enriched by 7300 links to molecular targets of the drugs, derived through text mining followed by manual curation. Links to the affected pathways are provided. The similarity to the medical compounds is expressed by the Tanimoto coefficient that gives the structural similarity of two compounds. A similarity score higher than 0.85 results in correct ATC prediction for 81% of all cases. As the biological effect is well predictable, if the structural similarity is sufficient, the web-server allows prognoses about the medical indication area of novel compounds and to find new leads for known targets. The combination of physicochemical property and similarity searching provides the possibility to detect new biologically active compounds and novel targets for drug-like compounds. SuperPred can be applied for drug repositioning purposes, too. A further intention of SuperPred is to find side effects elicited by drugs caused through off-target hits.

CTF
type: Resource
type: NamedIndividual
has db xref: OMICS_00480
IAO_0000115: Conditional random field (CRF) based transcription factor binding site (TFBS) finding system. The underlying CRF model can integrate features of different sources.

Wolfram Alpha Computational Knowledge Engine
type: Resource
type: NamedIndividual
has db xref: nif-0000-24917
synonym: Wolfram Alpha
IAO_0000115: Wolfram Alpha is a computational knowledge engine that to make all systematic knowledge computable. Although, this is not a specific neuroscience related resource, the computational and math element will be helpful. Wolfram Alpha's long-term goal is to make all systematic knowledge immediately computable and accessible to everyone. It aims to collect and curate all objective data; implement every known model, method, and algorithm; and make it possible to compute whatever can be computed about anything. It's goal is to build on the achievements of science and other systematizations of knowledge to provide a single source that can be relied on by everyone for definitive answers to factual queries. Wolfram Alpha aims to also bring expert-level knowledge and capabilities to the broadest possible range of peoplespanning all professions and education levels. It's goal is to accept completely free-form input, and to serve as a knowledge engine that generates powerful results and presents them with maximum clarity. Lastly, Wolfram Alpha is an ambitious, long-term intellectual endeavor that it intends to deliver increasing capabilities over the years and decades to come. With a world-class team and participation from top outside experts in countless fields, it's goal is to create something that will stand as a major milestone of 21st century intellectual achievement. As of now, Wolfram Alpha contains 10+ trillion pieces of data, 50,000+ types of algorithms and models, and linguistic capabilities for 1000+ domains. Built with Mathematicawhich is itself the result of more than 20 years of development at Wolfram ResearchWolfram Alpha's core code base now exceeds 5 million lines of symbolic Mathematica code. Running on supercomputer-class compute clusters, Wolfram Alpha makes extensive use of the latest generation of web and parallel computing technologies, including webMathematica and gridMathematica. Its knowledge base and capabilities already span a great many domains, and i…

FlyMine
type: Resource
type: NamedIndividual
has db xref: nif-0000-02845
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Integrated database of genomic, expression and protein data for Drosophila, Anopheles, C. elegans and other organisms. You can run flexible queries, export results and analyze lists of data. FlyMine presents data in categories, with each providing information on a particular type of data (for example Gene Expression or Protein Interactions). Template queries, as well as the QueryBuilder itself, allow you to perform searches that span data from more than one category. Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources, to modify existing template queries or to create your own template queries. Access our FlyMine data via our Application Programming Interface (API). We provide client libraries in the following languages: Perl, Python, Ruby and & Java API

LONI ShapeViewer
type: Resource
type: NamedIndividual
has db xref: nif-0000-23321
synonym: LONI Shape Viewer
synonym: ShapeViewer
IAO_0000115: Java-based geometry viewer that supports file formats used by Center for Computational Biology (CCB) researchers and provides necessary viewing functions. ShapeViewer uses ShapeTools library support to read and display LONI Ucf, VTX XML, FreeSurfer, Minc Obj (both binary and ascii), Open Dx, Gifti, and OFF format data files.

SuperTarget
type: Resource
type: NamedIndividual
has db xref: nif-0000-00416
has db xref: OMICS_01591
has db xref: r3d100012195
IAO_0000115: Database for analyzing drug-target interactions, it integrates drug-related information associated with medical indications, adverse drug effects, drug metabolism, pathways and Gene Ontology (GO) terms for target proteins. At present (May 2013), the updated database contains >6000 target proteins, which are annotated with >330 000 relations to 196 000 compounds (including approved drugs); the vast majority of interactions include binding affinities and pointers to the respective literature sources. The user interface provides tools for drug screening and target similarity inclusion. A query interface enables the user to pose complex queries, for example, to find drugs that target a certain pathway, interacting drugs that are metabolized by the same cytochrome P450 or drugs that target proteins within a certain affinity range.

LONI ShapeTools
type: Resource
type: NamedIndividual
has db xref: nif-0000-23323
abbrev: ShapeTools
IAO_0000115: Software library that is a collection of Java classes that enable Java programmers to model, manipulate and visualize geometric shapes and associated data values. It simplifies the creation of application programs by providing a ready-made set of support routines. * File format readers that implement ShapeIO interface (modeled after Java ImageIO) are automatically used when appropriate. * Storage of additional metadata of arbitrary type (other than shape vertices and interconnections) is enabled by the use of data attributes. * Shapes may contain a set of child shapes allowing for the construction and manipulation of complex hierarchies of shapes. * The various components of a shape are specified as interfaces with specific implementations, making it easy to create specialized implementations of a shape component when different performance characteristics are required.

FFT Library
type: Resource
type: NamedIndividual
has db xref: nif-0000-23324
synonym: Fast Fourier Transform (FFT) JavaLibrary
synonym: Fast Fourier Transform JavaLibrary
synonym: Fast Fourier Transform Library
synonym: FFT Java library
IAO_0000115: Java library used for the execution of discrete Fourier transforms in 1-D, 2-D and 3-D through the implementation of Fast Fourier Transform (FFT) algorithms. * The FFT library has been written in Java for portability across different platforms, integrated into a single jar file for easy implementation. * The FFT library provides forward and backward fast Fourier transforms in 1-D, 2-D and 3-D with an easy-to-use manner. * The FFT requires the length equal to a number with an integer power of two. This library automatically examines the input data and detects the length to prevent improper execution.

University of Basel; Basel; Switzerland
type: Organization
type: NamedIndividual
has db xref: nlx_24036
synonym: Universitat Basel
synonym: University of Basel
IAO_0000115: Public university in Basel, Switzerland that offers degree programs in theology, law, medicine, humanities and social sciences, science, psychology, and business and economics.

DrugBank
type: Resource
type: NamedIndividual
has db xref: nif-0000-00417
has db xref: OMICS_01580
has db xref: r3d100010544
IAO_0000115: Bioinformatics and cheminformatics database that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.

Aging Genes and Interventions Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-23326
synonym: Aging Genes Database
synonym: Aging Genes DB
synonym: Genes/Interventions Database
abbrev: AGEID
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 17,2023. A database of genes and interventions connected with aging phenotypes including those with respect to their effects on life-span or age-related neurological diseases. Information includes: organism, aging phenotype, allele type, strain, gene function, phenotypes, mutant, and homologs. If you know of published data (or your own unpublished data that you'd like to share) not currently in the database, please use the Submit a Gene/Intervention link.

Allopathfinder
type: Resource
type: NamedIndividual
has db xref: nif-0000-23327
synonym: Predicting allosteric communication in myosin via a conserved residue pathway
abbrev: AlloPathFinder
IAO_0000115: Software application and code base that allows users to compute likely allosteric pathways in proteins. The underlying assumption is that residues participating in allosteric communication should be fairly conserved and that communication happens through residues that are close in space. The initial application for the code provided was to study the allosteric communication in myosin. Myosin is a well-studied molecular motor protein that walks along actin filaments to achieve cellular tasks such as movement of cargo proteins. It couples ATP hydrolysis to highly-coordinated conformational changes that result in a power-stroke motion, or "walking" of myosin. Communication between a set of residues must link the three functional regions of myosin and transduce energy: the catalytic ATP binding region, the lever arm, and the actin-binding domain. They are investigating which residues are likely to participate in allosteric communication pathways. The application is a collection of C++/QT code, suitable for reproducing the computational results of the paper. (PMID 17900617) In addition, they provide input and alignment information to reproduce Figure 3 (a key figure) in the paper. Examples provided will show users how to use AlloPathFinder with other protein families, assumed to exhibit an allosteric communication. To run the application a multiple sequence alignment of representative proteins from the protein family is required along with at least one protein structure.

Super Drug Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-00418
abbrev: SDD
IAO_0000115: Public database of the structures of active ingredients in marketed drugs. It utilizes a web-query system with various search options, such as drug names, trade name, and synonyms.

Molecular Simulation Trajectories Archive of a Villin Variant
type: Resource
type: NamedIndividual
has db xref: nif-0000-23331
IAO_0000115: An archive of hundreds of all-atom, explicit solvent molecular dynamics simulations that were performed on a set of nine unfolded conformations of a variant of the villin headpiece subdomain (HP-35 NleNle). It includes scripts for accessing the archive of villin trajectories as well as a VMD plug-in for viewing the trajectories. In addition, all starting structures used in the trajectories are also provided. The simulations were generated using a distributed computing method utilizing the symmetric multiprocessing paradigm for individual nodes of the Folding_at_home distributed computing network. The villin trajectories in the archive are divided into two projects: PROJ3036 and PROJ3037. PROJ3036 contains trajectories starting from nine non-folded configurations. PROJ3037 contains trajectories starting from the native (folded) state. Runs 0 through 8 (in PROJ3036) correspond to starting configurations 0 through 8 discussed in the paper in J. Mol. Biol. (2007) 374(3):806-816 (see the publications tab for a full reference), whereas RUN9 uses the same starting configuration as RUN8. Each run contains 100 trajectories (named clone 0-99), each with the same starting configuration but different random velocities. Trajectories vary in their length of time and are subdivided into frames, also known as a generation. Each frame contains around 400 configurational snapshots, or timepoints, of the trajectory, with the last configurational snapshot of frame i corresponding to the first configurational snapshot of generation i+1. The goal is to allow researchers to analyze and benefit from the many trajectories produced through the simulations.

PANDAseq
type: Resource
type: NamedIndividual
has db xref: OMICS_05255
synonym: PAired-eND Assembler for DNA sequences
IAO_0000115: Software program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.

ToRNADo
type: Resource
type: NamedIndividual
has db xref: nif-0000-23335
IAO_0000115: A software application for animating and visualising RNA and other macromolecular structures. Users are able to use their intuition to interactively refold RNA structures and produce morphs from one structure to another. It allow researchers to explore and manipulate molecular structures Imported from BiositeMaps registry, to better understand structure:function relationships, folding pathways, and molecular motion.

SAFA Footprinting Software
type: Resource
type: NamedIndividual
has db xref: biotools:safa
has db xref: nif-0000-23336
synonym: Semi-Automated Footprinting Analysis Software
abbrev: SAFA
IAO_0000115: A software package that anayzes the structral details of RNA molecules through rapid quantification of a footprinting gel. By automating many of the steps involved in gel analysis, approximately one entire gel with thousands of bands can be quantified in less than 10 minutes using SAFA. In general, all the automated features have a manual override, such that even difficult or exceptional gels can be analyzed with the package.

BWH Research Imaging Core
type: Resource
type: NamedIndividual
has db xref: SciEx_8812
synonym: Brigham and Women's Hospital Research Imaging Core
synonym: BWH Research Imaging Core (BRIC)
abbrev: BRIC
IAO_0000115: Imaging Core facility that provides a comprehensive research imaging service to meet the needs of investigators and research subjects using imaging facilities at Brigham and Women's Hospital (BWH). A unique feature of BRIC is the complete anonymity of research subjects. Research image scheduling, image acquisition and image storage are all kept completely separate from BWH clinical Radiology systems. The BRIC provides the administrative infrastructure, customer service architecture and institutional support to promote investigative applications of imaging technologies.

NCBI database of Genotypes and Phenotypes (dbGap)
type: Resource
type: NamedIndividual
has db xref: biotools:dbgap
has db xref: nif-0000-23342
has db xref: OMICS_00263
has db xref: r3d100010788
synonym: Database of Genotypes and Phenotypes
synonym: database of Genotypes and Phenotypes (dbGaP)
synonym: dbGaP
synonym: NCBI
IAO_0000115: Database developed to archive and distribute clinical data and results from studies that have investigated interaction of genotype and phenotype in humans. Database to archive and distribute results of studies including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits.

leeHom
type: Resource
type: NamedIndividual
has db xref: biotools:leehom
has db xref: OMICS_05254
IAO_0000115: Software program for the Bayesian reconstruction of ancient DNA fragments. The algorithm removes the adaptors and reconstructs the original DNA sequences using a Bayesian maximum a posteriori probability approach.

University of Canterbury; Christchurch; New Zealand
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100008414
has db xref: grid.21006.35
has db xref: ISNI:0000 0001 2179 4063
has db xref: nlx_155455
has db xref: Wikidata:Q432475
synonym: University of Canterbury
abbrev: UC
IAO_0000115: Public university in New Zealand that offers degree programs in fields such as art, commerce, engineering, forestry, health sciences, and social work.

Poldracklab Portal
type: Resource
type: NamedIndividual
has db xref: nif-0000-00423
synonym: Poldracklab.org - Software projects
IAO_0000115: The Poldrack lab has developed software tools for fMRI data analysis (links on the site), experimental design, and informatics, in collaboration with several other groups. * pubbrain.org: Developed in collaboration with the UCLA Consortium for Neuropsychiatric Phenomics, this site is an automatic meta-analytic search aid that allows for visualizing PubMed searches based on published neuroanatomic findings. * LONI Probabilistic Atlas: Developed in collaboration with the UCLA Laboratory of Neuroimaging and Center for Cognitive Phenomics, this project provides free and open access to a probabilistic atlas of cortical structures in 40 healthy individuals, including all raw data. * fmripower.org: Software developed by Jeanette Mumford in the Poldrack lab for statistical power analysis for fMRI studies. * Automated ICA-based denoising: Toolbox developed by Jussi Tohka at the Tampere University of Technology in Finland in collaboration with our laboratory and the UCLA Laboratory of Neuroimaging. * Raw data diagnostics - An R program that reads in a 4-D data file and provides a diagnostic report. * Code to run various tasks used in the lab - all of these require MATLAB and the MATLAB Psychophysics toolbox: * - Stop signal task (for behavioral testing outside the scanner) * - File Stop signal task (for use in the scanner) * - File mixed gambles task (demo and scanning script)

BioPortal
type: Resource
type: NamedIndividual
has db xref: nif-0000-23346
has db xref: r3d100012344
synonym: BioPortal Knowledgebase
IAO_0000115: Open repository of biomedical ontologies that provides access via Web browsers and Web services to ontologies. It supports ontologies in OBO format, OWL, RDF, Rich Release Format (RRF), Protege frames, and LexGrid XML. Functionality includes the ability to browse, search and visualize ontologies as well as to comment on, and create mappings for ontologies. Any registered user can submit an ontology. The NCBO Annotator and NCBO Resource Index can also be accessed via BioPortal. Additional features: * Add Reviews: rate the ontology according to several criteria and describe your experience using the ontology. * Add Mappings: submit point-to-point mappings or upload bulk mappings created with external tools. Notification of new Mappings is RSS-enabled and Mappings can be browsed via BioPortal and accessed via Web services. * NCBO Annotator: Tool that tags free text with ontology terms. NCBO uses the Annotator to generate ontology annotations, creating an ontology index of these resources accessible via the NCBO Resource Index. The Annotator can be accessed through BioPortal or directly as a Web service. The annotation workflow is based on syntactic concept recognition (using the preferred name and synonyms for terms) and on a set of semantic expansion algorithms that leverage the ontology structure (e.g., is_a relations). * NCBO Resource Index: The NCBO Resource Index is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data linked via ontology terms. A set of annotations is generated automatically, using the NCBO Annotator, and presented in BioPortal. This service uses a concept recognizer (developed by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand them using ontology is_a relations. * Web services: Documentation on all Web services and example code is available at: BioPortal Web services.

Reflect
type: Resource
type: NamedIndividual
has db xref: nif-0000-23349
has db xref: OMICS_01196
synonym: Reflect: Protein small molecules
IAO_0000115: Web service that tags gene, protein, and small molecule names in any web page. Clicking on a tagged term opens a small popup showing summary information, and allows the user to quickly link to more detailed information. For each protein or gene, Reflect provides domain structure, sub-cellular localization, 3D structure, and interaction partners. For small molecules, it provides the chemical structure and interaction partners. Reflect can be installed as a plugin to Firefox or Internet Explorer, or can be used by entering a URL in the field provided. It can also be accessed programmatically via a REST or SOAP API, and a Reflect button can easily be added to any web page using Javascript or using a CGI proxy. Reflect was first-prize winner out of over 70 submissions in the Elsevier Grand Challenge, an international competition for systems that improve the way scientific information is communicated and used. Reflect can be edited and improved by the community.

PyNN
type: Resource
type: NamedIndividual
has db xref: nif-0000-23351
IAO_0000115: Software Python package for simulator-independent specification of neuronal network models. In other words, you can write the code for a model once, using the PyNN API, and then run it without modification on any simulator that PyNN supports (currently NEURON, NEST and PCSIM). The API has two parts, a low-level, procedural API (functions create(), connect(), set(), record(), record_v()), and a high-level, object-oriented API (classes Population and Projection, which have methods like set(), record(), setWeights(), etc.). The low-level API is good for small networks, and perhaps gives more flexibility. The high-level API is good for hiding the details and the book-keeping, and is intended to have a one-to-one mapping with FacetsML. The other thing that is required to write a model once and run it on multiple simulators is standard cell models. PyNN translates standard cell-model names and parameter names into simulator-specific names, e.g. standard model IF_curr_alpha is iaf_neuron in NEST and StandardIF in NEURON, while SpikeSourcePoisson is a poisson_generator in NEST and a NetStim in NEURON. Only a small number off cell models have been implemented so far.

Synapse Web Reconstruct
type: Resource
type: NamedIndividual
has db xref: nif-0000-23420
abbrev: Reconstruct
IAO_0000115: A Windows (Win32) software application for montaging, aligning, tracing, measuring, and reconstructing objects from serial microscopic section images. The software is designed for microscopy in which section resolution is much less than section thickness, such as transmitted electron microscopy (EM) where the resolution is a few nanometers while the section thickness is many tens of nanometers. Reconstruct can easily handle series with hundreds of very large, high-resolution section images. It facilitates image cropping, scaling and alignment. Multiple images can be placed side-by-side to make a montage of a section from a mosaic of images. The alignment of adjacent sections can be rapidly compared by either blending the two sections or by flickering between them. Sections can be moved while blended. Reconstruct aids in the calibration of image size. Images taken at different magnifications can be combined, calibrated and aligned. Tools for tracing and editing of objects on sections are provided. Objects can be surfaced from the traces and previewed in an OpenGL-based 3D scene window. The 3D scene can be saved as a bitmap or as a VRML file.

Phalanx Biotech Group
type: Resource
type: NamedIndividual
has db xref: SciEx_13118
synonym: Phalanx Biotech
IAO_0000115: Group service that provides expression profiling products and services. They manufacture DNA microarrays for gene expression and microRNA profiling.

CNSforum: Image Bank
type: Resource
type: NamedIndividual
has db xref: nif-0000-23576
synonym: CNS Forum Image Bank
synonym: Lundbeck Institute CNSforum Image Bank
IAO_0000115: A collection of downloadable central nervous system (CNS) images for teaching, presentations, articles, and other purposes. The following major categories of images are as follows: Brain anatomy, Brain physiology, Anxiety, Depression, Schizophrenia, Dementia, Parkinson's disease, Stroke, and Others.

Movement Disorder Virtual University (MDVU): Resource Library
type: Resource
type: NamedIndividual
has db xref: nif-0000-23698
synonym: MDVU Resource Library
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented April 15, 2016. The Movement Disorder Virtual University (MDVU) Resource Library contains detailed movement disorder information and resources including rating scales, scoring sheets, patient fact sheets, teaching slide sets, research news, meeting reports, anatomical illustrations, movement disorder treatment and rehabilitation directory, a glossary, support organizations, drug package information, and a library of links.

CRE Driver Network
type: Resource
type: NamedIndividual
has db xref: nif-0000-23753
synonym: CRE-Driver Network
synonym: CRE-driver Network
synonym: Mouse Models for Neuroscience Research
synonym: NIH Neuroscience Blueprint CRE Driver Network
IAO_0000115: Project to provide Neuroscience Community with mouse strains that are suitable for tissue and cell-type-specific perturbation of gene function in nervous system. NIH Neuroscience Blueprint has established three centers in the USA for generation of genetically modified mice expressing CRE recombinases in nervous system on the C57BJ/6 genetic background. Mouse lines are generated at Cold Spring Harbor Lab, at Scripps Research Institute, and at Baylor College of Medicine.

Gene Expression Nervous System Atlas
type: Resource
type: NamedIndividual
has db xref: nif-0000-00130
synonym: GENSAT
IAO_0000115: Gene expression data and maps of mouse central nervous system. Gene expression atlas of developing adult central nervous system in mouse, using in situ hybridization and transgenic mouse techniques. Collection of pictorial gene expression maps of brain and spinal cord of mouse. Provides tools to catalog, map, and electrophysiologically record individual cells. Application of Cre recombinase technologies allows for cell-specific gene manipulation. Transgenic mice created by this project are available to scientific community.

iGentBio
type: Commercial Organization
type: NamedIndividual
has db xref: SciEx_11268
IAO_0000115: A commercial facility handling induced pluripotent stem cell (iPSC) generation, cellular characterization, teratoma formation, karyotyping, and KO-mouse generation.

Mapix
type: Resource
type: NamedIndividual
has db xref: OMICS_00844
synonym: Innopsys Mapix
IAO_0000115: System control software used for data acquisition and analysis for microarray images., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Rainbow
type: Resource
type: NamedIndividual
has db xref: biotools:rainbow
has db xref: OMICS_03722
has db xref: SCR_015992
synonym: Bio-rainbow
synonym: RAD-seq
synonym: RAD-seq: Restriction-site Associated DNA sequencing
IAO_0000115: Software developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq.

Database of Secondary Structure Assignments
type: Resource
type: NamedIndividual
has db xref: biotools:dssp
has db xref: nif-0000-23901
has db xref: OMICS_06247
abbrev: DSSP
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB) and the program that calculates DSSP entries from PDB entries. DSSP is distributed on a basis of trust and instructions are available on the site. * Precompiled executables are also available for Linux and Windows. (The Windows .exe file was compiled under Linux using Mingw32, has never seen a Windows environment and should thus be virus-free. Download the source if you want to be 100% sure.) Under Windows the DSSP output does not make it to the console, so redirect it to a file instead: dsspcmbi source.pdb destination.dssp > messages.txt * Several changes have been made to the DSSP program to solve problems with recent PDB files. These are documented in the source code. * FTP access to the DSSP files resides at the CMBI: ftp.cmbi.kun.nl/pub/molbio/data/dssp or ftp://ftp.ebi.ac.uk/pub/databases/dssp/. If you have problems downloading the DSSP files, it is likely that your FTP program is not able to handle tens of thousands of files in one directory. In this case, install a proper FTP program, for example NCFTP. However, it is recommended that you download DSSP files with the rsync command.

Fungal C-values Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02857
synonym: Fungal Genome Size Database
IAO_0000115: Database for scientists interested in fungal genomics. Multiple species are included, and the database provides information on DNA C-values and genomic size. It also gives information derived from electrophoresis experiments and genome sequencing projects. The database accepts data submissions. We appreciate receiving published offprints, preprints, and personal communications providing C-value estimates for fungi.

Rodent Brain WorkBench
type: Resource
type: NamedIndividual
has db xref: nif-0000-00424
synonym: Rodent Brain Work Bench
abbrev: rbwb
IAO_0000115: The Rodent Brain WorkBench is the portal to atlases, databases and tools developed by the Neural Systems and Graphics Computing Laboratory (NeSys) at the Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo, Oslo, Norway. The Rodent Brain WorkBench presents a collection of brain mapping and atlasing oriented database applications and tools. The main category of available data is high resolution mosaic images covering complete histological sections through the rat and mouse brain. A highly structured relational database system for archiving, retrieving, viewing, and analysing microscopy and imaging data, aiming at presentation in standardized brain atlas space, is used to present a series of web applications for individual research projects. * Brain Connectivity * Atlases of Mouse Brain Promoter Gene Expression * General Brain Atlas and Navigation Systems * Downloadable tools for 3-DVisualization Open Access: * Atlas 3D * Cerebro-Cerebellar I * Cerebro-Cerebellar II * Neurotransporter Atlas * Rat Hippocampus * Tet-Off Atlas I (PrP) * Tet-Off Atlas II (PrP/CamKII) * Whole Brain Connectivity Atlas The data presented have been produced in collaboration with a large number of laboratories in Europe and the United States.

CASBAH
type: Resource
type: NamedIndividual
has db xref: OMICS_03304
synonym: CAspase Substrate dataBAse Homepage
synonym: The CASBAH
synonym: The CAspase Substrate dataBAse Homepage
IAO_0000115: Database which contains information pertaining to all currently known caspase substrates.

FunSimMat
type: Resource
type: NamedIndividual
has db xref: nif-0000-02860
synonym: FunSimMat - Functional Similarity Matrix
IAO_0000115: FunSimMat is a comprehensive resource of semantic and functional similarity values. It allows ranking disease candidate proteins for OMIM diseases and searching for functional similarity values for proteins (extracted from UniProt), and protein families (Pfam, SMART). FunSimMat provides several different semantic and functional similarity measures for each protein pair using the Gene Ontology annotation from UniProtKB and the Gene Ontology Annotation project at EBI (GOA). There are several search options available: Disease candidate prioritization: * Rank candidate proteins using any OMIM disease entry * Compare a list of proteins to any OMIM disease entry * Compare all human proteins to any OMIM disease entry Functional similarity: * Compare one protein / protein family to a list of proteins / protein families * Compare a list of GO terms to a list of proteins / protein families Semantic similarity: * For a list of GO terms, FunSimMat performs an all-against-all comparison and displays the semantic similarity values. FunSimMat provides an XML-RPC interface for performing automatic queries and processing of the results as well as a RestLike Interface. Platform: Online tool

TelSeq
type: Resource
type: NamedIndividual
has db xref: OMICS_03276
IAO_0000115: Software that measures average telomere length from whole genome or exome shotgun sequence data.

Automated recognition of brain region mentions in neuroscience literature.
type: Resource
type: NamedIndividual
has db xref: nif-0000-24027
synonym: WhiteText - annotated neuroscience text
abbrev: WhiteText
IAO_0000115: Freely available corpus of manually annotated brain region mentions created to facilitate text mining of neuroscience literature. The corpus contains 1,377 abstracts with 18,242 brain region annotations. Interannotator agreement was evaluated for a subset of the documents, and was 90.7% and 96.7% for strict and lenient matching respectively. We observed a large vocabulary of over 6,000 unique brain region terms and 17,000 words. For automatic extraction of brain region mentions we evaluated simple dictionary methods and complex natural language processing techniques. The dictionary methods based on neuroanatomical lexicons recalled 36% of the mentions with 57% precision. The best performance was achieved using a conditional random field (CRF) with a rich feature set. Features were based on morphological, lexical, syntactic and contextual information. The CRF recalled 76% of mentions at 81% precision, by counting partial matches recall and precision increase to 86% and 92% respectively. We suspect a large amount of error is due to coordinating conjunctions, previously unseen words and brain regions of less commonly studied organisms. We found context windows, lemmatization and abbreviation expansion to be the most informative techniques. We encourage you to test new methods and applications of the dataset. Please contact us if you do, we would like to hear about and link to your work. The abstracts are from PubMed/Medline, specifically The Journal of Comparative Neurology.

Pathview
type: Resource
type: NamedIndividual
has db xref: biotools:pathview
has db xref: OMICS_05212
synonym: path view
IAO_0000115: A tool set for pathway-based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.

SelectScience
type: Resource
type: NamedIndividual
has db xref: nif-0000-24033
IAO_0000115: SelectScience.net is a leading online resource for applied chemists, clinical chemists and life scientists. It provides up-to-date product and industry news, an extensive product directory and end-user product reviews, as well as the ability for visitors to review the products they use. Scientists can also use the site to search for jobs, application notes and scientific conferences. Sponsors: The company is run by independent scientists and funded from Government and Corporate sponsorship.

Wellesley College Neuroscience
type: Organization
type: NamedIndividual
has db xref: nif-0000-24036
synonym: Wellesley Neuroscience
IAO_0000115: Neuroscience was implemented as a new interdisciplinary major in 1999, replacing the Psychobiology Program and providing a base of experiences in biology, chemistry and psychology. Our students benefit from being able to work in small classes and to experience investigative lab experiences even in their introductory courses. Wellesley's neuroscience majors graduate with a liberal arts background coupled with sufficient concentration in this specialized field to be competitive among students coming from exclusively research-oriented institutions. The best proofs of the success of this approach are its products: * 60% of our graduates proceed to medical school; * 15% of our graduates continue on with graduate work in neuroscience, psychology, or neuropsychology; * 10% of our graduates pursue careers that intersect with neuroscience - for example, patent law or work in the biotech industry. Neuroscience is the study of the structure and function of neurons and how they are assembled to produce behaviors. This topic uses a multidisciplinary approach that extends from the molecular, through the cellular, and to the behavioral level.

Genes to Cognition Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02864
synonym: Genes-to-Cognition Database
abbrev: G2Cdb
IAO_0000115: Database of protein complexes, protocols, mouse lines, and other research products generated from the Genes to Cognition project, a project focused on understanding molecular complexes involved in synaptic transmission in the brain.

Erasmus MC Department of Neuroscience
type: Organization
type: NamedIndividual
has db xref: nif-0000-24051
synonym: Neuroscience
IAO_0000115: The department of Neuroscience was founded in 2001, resulting from a merger between the Physiology and Anatomy department. In 2008, the BNT department joined forces. At present we consist of about 150 people. Our research is dedicated to Plasticity and Dynamics of Sensori-Motor Systems, which we investigate at the physiological, anatomical end molecular level in 18 different research groups. We have teaching responsibilities within the whole bachelor's phase of the medical curriculum at the Erasmus MC, teaching both basic anatomy and physiology, as well as neuroscience. The department hosts its own Master of Neuroscience program. The department of Neuroscience is embedded in the ONWAR, Helmholtz, and MGC research school

AGing Integrated Database
type: Resource
type: NamedIndividual
has db xref: rid_000108
synonym: AGing Integrated Database (AGID)
abbrev: AGID
IAO_0000115: An on-line database and query system based on Administration-on-Aging (AoA)-related data files and surveys, and includes population characteristics from the Census Bureau for comparison purposes. Four options or paths through AGID were designed to provide different levels of focus and aggregation of the data from individual data elements within Data-at-a-Glance, to State-level summaries in State Profiles, to detailed, multi-year tables in Custom Tables, and finally, to full database access within Data Files.

GLProbs
type: Resource
type: NamedIndividual
has db xref: OMICS_03732
IAO_0000115: Software implementing a simple and effective approach to improve the accuracy of multiple sequence alignment.

International Graduate Program Medical Neurosciences
type: Resource
type: NamedIndividual
has db xref: nif-0000-24040
synonym: MedNeuro
IAO_0000115: Program integrates basic laboratory research and the clinic in terms of faculty, students, course content and infrastructure. This university's rigorous and comprehensive Master program provides a structured education in basic neuroscience to medical students and trains students of the life sciences in medical topics and approaches concerning the central and peripheral nervous system. Besides in depth theoretical training, the MSc program emphasizes state-of-the art practical lab experience, preparing graduates for continued research as PhD students. The PhD program places a high emphasis on scientific excellence, provides a multidisciplinary research and learning environment and offers extensive supervision and tutoring allowing students to complete their projects within 3 years. The supervised research project stands in the center of the PhD program, complemented by colloquia, workshops and training in professional skills. Our PhD students are member of the undefined Humboldt-Graduate-School providing an excellent service and training in transferable skills.

Neuroscience Berlin
type: Resource
type: NamedIndividual
has db xref: nif-0000-24042
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 10, 2017. In the last few years the Berlin neuroscience community has been highly successful in creating new research projects. Not the least of these is the cluster of excellence, NeuroCure, which has brought nine new professors and their research groups to Berlin. Along with the increasing levels of research, a number of new neuroscience training programs have recently been established. In 2002 the International Graduate Program Medical Neurosciences was the only structured Masters and PhD program: as of 2009 Berlin hosts four neuroscience schools and several DFG funded research training groups. The purpose of this website to highlight the many projects and people involved in the Berlin neuroscience community. We hope that you, the reader, can benefit from this summary., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Center for Stroke Research Berlin
type: Resource
type: NamedIndividual
has db xref: nif-0000-24043
abbrev: CSB
IAO_0000115: Stroke research group that performs disease-oriented basic research, clinical research, epidemiology and health services research.

Emotion Mining Company, Inc.
type: Resource
type: NamedIndividual
has db xref: nif-0000-24045
synonym: Emotion Mining
IAO_0000115: Emotion Mining enables scientists to measure the emotions of subjects before, during, and after research protocols in a reliable, sensitive, and convenient manner. Furthermore, Emotion Minings easy to use online data collection methodology leads to deep insights into the problems facing respondents and their solutions. :Emotion Minings unique measurement of emotion is clarified emotion emotion from which normal research biases, including subject state and trait biases, are removed. Using "clarified" emotion, researchers can gain insight into what research subjects really feel beneath and beyond what they self-report. More specifically, Emotion Mining engages respondents in a game-like exercise that enables them to express their deep-seated idiosyncratic responses and emotions. Built-in consideration of all possible emotion words produces "whole" emotional profiles in Emotion Mining analyses. Emotion Mining is applicable to social, cognitive, and behavioral research challenges and goals. Because it can distinguish conscious, subconscious, and even unconscious emotional responses to an unlimited range of topics, it is particularly applicable to the following areas: Social Psychology Personality Psychology Cognition and Social Cognition Cognitive Neuroscience Behavioral Neuroscience Political Psychology Their online methodology provides an engaging, controlled environment where subjects feel free to express themselves. Emotion Mining collects vital emotional responses in a way that no other methodology can. Emotion Mining also allows: :- Identification of unappreciated but recognizable emotional responses :- Prioritization of most unique, least biased emotional responses :- Aggregation through structured emotion analysis :- Collection of rich emotional verbatim :- Keyword analysis of verbatim You can experience and determine the face validity of Emotion Mining for yourself by registering to use Emotion Mining for personal decision making. You may also wish to have your…

rBiopaxParser
type: Resource
type: NamedIndividual
has db xref: biotools:rbiopaxparser
has db xref: OMICS_05211
synonym: rBiopaxParser - Parses BioPax files and represents them in R
IAO_0000115: A software package that provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. At the moment BioPAX level 2 and level 3 are supported.

Bird Base
type: Resource
type: NamedIndividual
has db xref: nif-0000-02869
synonym: Bird Base: A Database of Avian Genes & Genomes
synonym: Bird Base: A Model Organism Database for Birds
synonym: BirdBase
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Birdbase is a centralized resource for avian genomics and other aspects of avian biology. BirdBase Objectives: * Provide a community driven platform for information about bird genomes and genomics. * Stimulate scientific advancement by integrating information from a variety of bird species * Promote collaboration and cooperation between scientists using birds as model organisms and those studying agricultural traits of birds. * Help coordinate solutions to common issues such as gene nomenclature and ontology development * Provide a conduit for sharing reagents and protocols

Genes to Cognition Online
type: Resource
type: NamedIndividual
has db xref: nif-0000-25051
synonym: G2C Online
abbrev: G2C
IAO_0000115: Genes to Cognition (G2C) Online is about modern neuroscience. It focuses on cognitive disorders, cognitive processes, and research approaches. Use the dynamic network maps to explore our library of 750+ unique items. Or, use the linear Selected Items menu on top of each map to tour selected content. Read the G2C blog, use simple mapper, or the 3-D brain, an interactive model of the brain. Disorders included in this site: ADHD, Alzheimer's Disease, Autism, Bipolar Disorder, Depression, Schizophrenia Cognitive Processes include: Attention, Language, Learning and Memory, Perception, and Thinking Research Approaches include: Bioinformatics, Ethics, Gene Finding, Model systems, Neuroimaging, Psychology. Navigation: Interact with the dynamic Networks Maps to explore the full catalog of content. Roll-over a node on the map for a preview and click to open the content. Move on to other content by returning to the network map. Each node you visit on the map gets flagged. Follow the Selected Items Subway Line for an overview of a topic. Roll-over a subway node for a preview and click to open the content. Other Features: Most content items include links to Related Items, which allow you to explore further. The Glossary includes over 300 neuroscience keywords. Search for content using keywords or id number. Select a preferred network map to view the content in context. Open/close the History at the lower left to view visited content. Your history is stored until you clear it. Simple Mapper - We developed Simple Mapper to power this web site on the brain. Now, you can use it to organize what comes out of yours! With Simple Mapper create and save concept maps, network diagrams, or flowcharts for personal use or to share with others. 3-D Brain - The G2C Brain is an interactive 3-D model of the brain, with 29 structures that can be rotated in three-dimensional space. Each structure has information on brain disorders, brain damage, case studies, and links to modern neuroscience resea…

Arthur Prochazka Laboratory, University of Alberta
type: Resource
type: NamedIndividual
has db xref: nif-0000-24047
synonym: University of Alberta Arthur Prochazka Laboratory
abbrev: Arthur Prochazka's Lab
IAO_0000115: The lab of Arthur Prochazka, whose research focuses on routing electrical current from surface electrodes to deep-lying nerves using implanted conductors. His research mostly focuses on muscle physiology. Current fields of research: * Stimulus Router System: A new family of implanted neuroprostheses. It comprises an implanted lead that picks up some of the current delivered through the skin by a surface stimulator and delivers it to a target nerve via a nerve cuff. The SRS has the advantages of an implanted stimulator: selectivity, reproducibility and convenience, at a fraction of the cost * Bionic Glove: Hand opening and closing stimulator for C5-C6 tetraplegic people. It is based on Functional Electrical Stimulation (FES). * In-home Telerehabilitation: Providing exercise sessions over the internet. * Interactive Receptor Model: An online model explaining muscle spindles and tendon organs. * Spinal Motoneuron Activity During Gait * Robocats: Mathematical models for locomotion. * Rigidity Analyzer: A better means of assessing rigidity. * General Research: Fundamental questions in our field of neurophysiology. * Spinal Cord Microstimulation: Restoring bladder function after spinal cord injury.

NUTMEG
type: Resource
type: NamedIndividual
has db xref: nif-0000-24052
synonym: Neurodynamic Utility Toolbox for Magnetoencephalography and Electroencephalography
IAO_0000115: Software MEG/EEG analysis toolbox for reconstructing neural activation and overlaying it onto structural MR images. Toolbox runs under MATLAB in conjunction with SPM2 and can be used with Linux/UNIX, Mac OS X, and Windows platforms.

Stanley Neuropathology Consortium Integrative Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-24103
abbrev: SNCID
IAO_0000115: A database of 1749 neuropathological markers measured in 12 different brain regions from 60 brains in the Consortium Collection from the Stanley Medical Research Institute combined with microarray data and statistical tools. Fifteen brains each are from patients diagnosed with schizophrenia, bipolar disorder, or major depression, and unaffected controls. The four groups are matched by age, sex, race, postmortem interval, pH, side of brain, and mRNA quality. A Repository of raw data is also included. Users must register for access.

Mendeley
type: Resource
type: NamedIndividual
has db xref: nif-0000-24120
synonym: Mendeley Data
synonym: Mendeley Research Network
IAO_0000115: Web application as free reference manager and academic social network to organize your research, collaborate with others online, and discover the latest research. Automatically generate bibliographies, Collaborate easily with other researchers online, Easily import papers from other research software, Find relevant papers based on what you're reading, Access your papers from anywhere online, Read papers on the go with the iPhone app. The software, Mendeley Desktop, offers: * Automatic extraction of document details * Efficient management of your papers * Sharing and synchronization of your library (or parts of it) * Additional features: A plug-in for citing your articles in Microsoft Word, OCR (image-to-text conversion, so you can full-text search all your scanned PDFs), etc The website, Mendeley Web, complements Mendeley Desktop by offering these features: * An online back up of your library * Statistics of all things interesting * A research network that allows you to keep track of your colleagues' publications, conference participations, awards etc * A recommendation engine for papers that might interest you.

Community Epidemiology Work Group
type: Resource
type: NamedIndividual
has db xref: nif-0000-24121
synonym: Community Epidemiology Work Group (CEWG)
abbrev: CEWG
IAO_0000115: A network composed of researchers from major metropolitan areas of the United States and selected foreign countries which meet semiannually to discuss the current epidemiology of drug abuse. The primary mission of the Work Group is to provide ongoing community-level surveillance of drug abuse through analysis of quantitative and qualitative research data. Through this program the CEWG provides current descriptive and analytical information regarding the nature and patterns of drug abuse, emerging trends, characteristics of vulnerable populations and social and health consequences. Reports Reports are available from the biannual meetings at which the network members discuss current and emerging problems of substance abuse. At the meetings, CEWG members present data on drug abuse from a variety of city, State, Federal, and other sources. These data are enhanced with information gathered through ethnographic research, focus groups, interviews, and other qualitative methods. This integration of quantitative with qualitative data provides invaluable insight into emerging drug use trends. Book In 1998, the National Institute on Drug Abuse (NIDA) published the first edition of Assessing Drug Abuse Within and Across Communities: Community Epidemiology Surveillance Networks on Drug Abuse to share information on establishing drug abuse epidemiology networks at community and State levels. Its purpose is to provide guidelines for establishing epidemiology networks to monitor and assess drug abuse patterns and trends and emerging drug problems at community and State levels to provide a foundation of information for public health response. The second edition differs from the first in format. For each data source, there is a description of the source and database, followed by guidelines on how to access the data (including Web sites) and what to request, and examples of how the data have been used by epidemiology work groups or Federal agencies. NIDA hopes that this revised guide …

Digital Repository Infrastructure Vision for European Research
type: Resource
type: NamedIndividual
has db xref: nif-0000-24122
abbrev: DRIVER
IAO_0000115: Data infrastructure project that merged with OpenAIRE. Cohesive, robust and flexible, pan-European infrastructure for digital repositories, offering sophisticated services and functionalities for researchers, administrators and the general public. Access the network of freely accessible digital repositories with content across academic disciplines with over 3,500,000 scientific publications, found in journal articles, dissertations, books, lectures, reports, etc., harvested regularly from more than 295 repositories, from 38 countries. DRIVER has established a network of relevant experts and Open Access repositories. DRIVER-II will consolidate these efforts and transform the initial testbed into a fully functional, state-of-the art service, extending the network to a larger confederation of repositories. It aims to optimize the way the e-Infrastructure is used to store knowledge, add value to primary research data and information making secondary research more effective, provide a valuable asset for industry, and help bridging research and education. The objectives of DRIVER-II, the second phase of the project, include efforts to expand, enrich, and strengthen the results of DRIVER, in the following areas: * strategic geographic and community expansion by means of the DRIVER confederation * establish a robust, scalable repository infrastructure accompanied by an open source software package D-Net * broader coverage of content through the use of enhanced publications * advanced end-user functionality to support scientific exploration of complex digital objects * larger outreach and advocacy programs * continued repository support * guidelines for interoperability in the larger European digital library community

Society for Research on Nicotine and Tobacco
type: Organization
type: NamedIndividual
has db xref: grid.430369.b
has db xref: ISNI: 0000 0004 0370 3617
has db xref: nif-0000-24137
has db xref: Wikidata: Q23583082
synonym: SRNT
IAO_0000115: With over a thousand members, including many of the top experts on nicotine and tobacco from over 20 countries around the world, the Society for Research on Nicotine and Tobacco's mission is to stimulate the generation of new knowledge concerning nicotine in all its manifestations - from molecular to societal. The Society has the following goals: 1. To sponsor scientific meetings and publications fostering the exchange of information on the biological, behavioral, social, and economic effects of nicotine; these activities shall include basic research and research on mechanisms of action and the use of nicotine as a probe for studying nervous systems function as well as applied research on the behavioral and pharmacological aspects of tobacco use, nicotine dependence, the therapeutic uses of nicotine, and related areas. 2. To encourage scientific research on public health efforts for the prevention and treatment of cigarette and tobacco use. 3. To provide the means by which various legislative, governmental, regulatory, and other public agencies and the ethical drug industry can obtain expert advice and consultation on critical issues concerning tobacco use, nicotine dependence, and the therapeutic uses of nicotine. Membership dues will be used to plan an annual meeting, to publish a newsletter, to compile a directory, to conduct advocacy and liaison activities for nicotine research, and to begin work on professional publications such as a journal. Though the Society will meet at least once per year in North America and will be incorporated in the United States, the intent is to be international in scope, with co-sponsorship of meetings in other countries and active recruitment of members outside the United States. By clicking on the various links on the website you can gain access to further information about the society, its publications, activities and membership. In 2004, the Society for Research on Nicotine and Tobacco celebrated the tenth anniversary of its fou…

DSS
type: Resource
type: NamedIndividual
has db xref: OMICS_03273
synonym: Dispersion Shrinakge for Sequencing data
synonym: DSS - Dispersion shrinakge for sequencing data
IAO_0000115: Software R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.

Gabi Primary Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02866
has db xref: r3d100012432
synonym: GabiPD
abbrev: GABI
IAO_0000115: Database that collects, integrates and links all relevant primary information from the GABI plant genome research projects and makes them accessible via internet. Its purpose is to support plant genome research in Germany, to yield information about commercial important plant genomes, and to establish a scientific network within plant genomic research. GreenCards is the main interface for text based retrieval of sequence, SNP, mapping data etc. Sharing and interchange of data among collaborating research groups, industry and the patent- and licensing agency are facilitated. * GreenCards: Text based search for sequence, mapping, SNP data etc. * Maps: Visualization of genetic or physical maps. * BLAST: Secure BLAST search against different public databases or non-public sequence data stored in GabiPD. * Proteomics: View interactive 2D-gels and view or download information for identified protein spots. Registered users can submit data via secure file upload.

GATE
type: Resource
type: NamedIndividual
has db xref: biotools:gate
has db xref: OMICS_03065
synonym: Genomic Annotation from Time-couse Epigenomic data
synonym: Genomic Annotation from Time-couse Epigenomic data (GATE)
IAO_0000115: Model-based, open source software analysis tool for chromatin states prediction based on time-course epigenetic marks data. It uses a combinatory Finite Mixture model nested with HMM to model the time course marks data in which each single hidden markov model describes the hidden states for a region set across different time points.

NetPathMiner
type: Resource
type: NamedIndividual
has db xref: biotools:netpathminer
has db xref: OMICS_05210
synonym: NetPathMiner: R package for network path mining through gene expression
IAO_0000115: Software that implements a flexible module-based process flow for network path mining and visualization, which can be fully inte-grated with user-customized functions. It supports construction of various types of genome scale networks from three different pathway file formats (KGML, SBML and BioPAX), enabling its utility to most common pathway databases. In addition, it provides different visualization techniques to facilitate the analysis of even thousands of output paths.

NMR metabolomics database of Linkoping
type: Resource
type: NamedIndividual
has db xref: OMICS_02853
synonym: Magnetic Resonance Metabolomics Database
synonym: MDL - The Magnetic Resonance Metabolomics Database
abbrev: MDL
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. An on-line database and publically accessible depository that is dedicated to the omics of small biomolecules.

SumsDB
type: Resource
type: NamedIndividual
has db xref: nif-0000-00016
has db xref: r3d100010169
synonym: Sums database
synonym: Sums DB
synonym: SumsDB (Surface Management System Database) and WebCaret Online Visualization
synonym: SumsDB (Surface Management System Database) WebCaret Online Visualization
synonym: SumsDB and WebCaret
synonym: SumsDB Database
synonym: SumsDB WebCaret
synonym: Surface Management System Database
synonym: Surface Management System Database and WebCaret Online Visualization
synonym: Web Caret
synonym: WebCaret Online Visualization
abbrev: WebCaret
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 11, 2016. Repository of brain-mapping data (surfaces and volumes; structural and functional data) derived from studies including fMRI and MRI from many laboratories, providing convenient access to a growing body of neuroimaging and related data. WebCaret is an online visualization tool for viewing SumsDB datasets. SumsDB includes: * data on cerebral cortex and cerebellar cortex * individual subject data and population data mapped to atlases * data from FreeSurfer and other brainmapping software besides Caret SumsDB provides multiple levels of data access and security: * Free (public) access (e.g., for data associated with published studies) * Data access restricted to collaborators in different laboratories * Owner-only access for work in progress Data can be downloaded from SumsDB as individual files or as bundles archived for offline visualization and analysis in Caret WebCaret provides online Caret-style visualization while circumventing software and data downloads. It is a server-side application running on a linux cluster at Washington University. WebCaret "scenes" facilitate rapid visualization of complex combinations of data Bi-directional links between online publications and WebCaret/SumsDB provide: * Links from figures in online journal article to corresponding scenes in WebCaret * Links from metadata in WebCaret directly to relevant online publications and figures

GenBank
type: Resource
type: NamedIndividual
has db xref: nif-0000-02873
has db xref: OMICS_01650
has db xref: r3d100010528
synonym: Gen Bank
abbrev: GB
IAO_0000115: NIH genetic sequence database that provides annotated collection of all publicly available DNA sequences for almost 280 000 formally described species (Jan 2014) .These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. It is part of International Nucleotide Sequence Database Collaboration and daily data exchange with European Nucleotide Archive (ENA) and DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through NCBI Entrez retrieval system, which integrates data from major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of GenBank database are available by FTP.

Washington National Primate Research Center
type: Resource
type: NamedIndividual
has db xref: nif-0000-24361
abbrev: WaNPRC
IAO_0000115: Center that aims to provide an environment to support biomedical research directed towards human health issues and nonhuman primate health and biology. To meet this mission, the WaNPRC supports biomedical research activities, professional research staff, specifically bred and maintained nonhuman primate colonies, and dedicated facilities and equipment required for nonhuman primate research protocols.

HINT
type: Resource
type: NamedIndividual
has db xref: biotools:hint
has db xref: OMICS_02898
synonym: High-quality INTeractomes
IAO_0000115: A database of high-quality protein-protein interactions in different organisms.

RNAplex
type: Resource
type: NamedIndividual
has db xref: biotools:rnaplex
has db xref: rid_000107
IAO_0000115: Software tool to rapidly search for short interactions between two long RNAs.

Coding Potential Calculator
type: Resource
type: NamedIndividual
has db xref: biotools:cpc
has db xref: rid_000106
abbrev: CPC
IAO_0000115: A Support Vector Machine-based classifier to assesses the protein-coding potential of a transcript based on six biologically meaningful sequence features. CPC can discriminate coding from noncoding transcripts with high accuracy and speed. In addition to predicting the coding potential of the input transcripts, the CPC web server also graphically displays detailed sequence features and additional annotations of the transcript that may facilitate users' further investigation. The coding potential calculator tool reads FASTA data format as input.

Primate Embryo Gene Expression Resource
type: Resource
type: NamedIndividual
has db xref: nif-0000-24366
synonym: PREGER Online
synonym: Preger.org
abbrev: PREGER
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Sample collection of oocytes obtained from various sized antral follicles, and embryos obtained through a variety of different protocols. The PREGER makes it possible to undertake quantitative gene-expression studies in rhesus monkey oocytes and embryos through simple and cost-effective hybridization-based methods.

libCSAM
type: Resource
type: NamedIndividual
has db xref: biotools:libcsam
has db xref: OMICS_03750
IAO_0000115: Contains several C++ codes for compress, decompress, and access each of the fields of any SAM format file.

Macaque.org
type: Resource
type: NamedIndividual
has db xref: nif-0000-24370
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on June 8, 2020.Macaque genomic and proteomic resources and how they are providing important new dimensions to research using macaque models of infectious disease. The research encompasses a number of viruses that pose…

National Gnotobiotic Rodent Resource Center
type: Resource
type: NamedIndividual
has db xref: nif-0000-24375
synonym: NGRRC
IAO_0000115: Material resource that provides germ-free and selectively colonized rodents to requesting investigators. Germ-free rodents are axenic, with no detectible bacteria, yeast, molds, parasites or viruses (except retroviruses).

Peromyscus Genetic Stock Center
type: Resource
type: NamedIndividual
has db xref: nif-0000-24376
IAO_0000115: The deer mouse (Peromyscus maniculatus) and congeneric species are the most common native North American mammal. Laboratory stock of both wild-type and genetically variant Peromyscus are used for investigations in which laboratory-based studies can be interfaced with those of natural populations. The major function of the Stock Center is to provide genetically characterized types of Peromyscus in limited quantities to scientific investigators. It provides a reliable source of genetically defined and virus-free animals and related materials to the scientific and educational communities. The center currently keeps nine species and more than 27 distinctive mutant and other genetically defined stocks. Included among the species maintained are P. californicus, P. leucopus, P. eremicus, P. aztecus, P. melanophrys as well as two subspecies each of P. maniculatus and P. polionotus and three inbred lines of P. leucopus. Among the mutant stocks are 17 with altered coat phenotypes, 3 with neurological symptoms, and 6 others with developmental/physiological effects. One of these is a line deficient in alcohol dehydrogenase that has been widely used in studies of alcohol metabolism. The stock center also supplies biological materials, including fresh, frozen, and preserved tissues; molecular probes, and libraries. The center functions as a clearinghouse for information regarding this genus by sponsoring an Internet database and the semi-annual Peromyscus Newsletter. The center maintains a collection of over 3,000 Peromyscus-related reprints of published articles, books, and journals-photocopies of which are available upon request. Continuation of the center is dependent upon significant external utilization, therefore potential users are encouraged to take advantage of this resource. Sufficient animals of the mutant types generally can be provided to initiate a breeding stock. Some what larger numbers, up to about 50 animals, can be provided from the wild-type stocks. A user fee…

New Science of Addiction: Genetics and the Brain
type: Resource
type: NamedIndividual
has db xref: nif-0000-00430
abbrev: New Science of Addiction
IAO_0000115: A physiologic and molecular look at drug addiction involving many factors including: basic neurobiology, a scientific examination of drug action in the brain, the role of genetics in addiction, and ethical considerations. Designed to be used by students, teachers and members of the public, the materials meet selected US education standards for science and health. Drug addiction is a chronic disease characterized by changes in the brain which result in a compulsive desire to use a drug. A combination of many factors including genetics, environment and behavior influence a person's addiction risk, making it an incredibly complicated disease. The new science of addiction considers all of these factors - from biology to family - to unravel the complexities of the addicted brain. * Natural Reward Pathways Exist in the Brain: The reward pathway is responsible for driving our feelings of motivation, reward and behavior. * Drugs Alter the Brain's Reward Pathway: Drugs work over time to change the reward pathway and affect the entire brain, resulting in addiction. * Genetics Is An Important Factor In Addiction: Genetic susceptibility to addiction is the result of the interaction of many genes. * Timing and Circumstances Influence Addiction: If you use drugs when you are an adolescent, you are more likely to develop lifetime addiction. An individual's social environment also influences addiction risk. * Challenges and Issues in Addiction: Addiction impacts society with many ethical, legal and social issues.

RNA Abundance Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-00133
has db xref: OMICS_00869
has db xref: r3d100000017
synonym: RNA Abundance Database
abbrev: RAD
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, Documented on March 24, 2014. A resource for gene expression studies, storing highly curated MIAME-compliant studies (i.e. experiments) employing a variety of technologies such as filter arrays, 2-channel microarrays, Affymetrix chips, SAGE, MPSS and RT-PCR. Data were available for querying and downloading based on the MGED ontology, publications or genes. Both public and private studies (the latter viewable only by users having appropriate logins and permissions) were available from this website. Specific details on protocols, biomaterials, study designs, etc., are collected through a user-friendly suite of web annotation forms. Software has been developed to generate MAGE-ML documents to enable easy export of studies stored in RAD to any other database accepting data in this format. RAD is part of a more general Genomics Unified Schema (http://gusdb.org), which includes a richly annotated gene index (http://allgenes.org), thus providing a platform that integrates genomic and transcriptomic data from multiple organisms. NOTE: Due to changes in technology and funding, the RAD website is no longer available. RAD as a schema is still very much active and incorporated in the GUS (Genomics Unified Schema) database system used by CBIL (EuPathDB, Beta Cell Genomics) and others. The schema for RAD can be viewed along with the other GUS namespaces through our Schema Browser.

La Jolla Interdisciplinary Neurosciences Center
type: Resource
type: NamedIndividual
has db xref: nif-0000-00436
synonym: La Jolla Interdisciplinary Neuroscience Center Core (Burnham-Salk-Scripps-UCSD)
abbrev: La Jolla Neuroscience Center Cores
IAO_0000115: Our NINDS Center Core Grant supports centralized resources and facilities shared by investigators with existing NINDS-funded research projects. Our Center is composed of three research cores, each of which will enrich the effectiveness of ongoing research, and promote new research directions. The three Core facilities support Electrophysiology, Neuropathology / Histology, and High-Throughput/High-Content Chemical and Genomic Library screening. By making these important Core Services available to the local Neuroscience community, the La Jolla Neurosciences Program hopes to promote the study of how the nervous system works and develop treatments for nervous system diseases. The cores and their services are available to La Jolla neuroscientists. Core services are available to NINDS-supported neuroscience projects from local investigators as well as young neuroscientists prior to obtaining their first NIH-funded grant. * Electrophysiology: SBMRI Electrophysiology ** The Electrophysiology Core consists of the Sanford-Burnham Electrophysiology Facility. This facility can perform patch-clamp intracellular and extracellular field recordings on a range of material including cultured cells and brain slices. The Sanford-Burnham facility emphasizes electrophysiological analysis of cultured cells and the detailed electrical properties of channels, receptors and recombinant proteins expressed in Xenopus oocytes or mammalian cells. * Neuropathology: UCSD Neuropathology ** The Neuropathology laboratory applies immunocytochemistry, neurochemistry, molecular genetics, transgenic models of disease, and imaging by scanning laser confocal microscopy to analysis of neurological disease in animal models. * Chemical Library Screening: SBIMR Assay Development, SBIMR Chemical Library Screening, SBIMR Cheminformatics, SBIMR High-content Screening ** The Chemical Library Screening core offers high-throughput screening (HTS) of biochemical and cell-based array using traditional HTS readouts and…

GeneCards
type: Resource
type: NamedIndividual
has db xref: nif-0000-02879
has db xref: OMICS_01652
has db xref: r3d100012015
synonym: GeneCards - The Human Gene Compendium
IAO_0000115: Database of human genes that provides concise genomic, proteomic, transcriptomic, genetic and functional information on all known and predicted human genes. Information featured in GeneCards includes orthologies, disease relationships, mutations and SNPs, gene expression, gene function, pathways, protein-protein interactions, related drugs and compounds and direct links to cutting edge research reagents and tools such as antibodies, recombinant proteins, clones, expression assays and RNAi reagents.

GeneDB
type: Resource
type: NamedIndividual
has db xref: nif-0000-02880
has db xref: r3d100010626
synonym: GDB
synonym: Gene DB
IAO_0000115: Database of genomes at various stages of completion, from early access to partial genomes with automatic annotation through to complete genomes with extensive manual curation. Its primary goals are: 1) to provide reliable access to the latest sequence data and annotation/curation for the whole range of organisms sequenced by the Pathogen group, and 2) to develop the website and other tools to aid the community in accessing and obtaining the maximum value from these data.

Scanalytics IPLab
type: Resource
type: NamedIndividual
has db xref: rid_000102
abbrev: IPLab
IAO_0000115: Image processing software package that provides scientific image acquisition, visualization, analysis and laboratory automation in single package. Allows users to acquire grayscale and color images from most video cameras, variety of cooled CCD digital cameras and high resolution flatbed scanners. Capable of analyzing image data in seven different data types, this program can calculate integrated intensity, mean, min, and max values plus several morphometric parameters on object regions within images., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

NIS-Elements Basic Research
type: Resource
type: NamedIndividual
has db xref: SciRes_000190
abbrev: NIS-Elements BR
IAO_0000115: Software tool for acquisition and device control for standard research applications, requiring four dimensional imaging. Provides access to advanced image capture, archiving, and analysis solutions that are easy-to-use and provide maximum workflow. Handles multi dimensional imaging with support for capture, display, data management, analysis and additional options for peripheral device control, and multi-dimensional acquisition. Provides advanced image processing options such as database capabilities and report generation, intensity over time measurement, and Extended Depth of Focus functionality.

CNS Forum
type: Resource
type: NamedIndividual
has db xref: nif-0000-00435
synonym: Lundbeck Institute CNS Forum
synonym: Lundbeck Institute CNSforum
abbrev: CNSforum
IAO_0000115: Forum within psychiatry and neurology aimed at providing updated evidence-based educational resources and information for health care professionals including an opportunity to exchange knowledge and experiences online. The CNSforum includes Educational resources, Clinical resources, Patient Websites, Publications, and a Community forum. Educational resources: * Brain Explorer - A graphical and educational presentation of the brain and the disorders affecting it, aimed at GPs and specialists in training. * Image Bank - A collection of CNS images for download and free use in presentations. Expert Talks Online presentations by leading experts on scientific topics. * Journal Links - A collection of links to websites of scientific journals in neurology and psychiatry. * Film Forum - Specialists discuss mainstream films with a psychiatric or neurological element from an educational point of view. Clinical resources: * Psychiatry Quality Measurement, PQM PQM is and electronic patient database/journal for use by psychiatrists. * Psychotropics - A database of psychotropic and neurological drugs. Rating scales Descriptions of and references to central scales used in psychiatry and neurology as well as an introduction to the topic. * Commented Articles - Commented articles written for CNSforum by leading international specialists. Patient Websites: * DepNet - An online community and information website for people affected by depression. * DementiaNet - An online community and information website for people affected by dementia and their relatives. * Publications (A catalogue of The Lundbeck Institute's publications on topics of clinical relevance in psychiatry and neurology.) * Institute Books, Institute Magazine Community forum: available only for former seminar participants and other members of The Lundbeck Institute Network., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

BINOCh
type: Resource
type: NamedIndividual
has db xref: OMICS_00500
synonym: Binding Inference from Nucleosome Occupancy Changes
synonym: Binding Inference from Nucleosome Occupancy Changes (BINOCh)
synonym: BINOCh - Binding Inference from Nucleosome Occupancy Changes
IAO_0000115: Software that infers the identity of transcription factors used to regulate cell response to stimulus or determine a program of differentiation. It uses genome wide information on enhancer proximal nucleosome occupancy, acquired using ChIP-seq targeting enhancer related histone modifications., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

GeneSpeed- A Database of Unigene Domain Organization
type: Resource
type: NamedIndividual
has db xref: nif-0000-02887
synonym: GeneSpeed Database
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Database and customized tools to study the PFAM protein domain content of the transcriptome for all expressed genes of Homo sapiens, Mus musculus, Drosophila melanogaster, and Caenorhabditis elegans tethered to both a genomics array repository database and a range of external information resources. GeneSpeed has merged information from several existing data sets including the Gene Ontology Consortium, InterPro, Pfam, Unigene, as well as micro-array datasets. GeneSpeed is a database of PFAM domain homology contained within Unigene. Because Unigene is a non-redundant dbEST database, this provides a wide encompassing overview of the domain content of the expressed transcriptome. We have structured the GeneSpeed Database to include a rich toolset allowing the investigator to study all domain homology, no matter how remote. As a result, homology cutoff score decisions are determined by the scientist, not by a computer algorithm. This quality is one of the novel defining features of the GeneSpeed database giving the user complete control of database content. In addition to a domain content toolset, GeneSpeed provides an assortment of links to external databases, a unique and manually curated Transcription Factor Classification list, as well as links to our newly evolving GeneSpeed BetaCell Database. GeneSpeed BetaCell is a micro-array depository combined with custom array analysis tools created with an emphasis around the meta analysis of developmental time series micro-array datasets and their significance in pancreatic beta cells.

AliView
type: Resource
type: NamedIndividual
has db xref: OMICS_05209
IAO_0000115: Software for aligning viewing and editing dna / aminiacid sequences, intuitive, fast and leightweight. It has been designed to meet the requirements of next generation sequencing era phylogenetic datasets.

bioDBcore
type: Resource
type: NamedIndividual
has db xref: nif-0000-24395
abbrev: BioDBCore
IAO_0000115: A community-defined, uniform, generic description of the core attributes of biological databases. The BioDBCore checklist is overseen by the International Society for Biocuration (ISB), in collaboration with the BioSharing forum. A catalogue of databases, described according to the BioDBcore guidelines, along with the standards used within them have been partly compiled with the support of Oxford University Press and Re3Data.org. Database providers are encouraged to either create or claim their BioDBCore entry and update it as appropriate., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

BioNumbers
type: Resource
type: NamedIndividual
has db xref: biotools:bionumbers
has db xref: nif-0000-24396
synonym: BioNumbers: The Database of Useful Biological Numbers
IAO_0000115: Database of key numbers in molecular and cell biology--the quantitative properties of biological systems of interest to computational, systems and molecular cell biologists. Contents of the database range from cell sizes to metabolite concentrations, from reaction rates to generation times, from genome sizes to the number of mitochondria in a cell. Along with the numbers, you'll find the relevant references to the original literature, useful comments, and related numbers. While always of importance to biologists, having numbers in hand is becoming increasingly critical for experimenting, modeling, and analyzing biological systems. BioNumbers was motivated by an appreciation of how long it can take to find even the simplest number in the vast biological literature. All numbers are taken directly from a literature source and that reference is provided with the number. BioNumbers is designed to be highly searchable and queries can be performed by keywords or browsed by menus. BioNumbers is a collaborative community platform where registered users can add content and make comments on existing data. All new entries and commentary are curated to maintain high quality.

Short Course on the Genetics and Epigenetics of Addiction National Institute on Drug Abuse: Archived Video
type: Resource
type: NamedIndividual
has db xref: nif-0000-00438
synonym: Genetics and Epigenetics of Addiction
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. An archived video on the web providing comprehensive and hands-on training in genetics and epigenetic methodology. The purpose of the course is to provide an introduction to approaches and tools for identifying genes that confer vulnerability to addiction and individual differences in responses to treatments. The course is targeted to those who are new to the field of addiction genetics. The course was held over 5 days with lectures and hands-on demonstrations given each day. Viewers of the course will gain familiarity with conceptual and practical approaches to complex disorders using relevant genetic and epigenetic databases, and appropriate statistical and empirical approaches. Topics covered Behavioral genetics, genetic epidemiology, twin and adoption studies, statistical genetic concepts and approaches for mapping complex traits, haplotype based approaches for association mapping, genome-wide scans for addictive disorders, application of linkage for mapping genes and genetic loci for addictive disorders, pharmacogenomics of treatment of addictive disorders, Baysian Methods for identifying gene-gene interactions, analysis of copy number variation, practical use of genetic databases, mapping of complex traits in mice, methods for analyzing gene expression, and methods for doing epigenetic analysis are covered. The course was held April 4, 2008, at the Bethesda North Marriott Hotel and Conference Center, 5701 Marinelli Road, Bethesda, MD 20852.

W3C Provenance Incubator Group Wiki
type: Resource
type: NamedIndividual
has db xref: nif-0000-00439
synonym: Provenance Incubator Group Wiki
synonym: W3C Provenance Incubator Group
abbrev: Provenance Incubator Group
IAO_0000115: Group to provide a state-of-the art understanding and develop a roadmap in the area of provenance for Semantic Web technologies, development, and possible standardization., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Centre for Modeling Human Disease Gene Trap Resource
type: Resource
type: NamedIndividual
has db xref: nif-0000-02891
synonym: Centre for Modeling Human Disease (CMHD) Gene Trap Resource
abbrev: CMHD Gene Trap Resource
IAO_0000115: Generate gene trap insertions using mutagenic polyA trap vectors, followed by sequence tagging to develop a library of mutagenized ES cells freely available to the scientific community. This library is searchable by sequence or key word searches including gene name or symbol, chromosome location, or Gene Ontology (GO) terms. In addition,they offer a custom email alert service in which researchers are able to submit search criteria. Researchers will receive automated e-mail notification of matching gene trap clones as they are entered into the library and database. The resource features the use of complementary second and third generation polyA trap vectors developed by the Stanford lab and the laboratory of Professor Yasumasa Ishida of the Nara Institute of Science and Technology (NAIST) in Japan to mutagenize murine embryonic stem (ES) cells. CMHD gene trap clones are distributed by the Canadian Mouse Mutant Repository(CMMR). Information about ordering, services, and pricing can be found on their web site (http://www.cmmr.ca/services/index.html)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

GenePaint E15 Atlas
type: Resource
type: NamedIndividual
has db xref: nif-0000-24447
synonym: GenePaint E15.5 Mouse Atlas
abbrev: GenePaint Map E15.5
IAO_0000115: Abbreviated reference atlas for the Embryonic 15.5 post conception day mouse. All sections were nissl stained and digitized. To assist in the initial identification of sites of gene expression sites, maps of brains are available for E15.5, P7 and the adult. These maps depict the boundaries of major brain regions (cortex, thalamus, striatum, globus pallidus, ventral striatum, septum, basal forebrain, hippocampus, midbrain, pons, medulla, cerebellum) and also show the more prominent nerve tracts. Maps are most efficiently used by placing the window depicting the map of interest next to the gene expression image. Browsing between planes of sectioning is permitted thus allowing the most appropriate plane to be selected. The annotation of anatomical details such as brain nuclei is currently beyond the scope of the GenePaint database. Hence, such information on the anatomy of the brain and embryo should be obtained from published atlases of mouse anatomy (Kaufman, 1995; Paxinos and Franklin, 2001; Jacobowitz and Abbott, 1997; Schambra et al., 1992; Valverde1998).

GenePaint P7 Atlas
type: Resource
type: NamedIndividual
has db xref: nif-0000-24449
synonym: GenePaint Mouse Brain Map P7
abbrev: GenePaint Map P7
IAO_0000115: Abbreviated reference atlas for the P56 mouse. All sections were nissl stained and digitized. To assist in the initial identification of sites of gene expression sites, maps of brains are available for E15.5, P7 and the adult. These maps depict the boundaries of major brain regions (cortex, thalamus, striatum, globus pallidus, ventral striatum, septum, basal forebrain, hippocampus, midbrain, pons, medulla, cerebellum) and also show the more prominent nerve tracts. Maps are most efficiently used by placing the window depicting the map of interest next to the gene expression image. Browsing between planes of sectioning is permitted thus allowing the most appropriate plane to be selected. The annotation of anatomical details such as brain nuclei is currently beyond the scope of the GenePaint database. Hence, such information on the anatomy of the brain and embryo should be obtained from published atlases of mouse anatomy (Kaufman, 1995; Paxinos and Franklin, 2001; Jacobowitz and Abbott, 1997; Schambra et al., 1992; Valverde1998).

GenePaint P56 Mouse Atlas
type: Resource
type: NamedIndividual
has db xref: nif-0000-24450
synonym: GenePaint Mouse Brain Map P56
abbrev: GenePaint Map P56
IAO_0000115: Abbreviated reference atlas for the P56 mouse. All sections were nissl stained and digitized. To assist in the initial identification of sites of gene expression sites, maps of brains are available for E15.5, P7 and the adult. These maps depict the boundaries of major brain regions (cortex, thalamus, striatum, globus pallidus, ventral striatum, septum, basal forebrain, hippocampus, midbrain, pons, medulla, cerebellum) and also show the more prominent nerve tracts. Maps are most efficiently used by placing the window depicting the map of interest next to the gene expression image. Browsing is permitted between planes of sectioning thus allowing the most appropriate plane to be selected. Abbreviations are found in a list accessed by clicking the see abbreviation link at the bottom of each map. Alternatively, passing the cursor directly across the abbreviation on the map will result in the appearance of the appropriate term in the rider on top of the map panel. The annotation of anatomical details such as brain nuclei is currently beyond the scope of the GenePaint database. Hence, such information on the anatomy of the brain and embryo should be obtained from published atlases of mouse anatomy (Kaufman, 1995; Paxinos and Franklin, 2001; Jacobowitz and Abbott, 1997; Schambra et al., 1992; Valverde1998).

Dana Foundation
type: Resource
type: NamedIndividual
has db xref: nif-0000-24463
synonym: The Dana Foundation
IAO_0000115: A private philanthropy with principal interests in brain science, immunology, and education. The portal provides general information about the brain and current brain research, links to validated sites related brain disorders, education resources and lesson plans, and support for the training of in-school arts specialists. The Dana Foundation science and health grants support brain research in neuroscience and immunology and their interrelationship in human health and disease. The grant sections include brain and immuno-imaging, clinical neuroscience research, human immunology and neuroimmunology. The Foundation also occasionally sponsors workshops and forums for working scientists, as well as offering funding for selected young researchers to continue their education or to attend seminars and workshops elsewhere.

TherMos
type: Resource
type: NamedIndividual
has db xref: OMICS_00498
IAO_0000115: Software used for estimating protein-DNA binding energies from in vivo binding profiles. It is a de novo motif discovery algorithm that exploits the information in transcription factor ChIP-seq or ChIP-exo datasets based on a more natural thermodynamic formalism., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

ANDES
type: Resource
type: NamedIndividual
has db xref: biotools:andes
has db xref: OMICS_01119
synonym: Statistical tools for the ANalyses of Deep Sequencing
synonym: Statistical tools for the Analyses of Deep Sequencing
synonym: Statistical tools for the Analyses of Deep Sequencing (ANDES)
IAO_0000115: Software library and a suite of applications, written in Perl and R, for deep sequencing statistical analyses.

Diseasome
type: Resource
type: NamedIndividual
has db xref: nif-0000-24580
synonym: Diseaseome
IAO_0000115: A disease / disorder relationships explorer and a sample of a map-oriented scientific work. It uses the Human Disease Network dataset and allows intuitive knowledge discovery by mapping its complexity. The Human Disease Network (official) dataset, a poster of the data and related book (Biology - The digital era, ISBN: 978-2-271-06779-1) are available. This kind of data has a network-like organization, and relations between elements are at least as important as the elements themselves. More data could be integrated to this prototype and could eventually bring closer phenotype and genotype. Results should be visual, but also printable. Creating posters can enhance collaborative work. It facilitates discussion and sharing of ideas about the data. This website initiative is an invitation to think about the benefits of networks exploration but above all it tries to outline future designs of scientific information systems.

Cognitive Atlas
type: Resource
type: NamedIndividual
has db xref: nif-0000-24591
synonym: cognitive atlas - a collaboratively developed cognitive science ontology
IAO_0000115: Knowledge base (or ontology) that characterizes the state of current thought in cognitive science that captures knowledge from users with expertise in psychology, cognitive science, and neuroscience. There are two basic kinds of knowledge in the knowledge base. Terms provide definitions and properties for individual concepts and tasks. Assertions describe relations between terms in the same way that a sentence describes relations between parts of speech. The goal is to develop a knowledge base that will support annotation of data in databases, as well as supporting improved discourse in the community. It is open to all interested researchers. A fundamental feature of the knowledge base is the desire and ability to capture not just agreement but also disagreement regarding definitions and assertions. Thus, if you see a definition or assertion that you disagree with, then you can assert and describe your disagreement. The project is led by Russell Poldrack, Professor of Psychology and Neurobiology at the University of Texas at Austin in collaboration with the UCLA Center for Computational Biology (A. Toga, PI) and UCLA Consortium for Neuropsychiatric Phenomics (R. Bilder, PI). Most tasks used in cognitive psychology research are not identical across different laboratories or even within the same laboratory over time. A major advantage of anchoring cognitive ontologies to the measurement level is that the strategy for determining changes in task properties is easier than tracking changes in concept definitions and usage. The process is easier because task parameters are usually (if not always) operationalized objectively, offering a clear basis to judge divergence in methods. The process is also easier because most tasks are based on prior tasks, and thus can more readily be considered descendants in a phylogenetic sense.

BLOCK-iT RNAi Designer
type: Commercial Organization
type: NamedIndividual
has db xref: rid_000099
IAO_0000115: A free tool to design effective RNAi molecules that includes the following target design options: Stealth RNAi siRNA, siRNA, miR RNAi, shRNA, siRNA to Stealth RNAi siRNA, and siRNA to shRNA.

Code Analysis Repository and Modelling for e-Neuroscience
type: Resource
type: NamedIndividual
has db xref: nif-0000-00442
has db xref: r3d100012284
synonym: Code Analysis Repository & Modelling for E-Neuroscience
abbrev: CARMEN
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE.Documented on January 14, 2023. Infrastructure for sharing data, tools and services, this virtual research environment (VRE) supports e-Neuroscience and is designed to provide services for data and processing of that data. While the system is initially focused on electrophysiology data (neural activity recordings are the primary data types), it is equally applicable to many domains outside neuroscience. The Portal Provides: * User login and customization. * Data upload/download. * Data handling including custom permissions for public, shared or private data. * The ability to invoke custom public, shared or private services that consume and produce data. For example, it would allow spike series to be run through a sorter, producing new data representing the sorted spikes. * The ability to host services written in a number of languages including, but not limited to Matlab, R, Python, Perl, Java. * A system to support metadata for data objects, which provides extensive support for entering metadata at the point of upload, and allows the generation of metadata from services to provide provenance information. * The ability to invoke additional visualization for the data, for example, via the Signal Data Explorer. A core part is the development of: (i) minimum reporting guidelines for annotation of data and other computational resources for the purpose of sharing, and; (ii) intermediate formats and APIs for translation between proprietary and bespoke data types. These recommendations are being implemented and the global community is encouraged both to engage in their specification and make use of them for their own data sharing systems. * MINI: Minimum Information about a Neuroscience Investigation - This framework represents the formalized opinion of the CARMEN consortium and its associates, and identifies the minimum reporting information required to support the use of electrophysiology in a neuroscience study, for submission to the…

PacmonSTR
type: Resource
type: NamedIndividual
has db xref: OMICS_05208
synonym: PacmonsTR - Tandem Repeat Detection for Long Read Sequence Data
IAO_0000115: Software that implements a reference-based probabilistic approach to identify the Tandem Repeat (TR) region and estimate the number of these TR elements in long DNA reads.

RMassBank
type: Resource
type: NamedIndividual
has db xref: OMICS_02657
IAO_0000115: Workflow software to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.

GraphPad Prism
type: Resource
type: NamedIndividual
has db xref: rid_000081
has db xref: SCR_015807
synonym: Graph Pad Prism
synonym: Graph pad Prism
synonym: Graph pad Prism 5
synonym: Graph Pad Prism 7
synonym: Graph pad Prism 8
synonym: Graphpad Prism
synonym: Graphpad Prism software
synonym: GraphPad Prism version 9.2.0
synonym: Prism 9.2.0
IAO_0000115: Statistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling.

FisHiCal
type: Resource
type: NamedIndividual
has db xref: OMICS_05207
synonym: FisHiCal: Iterative FISH-based Calibration of Hi-C Data
IAO_0000115: Software that integrates Hi-C and FISH data, offering a modular and easy-to-use tool for chromosomal spatial analysis.

Mutation Annotation and Genomic Interpretation
type: Resource
type: NamedIndividual
has db xref: OMICS_06145
synonym: MAGI - A tool for Mutation Annotation and Genomic Interpretation
abbrev: MAGI
IAO_0000115: A tool for annotating, exploring, and analyzing gene sets that may be associated with cancer.

Circleator
type: Resource
type: NamedIndividual
has db xref: OMICS_05206
synonym: Charm City Circleator
IAO_0000115: A Perl-based visualization software tool that generates circular figures of genome-associated data. Common uses of the tool include: * Displaying the sequence and/or genes in a GenBank flat file. * Highlighting differences and/or similarities in gene content between related organisms. * Comparing SNPs and indels between closely-related strains or serovars. * Comparing gene expression values across multiple samples or timepoints. * Visualizing coverage plots of RNA-Seq read alignments.

University of Southern California LONI Software
type: Resource
type: NamedIndividual
has db xref: nif-0000-00445
IAO_0000115: Portal provides list of software resources. LONI is leader in development of advanced computational algorithms and software for comprehensive and quantitative mapping of brain structure and function. Aims to encourage communication between users and LONI software engineers in order to improve effectiveness.

Predictions for Entire Proteomes
type: Resource
type: NamedIndividual
has db xref: biotools:predictprotein
has db xref: nif-0000-00136
has db xref: OMICS_07135
synonym: PredictProtein
IAO_0000115: Web application for sequence analysis and the prediction of protein structure and function. The user interface intakes protein sequences or alignments and returned multiple sequence alignments, motifs, and nuclear localization signals., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

GenProtEC
type: Resource
type: NamedIndividual
has db xref: nif-0000-02904
synonym: GenProtEC - E. coli genome and proteome database
synonym: GenProtEC- E. coli Genome and Proteome Database
IAO_0000115: GenProtEC is dedicated to the functions encoded by the Escherichia coli K-12 (strain MG1655) genome defined in the GenBank Accession No. NC_000913.2 deposit. All the data presented in GenProtEC is made easily accessible to the users through downloadable flat files in text format. GenProtEC presents information on the functions of E.coli K-12 MG1655 gene products from several points of view. E.coli proteins as single modules have been grouped in sequence similarity. Using the power of group membership of proteins of similar function, open reading frames within any group can be assigned the general function. In addition, the presence of domains of known function within E.coli proteins has been determined. Domain content permits annotation of some functional information to otherwise totally unknown sequences. The rich classification of cellular roles, MultiFun, has been applied, underlining the fact that many gene products have more than one cellular role. Our annotation work includes multiple types of information: 1. Sequence similarity to orthologues as defined by Darwin (start and end of aligned region, identity, and PAM distance). 2. Resolution of fused proteins into modular units with independent functions. 3. Identification of sequence similar protein groups within E. coli that are clustered by transitive relationships. The sequence similarity is limited to PAM 200 and an alignment of at least 83 amino acids. 4. Updated literature references. 5. Classification of gene products by their gene type and by their cellular role(s). The MultiFun classification system for cellular roles is used to assign gene products to one or more roles. MultiFun has been converted to Gene Ontology terms. 6. Familes of proteins related by structure and biochemical reaction mechanisms (work in progress). 7. SCOP superfamily identification and location (e.g. binding site domains) for E. coli proteins., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

IMEx - The International Molecular Exchange Consortium
type: Resource
type: NamedIndividual
has db xref: biotools:imex
has db xref: nif-0000-00447
has db xref: OMICS_01545
has db xref: r3d100010669
synonym: International Molecular Exchange Consortium
synonym: The International Molecular Exchange Consortium
abbrev: IMEx
IAO_0000115: Interaction database from international collaboration between major public interaction data providers who share curation effort and develop set of curation rules when capturing data from both directly deposited interaction data or from publications in peer reviewed journals. Performs complete curation of all protein-protein interactions experimentally demonstrated within publication and makes them available in single search interface on common website. Provides data in standards compliant download formats. IMEx partners produce their own separate resources, which range from all encompassing molecular interaction databases, such as are maintained by IntAct, MINT and DIP, organism-centric resources such as BioGrid or MPIDB or biological domain centric, such as MatrixDB. They have committed to making records available, via PSICQUIC webservice, which have been curated to IMEx rules and are available to users as single, non-redundant set of curated publications which can be searched at the IMEx website. Data is made available in standards-compliant tab-deliminated and XML formats, enabling to visualize data using wide range of tools. Consortium is open to participation of additional partners and encourages deposition of data, prior to publication, and will supply unique accession numbers which may be referenced within final article. Submitters may send their data directly to any of member databases using variety of formats, but should conform to guidelines as to minimum information required to describe data.

Islet Cell Resource Centers
type: Resource
type: NamedIndividual
has db xref: nif-0000-25418
abbrev: ICR
IAO_0000115: Group of 10 academic laboratories provide pancreatic islets of cGMP-quality to eligible investigators for use in FDA approved, IRB-approved transplantation protocols in which isolated human islets are transplanted into qualified patients afflicted with type 1 diabetes mellitus; optimize the harvest, purification, function, storage, and shipment of islets while developing tests that characterize the quality and predict the effectiveness of islets transplanted into patients with diabetes mellitus; and provide pancreatic islets for basic science studies. The centers are electronically linked through an Administrative and Bioinformatics Coordinating Center (ABCC). The ABCC manages a system with objectively defined criteria that establishes the order of priority for islet distribution. It also provides database and other informatics to track the utilization of pancreata and all distributed clinical grade islets for transplant and basic research, and supports the Islet Cell Resource Centers Consortium so that the research community has a single entry point to the program. Qualified researchers from domestic institutions may request islets by submitting a written application to the director of the ABCC. The ICRs will distribute Islets as appropriate for either clinical or basic science protocol use to eligible investigators who have received a favorable review and subsequent approval by the ICR Steering Committee (SC). The Administrative and Bioinformatics Coordinating Center (ABCC) manages the distribution according to a priority list. The ABCC will give preference to investigators who have peer-reviewed, NIH-funded research support.

GermOnline
type: Resource
type: NamedIndividual
has db xref: biotools:germonline
has db xref: nif-0000-02906
has db xref: r3d100010248
IAO_0000115: Cross-species microarray expression database focusing on high-throughput expression data relevant for germline development, meiosis and gametogenesis as well as the mitotic cell cycle. The database contains a unique combination of information: 1) High-throughput expression data obtained with whole-genome high-density oligonucleotide microarrays (GeneChips). 2) Sample annotation (mouse over the sample name and click on it) using the Multiomics Information Management and Annotation System (MIMAS 3.0). 3) In vivo protein-DNA binding data and protein-protein interaction data (available for selected species). 4) Genome annotation information from Ensembl version 50. 5) Orthologs are identified using data from Ensembl and OMA and linked to each other via a section in the report pages. The portal provides access to the Saccharomyces Genomics Viewer (SGV) which facilitates online interpretation of complex data from experiments with high-density oligonucleotide tiling microarrays that cover the entire yeast genome. The database displays only expression data obtained with high-density oligonucleotide microarrays (GeneChips)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Batch Oligo Selection Script
type: Resource
type: NamedIndividual
has db xref: OMICS_02334
abbrev: BOSS
IAO_0000115: Batch primer selection software program designed to select PCR oligos for gap closure for assemblies containing a large number of gaps. It will select oligos for gap closure of both contig and scaffold gaps.

Computational Neurobiology Laboratory at the Salk Institute
type: Resource
type: NamedIndividual
has db xref: nif-0000-24693
synonym: Computational Neurobiology Lab
IAO_0000115: The long range goal of this laboratory is to understand the computational resources of brains from the biophysical to the systems levels. The central issues being addressed are how dendrites integrate synaptic signals in neurons, how networks of neurons generate dynamical patterns of activity, how sensory information is represented in the cerebral cortex, how memory representations are formed and consolidated during sleep, and how visuo-motor transformations are adaptively organized. Additionally, new techniques have been developed for modeling cell signaling using Monte Carlo methods (MCell) and the blind separation of brain imaging data into functionally independent components (ICA).

GlycoMapsDB
type: Resource
type: NamedIndividual
has db xref: nif-0000-02913
synonym: GlycoMaps Database
abbrev: GlycoMaps DB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026. A data base system for the management of conformational maps and profiles, the system allows conformational maps to be archived in a standard format, and it provides search and comparison facilities. An interface to structures from Sweet-DB is implemented. GlycoMapsDB also offers scientists the possibility of adding their own publicized structures to the database via a web interface. GlycoMapsDB provides maps of 3D and 2D mono- and disaccharides. It provides users conformational information on carbohydrates and glycoproteins.

Gene Ontology
type: Resource
type: NamedIndividual
has db xref: biotools:go
has db xref: nif-0000-02915
has db xref: OMICS_02278
synonym: Gene Ontology Resource
synonym: GO
synonym: the Gene Ontology
IAO_0000115: Computable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases.

Blind Source Separation and Independent Component Analysis
type: Resource
type: NamedIndividual
has db xref: nif-0000-24771
synonym: BSS / ICA
synonym: BSS and ICA
synonym: ICA / BSS
abbrev: BSS/ICA
abbrev: ICA/BSS
IAO_0000115: Blind Source Separation and Independent Component Analysis (ICA) algorithms including: An efficient batch algorithm: JADE and Adaptive algorithms: relative gradient algorithms. Associated papers / documentation are included as well as thoughts on Multi-dimensional independent component analysis. * An efficient batch algorithm: JADE - For off-line ICA, an algorithm has been developed based on the (joint) diagonalization of cumulant matrices. "Good" statistical performance is achieved by involving all the cumulants of order 2 and 4 while a fast optimization is obtained by the device of joint diagonalization. JADE has been successfully applied to the processing of real data sets, such as found in mobile telephony and in airport radar as well as to bio-medical signals (ECG, EEG, multi-electrode neural recordings). The strongest point of JADE for applications of ICA is that it works off-the-shelf (no parameter tuning). They advocate using the code provided as a plug-in replacement for PCA (whenever one is willing to investigate if such a replacement is appropriate). The weakest point of the current implementation is that the number of sources (but not of sensors) is limited in practice (by the available memory) to something like 40 or 50 depending on your computer. The JADE algorithm was originally developed to process complex signals, motivated by applications to digital communications. Another implementation is now available which is tuned to process more efficiently real-valued signals. * Adaptive algorithms: relative gradient algorithms - For adaptive source separation, they have developed a class of equivariant algorithms. This means that their performance is independent of the mixing matrix. They are obtained as stochastic relative gradient algorithms. * Multi-dimensional independent component analysis - Performing ICA on ECG signals with the JADE algorithm, it was realized that an interesting extension of the notion of independent component analysis would be to co…

iontree
type: Resource
type: NamedIndividual
has db xref: biotools:iontree
has db xref: OMICS_02656
synonym: iontree: Data management and analysis of ion trees from ion-trap mass spectrometry
IAO_0000115: Software package that provides utility functions to manage and analyse MS2/MS3 fragmentation data from ion trap mass spectrometry. It was designed for high throughput metabolomics data with many biological samples and a large numer of ion trees collected. Tests have been done with data from low-resolution mass spectrometry but could be readily extended to precursor ion based fragmentation data from high resoultion mass spectrometry.

Mouse BIRN Atlasing Toolkit
type: Resource
type: NamedIndividual
has db xref: nif-0000-00039
synonym: MouseBIRN Atlasing Toolkit
abbrev: MBAT
IAO_0000115: Workflow environment bringing together heterogenous, online biological image resources, a user's image data and biological atlases in a concise, unified and intuitive workspace. The MBAT viewer displays multiple images on a single virtual canvas allowing easy side-by-side comparisons and image compositing. MBAT is written in Java so it is platform independent and is highly extensible through it's plugin architecture. MBAT integrates three distinct workspaces for online search, image alignment (registration) and image display: * Search Workspace: able to submit a query to multiple databases simultaneously and online literature searches. * Registration Workspace: performs 2D landmark based registration. * Viewer Workspace: displays & composites images and image volumes using high performance graphics hardware. * Atlas Viewer: allows navigation and interrogation of volumetric atlases. * Hierarchy Editor: create logical groupings of atlas labels.

Microcal Origin
type: Commercial Organization
type: NamedIndividual
has db xref: rid_000069
has db xref: SCR_016099
synonym: Origin Microcal software
abbrev: Origin
IAO_0000115: A complete graphing and data analysis software package that provides a suite of features catering to the needs of scientists and engineers. Main features: * Drag-and-drop import of data and images * Save import settings to a worksheet or external files for repeated use * Use saved settings to re-import files with a single click * Post-process imported data * Import Wizard with visual feedback * Handle non-standard files by programming

Temporal-Lobe: Hippocampal - Parahippocampal Neuroanatomy of the Rat
type: Resource
type: NamedIndividual
has db xref: nif-0000-24805
synonym: Parahippocampal hippocampal connectivity
synonym: Parahippocampal-hippocampal network
synonym: TEMPORAL-LOBE
abbrev: Temporal-lobe.com
IAO_0000115: Interactive diagram containing existing knowledge of hippocampal-parahippocampal connections in which any connection can be turned on or off at the level of cortical layers. It includes references for each connection.

Genomes Online Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02918
has db xref: r3d100010808
synonym: Genomes On Line Database (GOLD)
synonym: GOLD:Genomes Online Database
abbrev: GOLD
IAO_0000115: Database of information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. It also provides information related to organism properties such as phenotype, ecotype and disease. Both complete and ongoing projects, along with their associated metadata, can be accessed. Users can also register, annotate and publish genome and metagenome data.

Drug Information Portal
type: Resource
type: NamedIndividual
has db xref: nif-0000-24913
synonym: Drug Information Portal - Quick Access to Quality Drug Information
synonym: NLM Drug Information Portal
IAO_0000115: The NLM Drug Information Portal gives users a gateway to selected drug information from the U.S. National Library of Medicine and other key U.S. Government agencies. At the top of the page are links to individual resources with potential drug information, including summaries tailored to various audiences. Resources include the NLM search systems useful in searching for a drug, NLM research resources, resources organized by audience and class, and other NIH and government resources such as FDA and CDC. The search box in the middle of the page lets you search many of these resources simultaneously. More than 34,000 drugs can be searched using this facility. The portal covers drugs from the time they are entered into clinical trials (Clinicaltrials.gov) through their entry in the U.S. market place (Drugs@FDA). Many drugs in other countries are covered, but not as thoroughly as U.S. drugs. The PubMed link provides medical literature describing research, and TOXLINE provides toxicology literature. Resources such as MedlinePlus provide easy to read summaries of the uses and efficacy of a drug. You may search by a drug's trade name or generic name. For example, the trade name Advil and the generic name ibuprofen will retrieve the same drug record. As you type in a name, suggestions are given beneath the search box. A spell checker gives suggestions if the name is not found. You can find embedded portions of names by using an asterisk at the beginning and/or end of a search term. You can also search by the general Category of usage of a drug by checking that radio button. Suggestions are given as you type here too. Once a drug is found, a summary of the drug's type and usage is given, as well as links leading to further information at one of the portal's resources. Outside links open in a new window. Within a given drug record, you may click on the drug category and retrieve drugs with the same or similar uses. * View drug category descriptions. * View top By Name searches …

HSPH Trace Metals Laboratory
type: Resource
type: NamedIndividual
has db xref: nlx_156296
synonym: Harvard NIEHS Center for Environmental Health Trace Metals Lab
synonym: Trace Metals Laboratory (HSPH)
abbrev: HSPS Trace Metals Laboratory
IAO_0000115: Core facility that provides metals analytical capabilities to biomedical and non-biomedical researchers and serves as a source for study design consultation and sample QA/QC requirements. The transport, fate, exposure, and toxic effects of heavy metals is a primary focus of research at the Center. It operates as a modified fee-for-service laboratory. Researchers have the option of having the samples run by the Service staff, or of receiving instruction (for themselves or a doctoral or post doctoral trainee) on how to operate the analytical equipment and analyze their own samples. Both options have associated fees and, as with other services, facility access funds can be requested internal or external services when individual grant support is not yet available.

MicroVigene
type: Resource
type: NamedIndividual
has db xref: OMICS_00845
IAO_0000115: Automated software program for image analysis based on microarray based image application. Various output styles are available, including image overlay with warping and registration and scattered correlation plot with 2D or 3D spot profile. Outputs can be formatted in text, xml, excel, or custom format.

Phenoscape Knowledgebase
type: Resource
type: NamedIndividual
has db xref: nif-0000-24925
IAO_0000115: Knowledgebase that uses ontologies to integrate phenotypic data from genetic studies of zebrafish with evolutionary variable phenotypes from the systematic literature of ostariophysan fishes. Users can explore the data by searching for anatomical terms, taxa, or gene names. The expert system enables the broad scale analysis of phenotypic variation across taxa and the co-analysis of these evolutionarily variable features with the phenotypic mutants of model organisms. The Knowledgebase currently contains 565,158 phenotype statements about 2,527 taxa, sourced from 57 publications, as well as 38,189 phenotype statements about 4,727 genes, retrieved from ZFIN. 2013-01-26.

Marginalia Web Annotation
type: Resource
type: NamedIndividual
has db xref: nif-0000-02922
abbrev: Marginalia
IAO_0000115: Marginalia is an open source Javascript web annotation system that allows users of web applications to highlight text and write margin notes. Marginalia has been integrated into several web applications: * An extension to Moodle adds annotation to Moodle discussion forums. * A plug-in for Open Journal Systems allows readers to annotate journal articles. * Marginalia is part of the Bungeni parliamentary and legislative information system. * A stand-alone demo implementation provides a minimal sample implementation as a demonstration of how to integrate Marginalia with other web applications. The annotation feature supports recent versions of major browsers (Firefox, Safari, and IE), but works best and fastest in Firefox. The features are integrated into and work with a host web application with no need for special browser or other client software. Marginalia is the 2008 winner of the British Columbia Innovation Award in Educational Technology., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

FSL
type: Resource
type: NamedIndividual
has db xref: birnlex_2067
has db xref: nif-0000-00305
has db xref: SCR_007368
synonym: FMRIB Software Library
synonym: fMRIB Software Library
synonym: Functional Magnetic Resonance Imaging of the Brain Software Library
IAO_0000115: Software library of image analysis and statistical tools for fMRI, MRI and DTI brain imaging data. Include registration, atlases, diffusion MRI tools for parameter reconstruction and probabilistic taractography, and viewer. Several brain atlases, integrated into FSLView and Featquery, allow viewing of structural and cytoarchitectonic standard space labels and probability maps for cortical and subcortical structures and white matter tracts. Includes Harvard-Oxford cortical and subcortical structural atlases, Julich histological atlas, JHU DTI-based white-matter atlases, Oxford thalamic connectivity atlas, Talairach atlas, MNI structural atlas, and Cerebellum atlas.

National Natural Toxins Research Center
type: Resource
type: NamedIndividual
has db xref: nif-0000-24966
synonym: Viper Resource Center
abbrev: NNTRC
abbrev: VRC
IAO_0000115: Center to provide global research, training, and resources that will lead to the discovery of medically important toxins found in venoms. The Viper Resource Center (VRC) is located in the Natural Toxins Research Center at Texas A&M University-Kingsville.

Brigham Young University; Utah; USA
type: Organization
type: NamedIndividual
has db xref: nlx_156752
synonym: Brigham Young University
abbrev: BYU
IAO_0000115: Private, non-profit university in Utah. The university is a part of the Latter-day Saints Church Educational System.

American Physiological Society
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100005384
has db xref: grid.281274.a
has db xref: ISNI: 0000 0001 2243 2144
has db xref: nif-0000-00455
has db xref: Wikidata: Q3487625
synonym: APS - American Physiological Society
abbrev: APS
IAO_0000115: A nonprofit devoted to fostering education, scientific research, and dissemination of information in the physiological sciences. Founded in 1887 with 28 members, the APS now has over 10,500 members. Most members have doctoral degrees in physiology and/or medicine (or other health professions). APS is governed by an elected Council consisting of a President, President-Elect, Past President, and nine Councillors. The National headquarters of the Society is based in Bethesda, Maryland, on the campus of the Federation of American Societies for Experimental Biology (FASEB). The American Physiological Society Awards program demonstrates the Society's dedication to its members and biomedical research by recognizing the research efforts of outstanding APS members. Awards are offered by the Society and the various APS Sections. For questions regarding the Society awards (including Student awards), please send an email to awards_at_the-aps.org. For questions regarding the Section awards please contact the individual Sections directly www.the-aps.org/sections/.

HGNC
type: Resource
type: NamedIndividual
has db xref: biotools:genenames.org
has db xref: nif-0000-02955
has db xref: r3d100010901
synonym: HGNC - HUGO Gene Nomenclature Committee
synonym: HGNC Database
synonym: HUGO Gene Nomenclature Committee
synonym: HUGO symbols
synonym: Human Genome Organization Gene Symbols
IAO_0000115: Only worldwide authority that provides standardized nomenclature, i.e. gene names and symbols (short form abbreviations), for all known human genes, and stores all approved symbols in the HGNC database. Approved human gene nomenclature. Database of gene symbols and names. Manually curated genes into groups based on shared characteristics such as homology, function or phenotype. Data for protein-coding genes, pseudogenes and non-coding RNAs.

Primate Resource Referral Service
type: Resource
type: NamedIndividual
has db xref: nif-0000-24969
abbrev: PRRS
IAO_0000115: It provides the communications/database network needed for efficient acquisition and sharing of existing captive primates and primate-related resources by investigators and institutions both nationally and internationally. The overall goal of this service is to maximize the use of existing captive primates, thereby reducing the total number of primates needed for research, and in turn, helping to promote the conservation of primate populations in the wild. Services Provided PRRS services include 1) Referral Service, an immediate, staff-operated service designed to match investigator inquiries/requests to the available resource listings maintained in the PRRS master database; 2) CURRENT LISTINGS, a twice-monthly newsletter listing current availability of, as well as needs for, primates, tissues, equipment, and services; 3) ANNUAL RESOURCE GUIDE (ARG), an annual publication that lists subscribing suppliers of primates, laboratories, equipment, and commercial services such as transportation and quarantine facilities; and 4) Web site, an interactive site that includes the full text of CURRENT LISTINGS as well as online forms for posting resource availabilities/needs and listing updates, the current ARG, a diagram of primate taxonomy with illustrative photographs, online renewal and feedback forms, general service information, and links to other sites of interest to the primate research community. The PRRS also maintains a database of colonies, primates, and primate materials to which notices of availability and need can be referred. Services are available without charge to government-supported researchers and other scientists in the United States and abroad using primates in their work. Sponsors: The PRRS is made possible by grant RR-01240 from the National Center for Research Resources, National Institutes of Health.

Gramene
type: Resource
type: NamedIndividual
has db xref: biotools:gramene
has db xref: nif-0000-02926
has db xref: nlx_65829
has db xref: r3d100010856
synonym: GR GENE
synonym: GR PROTEIN
synonym: GR QTL
synonym: GR REF
synonym: Gramene: A Resource for Comparative Grass Genomics
synonym: RiceGenes
abbrev: GR
IAO_0000115: Curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. It currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database. In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data. Additionally you can access Gramene through an FTP site.

Greengenes
type: Resource
type: NamedIndividual
has db xref: nif-0000-02927
has db xref: OMICS_01512
has db xref: r3d100010549
IAO_0000115: Database that provides access to the current and comprehensive 16S rRNA gene sequence alignment for browsing, blasting, probing, and downloading. The data and tools can assist the researcher in choosing phylogenetically specific probes, interpreting microarray results, and aligning/annotating novel sequences. The 16S rRNA gene database provides chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. ARB users can use Greengenes to update local databases., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Database oDatabase of Predicted Subcellular Localization for Eukaryotic PDB Chainsf Predicted Subcellular Localization for Eukaryotic PDB Chains
type: Resource
type: NamedIndividual
has db xref: biotools:loc3d
has db xref: nif-0000-25200
synonym: LOC3d
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. LOC3d is a database of predicted subcellular localization for eukaryotic proteins of known 3-D structure taken from the Protein Databank. Subcellular localization is currently predicted using four different methods: predictNLS (nuclear localization signal), LOChom (using homology), LOCkey (using keywords) and LOC3d (neural network based prediction). The reported localization is based on the method which predicts localization of a given protein with the highest confidence. LOCtree is a novel system of support vector machines (SVMs) that predict the subcellular localization of proteins, and DNA-binding propensity for nuclear proteins, by incorporating a hierarchical ontology of localization classes modeled onto biological processing pathways. Biological similarities are incorporated from the description of cellular components provided by the gene ontology consortium (GO). GO definitions have been simplified and tailored to the problem of protein sorting. Technically the ontology has been implemented using a decision tree with SVMs as the nodes. LOCtree, was extremely successful at learning evolutionary similarities among subcellular localization classes and was significantly more accurate than other traditional networks at predicting subcellular localization. Whenever available, LOCtree also reports predictions based on the following: 1) Nuclear localization signals found by PredictNLS, 2) Localization inferred using Prosite motifs and Pfam domains found in the protein, and 3) SWISS-PROT keywords associated with a protein. Localization is inferred in the last two cases using the entropy-based LOCkey algorithm. Additional information can be found in the LOCtree manuscript and associated PredictNLS and LOCkey publications.

University of Chicago; Illinois; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100007234
has db xref: grid.170205.1
has db xref: ISNI:0000 0004 1936 7822
has db xref: nlx_50001
has db xref: Wikidata:Q131252
synonym: UChicago
synonym: University of Chicago
IAO_0000115: Private research university in Chicago, Illinois.

University of Cincinnati; Ohio; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100008102
has db xref: grid.24827.3b
has db xref: ISNI:0000 0001 2179 9593
has db xref: nlx_16657
has db xref: Wikidata:Q153265
abbrev: UC
IAO_0000115: Public research university in Ohio that offers degree programs in a variety of fields such as business, music and arts, and medical and human service.

GreenPhylDB
type: Resource
type: NamedIndividual
has db xref: biotools:greenphyldb
has db xref: nif-0000-02928
IAO_0000115: A database designed for plant comparative and functional genomics based on complete genomes. It comprises complete proteome sequences from the major phylum of plant evolution. The clustering of these proteomes was performed to define a consistent and extensive set of homeomorphic plant families. Based on this, lists of gene families such as plant or species specific families and several tools are provided to facilitate comparative genomics within plant genomes. The analyses follow two main steps: gene family clustering and phylogenomic analysis of the generated families. Once a group of sequences (cluster) is validated, phylogenetic analyses are performed to predict homolog relationships such as orthologs and ultraparalogs.

Exonic Splicing Enhancer Finder
type: Resource
type: NamedIndividual
has db xref: nif-0000-25204
synonym: ESEfinder
IAO_0000115: A web-based analysis service for identifying exonic splicing enhancers in eukaryotic genes. ESEfinder accept sequences in the FASTA format. A typical mammalian gene is composed of several relatively short exons that are interrupted by much longer introns. To generate correct mature mRNAs, the exons must be identified and joined together precisely and efficiently, in a process that requires the coordinated action of five small nuclear (sn)RNAs (U1, U2, U4, U5 and U6) and more than 60 polypeptides. The inaccurate recognition of exon/intron boundaries or the failure to remove an intron generates aberrant mRNAs that are either unstable or code for defective or deleterious protein isoforms. Exonic enhancers are thought to serve as binding sites for specific serine/arginine-rich (SR) proteins, a family of structurally related and highly conserved splicing factors characterized by one or two RNA-recognition motifs (RRM) and by a distinctive C-terminal domain highly enriched in RS dipeptides (the RS domain). The RRMs mediate sequence-specific binding to the RNA, and so determine substrate specificity, whereas the RS domain appears to be involved mainly in protein-protein interactions. SR proteins bound to ESEs can promote exon definition by directly recruiting the splicing machinery through their RS domain and/or by antagonizing the action of nearby silencer elements. Sponsors: ESEfinder is supported by the Cold Spring Harbor Laboratory.

Basic4Cseq
type: Resource
type: NamedIndividual
has db xref: OMICS_05202
synonym: Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
IAO_0000115: An R/Bioconductor package for basic filtering, analysis and subsequent near-cis visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.

Protein Information Resource
type: Resource
type: NamedIndividual
has db xref: biotools:pir
has db xref: nif-0000-00143
has db xref: nif-0000-21327
synonym: PIR - Protein Information Resource
abbrev: PIR
IAO_0000115: Integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies. Provides databases and protein sequence analysis tools to scientific community, including Protein Sequence Database which grew out from the Atlas of Protein Sequence and Structure. Conducts research in biomedical text mining and ontology, computational systems biology, and bioinformatics cyberinfrastructure. In 2002 PIR, along with its international partners, EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics), were awarded a grant from NIH to create UniProt, a single worldwide database of protein sequence and function, by unifying the PIR-PSD, Swiss-Prot, and TrEMBL databases. Currently, PIR major activities include: i) UniProt (Universal Protein Resource) development, ii) iProClass protein data integration and ID mapping, iii) PRO protein ontology, and iv) iProLINK protein literature mining and ontology development. The FTP site provides free download for iProClass, PIRSF, and PRO.

rDock
type: Resource
type: NamedIndividual
has db xref: OMICS_03835
IAO_0000115: A fast and versatile Open Source docking software program that can be used to dock small molecules against proteins and nucleic acids.

A.nnotate
type: Commercial Organization
type: NamedIndividual
has db xref: nif-0000-02933
synonym: A.nnotate.com
IAO_0000115: An online annotation, collaboration and indexing system for documents and images, supporting PDF and MS Office formats. Instead of emailing different versions of a document back and forth you can all comment on a single read-only copy online. Unlike online word processors, the document is displayed in high quality with fonts and layout just like the printed version. It is easy to use and runs in all common web browsers, with no software or plugins to install. Hosted solutions are available for individuals and workgroups. For enterprise users the full system is available for local installation. Special discounts apply for educational use. The FREE hosted solution offers single-user accounts for uploading up to 30 pages per month. Documents can be shared with any number of annotators.

hot scan
type: Resource
type: NamedIndividual
has db xref: biotools:hot_scan
has db xref: OMICS_05200
synonym: hot_scan
IAO_0000115: A free software to detect genomic regions unusually rich in translocation breakpoints. More generally, it may be used to detect a region that is unusually rich in a given character of a binary sequence.

University of Coimbra; Coimbra; Portugal
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100007474
has db xref: grid.8051.c
has db xref: ISNI:0000 0000 9511 4342
has db xref: nlx_155543
has db xref: Wikidata:Q368643
synonym: Universidade de Coimbra
synonym: University of Coimbra
abbrev: UC
IAO_0000115: Public university in Coimbra, Portugal that offers degree programs in a variety of fields including law, medicine, science and technology, pharmaceuticals, and sports sciences.

GenomEUtwin
type: Resource
type: NamedIndividual
has db xref: nif-0000-25218
synonym: GenomeEUtwin
synonym: GenomEUtwin Project
synonym: Studies of European Volunteer Twins to Identify Genes Underlying Common Diseases
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Study of genetic and life-style risk factors associated with common diseases based on analysis of European twins. The population cohorts used in the Genomeutwin study consist of Danish, Finnish, Italian, Dutch, English, Australian and Swedish twins and the MORGAM population cohort. This project will apply and develop new molecular and statistical strategies to analyze unique European twin and other population cohorts to define and characterize the genetic, environmental and life-style components in the background of health problems like obesity, migraine, coronary heart disease and stroke, representing major health care problems worldwide. The participating 8 twin cohorts form a collection of over 0.6 million pairs of twins. Tens of thousands of DNA samples with informed consents for genetic studies of common diseases have already been stored from these population-based twin cohorts. Studies targeted to cardiovascular traits are now being undertaken in MORGAM, a prospective case-cohort study. MORGAM cohorts include approximately 6000 individuals, drawn from population-based cohorts consisting of more than 80 000 participants who have donated DNA samples.

National Academies Press
type: Organization
type: NamedIndividual
has db xref: grid.431670.7
has db xref: ISNI: 0000 0004 0466 615X
has db xref: nif-0000-25219
has db xref: Wikidata: Q6970107
synonym: NAP
IAO_0000115: The National Academies Press (NAP) was created by the National Academies to publish the reports issued by the National Academy of Sciences, the National Academy of Engineering, the Institute of Medicine, and the National Research Council, all operating under a charter granted by the Congress of the United States. The NAP publishes more than 200 books a year on a wide range of topics in science, engineering, and health, capturing the most authoritative views on important issues in science and health policy. The institutions represented by the NAP are unique in that they attract the nation's leading experts in every field to serve on their award-winning panels and committees. This is the right place for definitive information on everything from space science to animal nutrition. Many books can be read on-line for free. NAP also offers many titles in electronic Adobe PDF format. Hundreds of these books can be downloaded for free by the chapter or the entire book, while others are available for purchase. Sponsors: This resource is supported by The National Academies.

Drosophila Genomics Resource Center
type: Serves Drosophila research community by collecting and distributing DNA clones and vectors, cell lines, developing and testing genomics technologies.
type: NamedIndividual
has db xref: nif-0000-25420
synonym: Drosophila Genomics Resource Center at Indiana University
abbrev: DGRC
IAO_0000115: Serves Drosophila research community by collecting and distributing DNA clones and vectors; collecting and distributing Drosophila cell lines; developing and testing genomics technologies for use in Drosophila and assisting members of the research community in their use.

International HapMap Project
type: Resource
type: NamedIndividual
has db xref: biotools:int_hapmap_project
has db xref: nif-0000-02940
has db xref: OMICS_00273
has db xref: r3d100011835
synonym: HapMap Project
abbrev: HapMap
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A multi-country collaboration among scientists and funding agencies to develop a public resource where genetic similarities and differences in human beings are identified and catalogued. Using this information, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. All of the information generated by the Project will be released into the public domain. Their goal is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. HapMap project related data, software, and documentation include: bulk data on genotypes, frequencies, LD data, phasing data, allocated SNPs, recombination rates and hotspots, SNP assays, Perlegen amplicons, raw data, inferred genotypes, and mitochondrial and chrY haplogroups; Generic Genome Browser software; protocols and information on assay design, genotyping and other protocols used in the project; and documentation of samples/individuals and the XML format used in the project.

General Clinical Research Centers Program
type: Resource
type: NamedIndividual
has db xref: nif-0000-25308
synonym: General Clinical Research Centers
synonym: General Clinical Research Centers (GCRC)
abbrev: GCRC
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Through the General Clinical Research Centers (GCRC) program, NCRR funds a national network that provides settings for medical investigators to conduct safe, controlled, state-of-the-art, in-patient and out-patient studies of both children and adults. GCRCs also provide infrastructure and resources that support several career development opportunities.

Tribolium castaneum Genome Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-25607
synonym: Tribolium
IAO_0000115: This portal provides information about the Tribolium castabeum Genome Project. The Tribolium castaneum genome sequence and its analysis has been published in Nature, two companion journal issues (IBMB and DGE) and numerous other publications listed below. The red flour beetle, Tribolium castaneum, a common pest that is also a genetic model for the Coleoptera. The genome has been sequenced to 7-fold coverage using a whole genome shotgun approach and assembled using the HGSC's assembly engine, Atlas, with methods employed for the Drosophila pseudoobscura genome assembly. Approximately 90% of the genome sequence has been mapped to chromosomes in collaboration with Dick Beeman (USDA ARS) and Sue Brown (Kansas State University). Access to the Data :- Genome Assembly: The long term home of the Tribolium genome is Beetlebase. Tcas 3.0 is now available in GenBank and on our FTP site. Note there are no restrictions of any kind on the Tribolium data as it has been published. Version 2 of the assembly, Tcas_2.0 is available for download using the FTP Data link in the sidebar. The assembly is described in detail in the README in that directory. T.cas_1.0 was a preliminary genome assembly that did not include large insert paired end information and has been moved to a previous assemblies folder. A genboree browser of the Tcas2.0 sequence is available here: There are also links to the genboree browser from the blast results (at the bottom of each reported HSP) if you use the blast server on this page. The original linear scaffold file, Tcas2.0/linearScaffolds/Tcas20050914-genome, posted on the ftp site did not include singleton contigs from the assembly and thus did not fully reflect the tribolium genome sequence, missing ~4.4Mb of sequence in 1860 contigs and reptigs or approximately 2.5% of the assembled sequence. A corrected Tcas20051011-genome file containing these missing sequences is now available on the ftp site. The blast databases have also been updated to reflect this c…

OpenSesame
type: Resource
type: NamedIndividual
has db xref: rid_000039
IAO_0000115: Software for the rapid development of psychological and neuroscientific experiments.

Sal-Site
type: Resource
type: NamedIndividual
has db xref: nif-0000-25309
synonym: Ambystoma Resources for Model Amphibians Database
IAO_0000115: Portal that supports Ambystoma-related research and educational efforts. It is composed of several resources: Salamander Genome Project, Ambystoma EST Database, Ambystoma Gene Collection, Ambystoma Map and Marker Collection, Ambystoma Genetic Stock Center, and Ambystoma Research Coordination Network.

Neurogenetics and Behavior Center
type: Resource
type: NamedIndividual
has db xref: nif-0000-25310
synonym: NBC
IAO_0000115: This center provides routine behavioral/cognitive testing of mice with phenotypes that are expressed as a consequence of alterations at the level of gene function, and that are relevant to basic neuroscience and to animal models of neurological and psychiatric disorders. Current Research Behavioral testing within the center involves a collaborative component in which mice provided by users are assessed for behavioral/cognitive functions. All research includes behavioral assessment of a variety of genetically altered mice provided by users. Services Provided The objective of the center is to provide a link between genetic and molecular analysis of neural function and the study of integrative systems and clinical conditions through behavioral assessment of animal models, and mouse behavioral phenotypes generated by genetic modification. Sponsors: This resource is supported by the National Center of Research Resources (Grant Number: P40 RR017688).

SMART Video-tracking
type: Commercial Organization
type: NamedIndividual
has db xref: rid_000052
synonym: Panlab SMART video tracking system
synonym: SMART Video tracking
abbrev: SMART
IAO_0000115: Software for the automated evaluation of behavior in a range of pre-clinical and neuroscience applications in basic and clinical psychopharmacology. Applications include phenotype characterization and studying the behavioral effects of pharmacologic substances.

VIPERdb
type: Resource
type: NamedIndividual
has db xref: biotools:viperdb
has db xref: nif-0000-03630
has db xref: nif-0000-25311
has db xref: r3d100012362
has db xref: SCR_007970
synonym: Virus Particle ExploreR
IAO_0000115: Database for icosahedral virus capsid structures. The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. In addition, all virus capsids are placed in a single icosahedral orientation convention, facilitating comparison between different structures. The web site includes powerful search utilities , links to other relevant databases, background information on virus capsid structure, and useful database interface tools. It is an information source for the analysis of high resolution virus structures. VIPERdb is a one-stop site dedicated to helping users around the world examine the many icosahedral virus structures contained within the Protein Data Bank (PDB) by providing them with an easy to use database containing current data and a variety of analytical tools. Sponsors: VIPERdb is funded by the NIH., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

BiGGR
type: Resource
type: NamedIndividual
has db xref: OMICS_02655
synonym: BiGGR - Constraint based modeling in R using metabolic reconstruction databases
IAO_0000115: Software package that provides an interface to simulate metabolic reconstruction from the BiGG database and other metabolic reconstruction databases. The package facilitates flux balance analysis (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs.

Virtual Physiological Human Network of Excellence
type: Resource
type: NamedIndividual
has db xref: nif-0000-25315
synonym: VPH NoE
IAO_0000115: The VPH NoE is a project which aims to help support and progress European research in biomedical modeling and simulation of the human body. This project will improve our ability to predict, diagnose and treat disease, and have a dramatic impact on the future of healthcare, the pharmaceutical and medical device industries. The VPH Network of Excellence (VPH NoE) is designed to foster, harmonize and integrate pan-European research in the field of i) patient-specific computer models for personalised and predictive healthcare and ii) ICT-based tools for modeling and simulation of human physiology and disease-related processes. The main objectives of the VPH Network of Excellence are to support the: :- Coordination of research portfolios of VPH NoE partners through initiation of Exemplar integrative research projects that encourage inter-institution and interdisciplinary VPH research; :- Integration of research infrastructures of VPH NoE partners through development of the VPH ToolKit: a shared and mutually accessible source of research equipment, managerial and research infrastructures, facilities and services; :- Development of a portfolio of interdisciplinary training activities including a formal consultation on, and assessment of, VPH careers; :- Establishment of a core set of VPH-related dissemination and networking activities which will engage everyone from partners within the VPH NoE/other VPH projects, to national policy makers, to the public at large; :- Creation of Industrial, Clinical and Scientific Advisory Boards that will jointly guide the direction of the VPH NoE and, through consultation, explore the practical and legal options for real and durable integration within the VPH research community; :- Implementation of key working groups that will pursue specific issues relating to VPH, notably integrating VPH research worldwide through international physiome initiatives. Finally, by involving clinical and industrial stakeholders, VPH NoE also plans to lay a…

mzR
type: Resource
type: NamedIndividual
has db xref: OMICS_02654
synonym: mzR - parser for netCDF mzXML mzData and mzML and mzIdentML files
IAO_0000115: Software that provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files.

PAPi
type: Resource
type: NamedIndividual
has db xref: OMICS_02653
synonym: PAPi - Predict metabolic pathway activity based on metabolomics data
synonym: Pathway Activity Profiling
IAO_0000115: An R package for predicting the activity of metabolic pathways based solely on a metabolomics data set containing a list of metabolites identified and their respective abundances in different biological samples. PAPi generates hypothesis that improves the final biological interpretation.

Health Protection Agency Culture Collections
type: Resource
type: NamedIndividual
has db xref: nlx_152376
synonym: Public Health England Culture Collections
IAO_0000115: Archival database of cell lines and microbial strains. Maintained by Public Health England, the database is used by scientists to determine the effects of various substances on human cells as well as for controls for diagnostic and antimicrobial susceptibility tests.

Human Tissue and Organ for Research Resource (HTORR)
type: Resource
type: NamedIndividual
has db xref: nif-0000-25417
synonym: Human Tissue Organ Resource for Research
synonym: Human Tissues and Organs for Research
synonym: Human Tissues and Organs for Research (HTOR)
synonym: Human Tissues Organs for Research
abbrev: HTORR
IAO_0000115: NDRI’s Human Tissue and Organs for Research Resource (HTORR) Program has been funded by the National Institutes of Health (NIH) for over 30 consecutive years to support research programs across multiple disciplines. It is through the HTORR program that NDRI provides academic biomedical investigators with donated normal and diseased human tissues and organs recovered from a diverse donor pool using customized procurement, processing, and preservation and distribution protocols. Our HTORR Program supports academic biomedical research investigators needs by providing: Access to a wide array of human biospecimens from any body system * Customized procurement in a variety of preservation formats including fresh, frozen, and fixed suitable for various analytical techniques * Reduced costs for tissue procurement * Technical support to design your studies utilizing human biospecimens * Letters of support and budgetary information for grant applications

pNovo+
type: Resource
type: NamedIndividual
has db xref: biotools.pNovo_3
has db xref: OMICS_02470
IAO_0000115: A de novo peptide sequencing algorithm using complementary higher-energy collisional dissociation (HCD) and electron transfer dissociation (ETD) tandem mass spectra.

WormAtlas
type: Resource
type: NamedIndividual
has db xref: nif-0000-00098
has db xref: nif-0000-25470
has db xref: SCR_007295
synonym: Worm Image Database
synonym: WormImage
IAO_0000115: Anatomical atlas about structural anatomy of Caenorhabditis elegans. Provides simple interface allowing user to easily navigate through every anatomical structure of worm. Contains set of images which can be sorted by different characteristics: sex, genotype, age, body portion or tissue type. Includes links to other major worm websites and databases. Application for viewing and downloading thousands of unpublished electron micrographs and associated data. These images have been generated by several labs in the C. elegans community, including the MRC, the Hall lab (Center for C. elegans Anatomy), and the Culotti and Riddle labs.

Annotation Ontology
type: Resource
type: NamedIndividual
has db xref: nif-0000-02943
synonym: annotation-ontology
synonym: AO - Annotation Ontology
abbrev: AO
IAO_0000115: Provides vocabulary for performing several types of annotation - comment, entities annotation (or semantic tags), textual annotation (classic tags), notes, examples, erratum... - on any kind of electronic document (text, images, audio, tables...) and document parts. AO is not providing any domain ontology but it is fostering the reuse of the existing ones for not breaking the principle of scalability of the Semantic Web.

HCV Databases
type: Resource
type: NamedIndividual
has db xref: nif-0000-02944
synonym: HCV Database
synonym: Hepatitis C Virus (HCV) Database Project
synonym: Hepatitis C Virus Database
synonym: Hepatitis C Virus Database Project
synonym: Hepatitis C Virus Databases
IAO_0000115: The Hepatitis C Virus (HCV) Database Project strives to present HCV-associated genetic and immunologic data in a user-friendly way, by providing access to the central database via web-accessible search interfaces and supplying a number of analysis tools.

National Resource Center for Cephalopods
type: Resource
type: NamedIndividual
has db xref: nif-0000-25474
abbrev: NRCC
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. The center serves the biomedical research community's increased needs for alternative invertebrate models by maintaining a consistent year-round supply of live cephalopod mollusks. These animals are suitable for a wide range of physiological and molecular biological investigations. Investigations are being conducted in the area of life history related to improved animal husbandry. Further studies focus on improving culture system design through development of computer automation and innovative water filtration technology. Current biomedical research on cephalopods includes neurophysiology of the giant axon; anatomy and neurophysiology of the equilibrium receptor organ as a comparative model of the vestibular system of invertebrates; chemoreception, basic nutrition, and protein metabolism; cellular receptor function; and brain, behavior, and learning. Services Provided: The center has built a computer-automated, environmentally controlled, recirculating seawater laboratory for the purpose of culturing cephalopods. The tank systems can be used to conduct a variety of experiments never before possible with cephalopods. Visiting researchers have access to dedicated facilities, including wet and dry laboratory space, office space, computer support and accommodations, as well as priority access to all available live animal resources. Off-site investigators can have live animals, dissected animal tissues/body fluids from all life stages, and a variety of molecular reagents (gene libraries and clones) delivered year-round. Staff expertise and an extensive literature library are available. All life stages of the squid (Sepioteuthis lessoniana) and the common cuttlefish (Sepia officinalis) are available year-round from laboratory culture populations. The sepiolid squid (Euprymna scolopes) can also be cultured on request. The squid Lolliguncula brevis is available year-round from local waters; the squids Lolig…

SPSS
type: Resource
type: NamedIndividual
has db xref: rid_000042
has db xref: SCR_017473
synonym: IBM SPSS Statistics:International Business Machines SPSS Statistics
synonym: IBM SPSS v16
synonym: IBM SPSS v17
synonym: IBM SPSS v18
synonym: Statistical Package for the Social Sciences
IAO_0000115: Software package used for interactive, or batched, statistical analysis in social science, health sciences and marketing. Software platform offers advanced statistical analysis, a library of machine-learning algorithms, text analysis, open-source extensibility, integration with big data and deployment into applications.Versions that were produced by SPSS Inc. before the IBM acquisition (Versions 18 and earlier) would be given origin or publisher of SPSS Inc. in Chicago.

Tuschl Laboratory: RNA Molecular Biology
type: Resource
type: NamedIndividual
has db xref: nif-0000-25546
synonym: Tuschl Lbaoratory
IAO_0000115: RNA is not only a carrier of genetic information, but also a catalyst and a guide for sequence-specific recognition and processing of other RNA molecules. This lab investigates the regulatory mechanisms of RNA interference, RNA-mediated translational control, and nuclear pre-mRNA splicing. Classical and combinatorial biochemical techniques are used to analyze the function of the RNA- and protein-components involved in those processes.

SharedCopy
type: Resource
type: NamedIndividual
has db xref: nif-0000-02946
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 12, 2017. Web application for annotation and collaboration on web pages. Its features include the ability to highlight words, comment, and share annotated copies of the web page that can be annotated by other users.

Patterns of Gene Expression in Drosophila Embryogenesis
type: Resource
type: NamedIndividual
has db xref: nif-0000-25550
has db xref: r3d100011327
synonym: BDGP Embryonic Expression Patterns
abbrev: BDGP insitu
IAO_0000115: Database of embryonic expression patterns using a high throughput RNA in situ hybridization of the protein-coding genes identified in the Drosophila melanogaster genome with images and controlled vocabulary annotations. At the end of production pipeline gene expression patterns are documented by taking a large number of digital images of individual embryos. The quality and identity of the captured image data are verified by independently derived microarray time-course analysis of gene expression using Affymetrix GeneChip technology. Gene expression patterns are annotated with controlled vocabulary for developmental anatomy of Drosophila embryogenesis. Image, microarray and annotation data are stored in a modified version of Gene Ontology database and the entire dataset is available on the web in browsable and searchable form or MySQL dump can be downloaded. So far, they have examined expression of 7507 genes and documented them with 111184 digital photographs.

HERVd - Human Endogenous Retrovirus database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02953
synonym: HERVd
IAO_0000115: HERVd is compiled from the human genome nucleotide sequences obtained mostly in the Human Genome Projects. We created a relatively simple and fast environment for screening human genome for Human endogenous retroviruses ( HERVs). The HERV database now contains retroviruses from more than 90 % of the human genome. Retroviral genomes or parts of their genomes are present in the DNA of many organisms. Studies of endogenous retroviral nucleotide sequences have become an important part of contemporary retrovirology as well as of molecular and cellular biology and genomics. Human endogenous retroviruses (HERVs) are of special interest also because their expression may be associated with several diseases, including cancer. Various groups of HERVs have been reported in the human genome. Their number can range from one copy to many thousand copies.

GenWay Biotech
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_152375
synonym: GenWay Biotech Inc
IAO_0000115: Commercial supplier of antibodies, reagents, PCR kits, and other materials for scientific research.

Support-of-PDF-annotations
type: Resource
type: NamedIndividual
has db xref: nif-0000-02947
synonym: How to express and exchange annotations
abbrev: Support of PDF annotations
IAO_0000115: Wiki that provides a listing (and associated links) of various formats to store and export annotations. Apparently everyone uses his own proprietary format to store and export annotations. The FDF format (or better its XML variant XFDF) is or was used by Acrobat to store form values and annotations, but third-party implementations focus on the forms-part of FDF instead of the annotations-part. * XML Forms Data Format Specification (XFDF) 2.0 (2007). * iText classes (no full FDF/XFDF implementation) ** FdfReader ** FdfWriter ** XfdfReader * The commercial software Adobe Digital Editions explicitly supports external annotations. The FAQ says Digital Editions supports bookmarks, highlights, and text notes via its bookmarks panel. These annotations are stored in an open XML format separately from publications to enable seamless annotation across PDF- and EPUB-based publications. They will set the stage for future social networking features (such as sharing annotations within a community of readers). * Okular has its own annotation exchange format, similar to PDF annotation (comparison is needed) ** internal API documentation ** There is no file format documentation, but the source code is mainly in the methods AnnotationUtils storeAnnotation and Annotation store * Xournal is open source and allows some annotation, but its PDF reading ability is very limited. It also uses its own format to store annotations * Mendeley supports annotations, which can be synced independent from the PDF files they refer to, and exported together with PDFs. There is no documentation of the API and format they use to exchange annotations. * Evernote is worth a view. But proprietary and no Linux client. * iAnnotate seems to be popular on the iPad - can it export and import annotations? In which format? There is a good article by Scott McLeod with screenshots about his use of iAnnotate and Evernote to take notes (June 15, 2010). http://blogs.edweek.org/edweek/LeaderTalk/2010/06/tools_for_school…

Toolbox at the European Bioinformatics Institute
type: Resource
type: NamedIndividual
has db xref: nif-0000-25553
synonym: EBI Bioinformatics Tools
IAO_0000115: The European Bioinformatics Institute (EBI) toolbox area provides a comprehensive range of tools for the field of bioinformatics. These are subdivided into categories in the left menu for convenience. EBI has developed a large number of very useful bioinformatics tools. A few examples include: - Similarity & Homology - the BLAST or FASTA programs can be used to look for sequence similarity and infer homology. - Protein Functional Analysis - InterProScan can be used to search for motifs in your protein sequence. - Proteomic Services NEW - UniProt DAS server allows researchers to show their research results in the context of UniProtKB/Swiss-Prot annotation. - Sequence Analysis - ClustalW2 a sequence alignment tool. - Structural Analysis - MSDfold can be used to query your protein structure and compare it to those in the Protein Data Bank (PDB). - Web Services - provide programmatic access to the various databases and retrieval/analysis services EBI provides. - Tools Miscellaneous - Expression Profiler a set of tools for clustering, analysis and visualization of gene expression and other genomic data. Sponsors: This resource is sponsored by EBI.

IgBLAST
type: Resource
type: NamedIndividual
has db xref: biotools:igblast
has db xref: nif-0000-25554
has db xref: OMICS_06083
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE.Documented on January 4,2023. IgBLAST was developed at NCBI to facilitate analysis of immunoglobulin V region sequences in GenBank. In addition to performing a regular BLAST search, IgBLAST has several additional functions: - Reports the germline V, D and J gene matches to the query sequence. - Annotates the immunoglobulin domains (FWR1 through FWR3). - Matches the returned hits (for databases other than germline genes) to the closest germline V genes, making it easier to identify related sequences. - Reveals the V(D)J junction details such as nucleotide homology between the ends of V(D)J segments and N nucleotide insertions. D and J gene reporting is only for nucleotide sequence search and requires a stretch of five or more nucleotide identity between the query and D or J genes. Sponsors: This resource is supported by the National Center for Biotechnology Information, a division of the U.S. National Library of Medicine.

CBS Prediction Servers
type: Resource
type: NamedIndividual
has db xref: nif-0000-25555
IAO_0000115: A portal to the on-line prediction services at Center for Biological Sequence Analysis. All of the servers are available as interactive input forms, and most of the servers are also available as stand-alone software packages with the same functionality. Ready-to-ship packages exist for the most common UNIX platforms. In addition, for some servers, programmatic access is provided in the form of SOAP-based Web Services.

COnsensus-DEgenerate Hybride Oligonucleotide Primers
type: Resource
type: NamedIndividual
has db xref: nif-0000-25557
synonym: CODEHOP
IAO_0000115: This COnsensus-DEgenerate Hybrid Oligonucleotide Primer (CODEHOP) strategy has been implemented as a computer program that is accessible over the World-Wide Web and is directly linked from the BlockMaker multiple sequence alignment site for hybrid primer prediction beginning with a set of related protein sequences. This is a new primer design strategy for PCR amplification of unknown targets that are related to multiply-aligned protein sequences. Each primer consists of a short 3' degenerate core region and a longer 5' consensus clamp region. Only 3-4 highly conserved amino acid residues are necessary for design of the core, which is stabilized by the clamp during annealing to template molecules. During later rounds of amplification, the non-degenerate clamp permits stable annealing to product molecules. The researchers demonstrate the practical utility of this hybrid primer method by detection of diverse reverse transcriptase-like genes in a human genome, and by detection of C5 DNA methyltransferase homologs in various plant DNAs. In each case, amplified products were sufficiently pure to be cloned without gel fractionation. Sponsors: This work was supported in part by a grant from the M. J. Murdock Charitable Trust and by a grant from NIH. S. P. is a Howard Hughes Medical Institute Fellow of the Life Sciences Research Foundation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Brazilian Ministry of Science Technology and Innovation
type: NamedIndividual
has db xref: nlx_155569
synonym: Ministry of Science and Technology (Brazil)
synonym: Ministry of Science Technology and Innovation (Brazil)
synonym: Ministério da Ciência
synonym: Ministério da Ciência e Tecnologia - Brazil
synonym: Tecnologia e Inovação
abbrev: MCT
abbrev: MCTI

Computational Biology Center
type: Resource
type: NamedIndividual
has db xref: nif-0000-25560
synonym: cBio
IAO_0000115: Computational biology research at Memorial Sloan-Kettering Cancer Center (MSKCC) pursues computational biology research projects and the development of bioinformatics resources in the areas of: sequence-structure analysis; gene regulation; molecular pathways and networks, and diagnostic and prognostic indicators. The mission of cBio is to move the theoretical methods and genome-scale data resources of computational biology into everyday laboratory practice and use, and is reflected in the organization of cBio into research and service components ~ the intention being that new computational methods created through the process of scientific inquiry should be generalized and supported as open-source and shared community resources. Faculty from cBio participate in graduate training provided through the following graduate programs: * Gerstner Sloan-Kettering Graduate School of Biomedical Sciences * Graduate Training Program in Computational Biology and Medicine Integral to much of the research and service work performed by cBio is the creation and use of software tools and data resources. The tools that we have created and utilize provide evidence of our involvement in the following areas: * Cancer Genomics * Data Repositories * iPhone & iPod Touch * microRNAs * Pathways * Protein Function * Text Analysis * Transcription Profiling

Dystonia Medical Research Foundation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100001595
has db xref: grid.433991.5
has db xref: ISNI: 0000 0001 0497 8290
has db xref: nif-0000-00464
abbrev: DMRF
IAO_0000115: Founded in 1976, the Dystonia Medical Research Foundation (DMRF) is a 501(c)3 organization dedicated to serving all people with dystonia and their families. Since its inception, the DMRF has grown from a small family-based foundation into a dynamic membership-driven organization led by a Board of Directors and network of volunteers with personal connections to dystonia. Because dystonia hits so close to home for our directors and volunteers, the DMRF leadership is motivated by an unrelenting drive to find a cure and an unwavering commitment to serving people affected by dystonia. Dystonia Medical Research Foundation (DMRF) prides itself on a long history of supporting dystonia research. Always the primary goal of the DMRF, research has led to a better understanding of dystonia as well as to breakthroughs in genetics and therapeutics.The funding which researchers obtain from the DMRF usually serves as seed money before generating even greater funding from the National Institutes of Health.Beyond the funding of research, the scientific program of the DMRF is multi-faceted, encompassing workshops, a residency elective program, and international medical symposiums, all to further the understanding of dystonia.

Centre for Vision Research
type: Resource
type: NamedIndividual
has db xref: nif-0000-25614
synonym: CVR
IAO_0000115: The Centre for Vision Research focuses on interdisciplinary research into human and machine vision and visual processes, into vision's interactions with other senses and with motor and cognitive processes, and in applications such as visually-guided robotics or clinical diagnosis and treatment. The Centre for Vision Research includes the following major research themes: - Human Visual Performance - Visual Human-Computer Interaction, Graphics and Virtual Reality - Visual Psychophysics - Eye Movements and Hand-Eye Coordination - Computational Modeling and Computer Vision - Electrophysiology - Clinical and Developmental Studies - Brain Imaging

HemBase
type: Resource
type: NamedIndividual
has db xref: nif-0000-02949
synonym: Hembase
IAO_0000115: Database designed for web-based examination of the human erythroid transcriptome. The database is organized to provide a cytogenetic band position, a unique name as well as a concise annotation for each entry. Search queries may be performed by name, keyword or cytogenetic location. Search results are linked to primary sequence data and three major human genome browsers for access to information considered current at the time of each search. Hembase provides interested scientists and clinical hematologists with a genome-based approach toward the study of erythroid biology. Red blood cells in the circulation arise from hematopoietic stem cells that proliferate as erythroid progenitors and differentiate into erythroid precursor cells in response to the hormone erythropoietin. Messenger RNA was isolated from those cells and used to generate gene libraries. Sequencing several thousand expressed sequence tags (EST) from those libraries was then performed. Those EST and sequences encoding several hundred additional genes with known expression in erythroid cells are compiled here as a database of human erythroid gene activity. The database is organized and linked according to the location of these sequences within the human genome., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026.

Psychophysics Toolbox
type: Resource
type: NamedIndividual
has db xref: rid_000041
synonym: Psychtoolbox
synonym: Psychtoolbox-3
abbrev: PTB
abbrev: PTB-2
abbrev: PTB-3
IAO_0000115: A free set of Matlab and GNU/Octave functions for vision research. It makes it easy to synthesize and show accurately controlled visual and auditory stimuli and interact with the observer.

OBD-PKB Interface
type: Resource
type: NamedIndividual
has db xref: nif-0000-25570
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This interface is for exploring data collected as part of the NIF Neurodegenerative Disease Ontology project. Not generally intended for public consumption yet, but people are welcome to look - large caveat emptor applies. Sponsors: This resource is part of the NIF project.

Pathway Genomics
type: Resource
type: NamedIndividual
has db xref: nif-0000-25571
synonym: Pathway
IAO_0000115: The mission of Pathway Genomics is to empower you with the most secure, comprehensive and affordable personal genomic information available and to become your partner in utilizing that information to improve your health and wellness. Pathway is the only DNA testing service with an on-site federal and state CLIA-licensed laboratory. This means it offers: - Better Science: Its certified geneticists are on-staff and on-site in our own state-of-the-art laboratory in California. Their 10,600 square foot, high-complexity CLIA licensed lab facility is equipped with the latest high-throughput robotics and Affymetrix, Illumina and Sequenom genotyping equipment. As scientists committed to staying on the cutting-edge, they diligently monitor all new developments in the rapidly evolving DNA research field allowing us to provide you immediate access to more meaningful markers than any other DNA testing firm. - Better Security: Because Pathway Genomics has its own laboratory, your DNA never leaves the building, and is never shared with third parties. At Pathway Genomics the integrity of your genetic material and information are protected. Instead, enjoy the security of our proprietary DNA Lockbox. Everyone has the right to know the secrets hidden within their own DNA. That's why Pathway has created the most secure, comprehensive and affordable way to unlock those secrets. This way you can: - Identify genetic health and drug response - Personalize your medical care - Help your doctor help you - Uncover your ancestral path - Explore the traits that make you unique With Personal DNA Testing, you can take preventative steps to improve your future, and even extend your life. Pathway Genomics provides cutting-edge research and easy-to-read scientific information customized for you, and you alone, based on your genes and your lifestyle. For the first time in human history, modern science has made it possible for you to learn your genetic predisposition for more than 90 diseases and cond…

Retina Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-25587
synonym: GENSAT - Retina Project
synonym: GENSAT Retina Project
synonym: Retina Project from GENSAT
synonym: The Retina Project
synonym: The Retina Project from GENSAT
IAO_0000115: Collection of images from cell type-specific protein expression in retina using BAC transgenic mice. Images from cell type-specific protein expression in retina using BAC transgenic mice from GENSAT project.

Special Mouse Strains Resource
type: Resource
type: NamedIndividual
has db xref: nif-0000-25593
synonym: Special Mouse Strains Resource (SMSR)
abbrev: SMSR
IAO_0000115: Resource of special strains of mice that are valuable tools for genetic analysis of complex diseases. They include panels of recombinant inbred (RI) and chromosome substitution (CS) strains.

COV2HTML
type: Resource
type: NamedIndividual
has db xref: OMICS_01302
IAO_0000115: An interactive web interface addressed to biologists, allowing both coverage visualization and analysis of NGS alignments performed on prokaryotic organisms (bacteria and phages). Its strength is to make NGS analysis without software installation, login or long training period.

New England National Primate Research Center
type: Resource
type: NamedIndividual
has db xref: nif-0000-25596
abbrev: NERPRC
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. A U.S. Regional Primate Research Center that focuses on AIDS, cancer, neuropsychiatric disorders, drug addiction, and neurodegenerative disease. The Division of Primate Resources provides researchers with the services and facilities to support biomedical research. It offers a broad spectrum of services ranging from analysis of tissue specimens to partnership investigations with leading biomedical research institutions. Outside investigators have access to tissue specimens, organs, blood, skeletal structures, and viral specimens. Services include veterinary services, animals and animal care, surgical and radiographic services, timed mating, biocontainment, pathology services, and professional and technical expertise. Additional diagnostic and research services at NEPRC include testing for antiviral antibodies, DNA cloning, and DNA sequencing. The colony of nine species includes rhesus macaques and other Old World monkeys and New World species including the common marmoset and squirrel monkey. Other species can be obtained. Animals with exceptional characteristics (specific-pathogen-free, timed pregnancy, surgically altered, etc.) can be made available if needed. Scientists wishing to conduct research at the center must have projects reviewed and approved by the center animal allocation committee.

Plant Metabolic Network
type: Resource
type: NamedIndividual
has db xref: nif-0000-25602
synonym: Plant Biochemical Pathway Databases
IAO_0000115: Collaborative project to bring together biochemical pathway databases and research communities focused on plant metabolism. Used to build broad network of plant metabolic pathway databases. Central feature of PMN is PlantCyc, comprehensive plant biochemical pathway database, containing curated information from literature and computational analyses about genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism.

Human Gene and Protein Database (HGPD)
type: Resource
type: NamedIndividual
has db xref: nif-0000-02956
synonym: HGPD
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.The Human Gene and Protein Database presents SDS-PAGE patterns and other informations of human genes and proteins. The HGPD was constructed from full-length cDNAs. For conversion to Gateway entry clones, we first determined an open reading frame (ORF) region in each cDNA meeting the criteria. Those ORF regions were PCR-amplified utilizing selected resource cDNAs as templates. All the details of the construction and utilization of entry clones will be published elsewhere. Amino acid and nucleotide sequences of an ORF for each cDNA and sequence differences of Gateway entry clones from source cDNAs are presented in the GW: Gateway Summary window. Utilizing those clones with a very efficient cell-free protein synthesis system featuring wheat germ, we have produced a large number of human proteins in vitro. Expressed proteins were detected in almost all cases. Proteins in both total and supernatant fractions are shown in the PE: Protein Expression window. In addition, we have also successfully expressed proteins in HeLa cells and determined subcellular localizations of human proteins. These biological data are presented on the frame of cDNA clusters in the Human Gene and Protein Database. To build the basic frame of HGPD, sequences of FLJ full-length cDNAs and others deposited in public databases (Human ESTs, RefSeq, Ensembl, MGC, etc.) are assembled onto the genome sequences (NCBI Build 35 (UCSC hg17)). The majority of analysis data for cDNA sequences in HGPD are shared with the FLJ Human cDNA Database (http://flj.hinv.jp/) constructed as a human cDNA sequence analysis database focusing on mRNA varieties caused by variations in transcription start site (TSS) and splicing.

Honey Bee Genome Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-25604
synonym: Honey Bee
IAO_0000115: The HGSC has sequenced the honey bee, Apis mellifera. The version 4.0 assembly was released in March 2006 and published in October 2006. The genome sequence is being upgraded with additional sequence coverage. The honey bee is important in the agricultural community as a producer of honey and as a facilitator of pollination. It is a model organism for studying the following human health issues: immunity, allergic reaction, antibiotic resistance, development, mental health, longevity and diseases of the X chromosome. In addition, biologists are interested in the honey bee's social organization and behavioral traits. This project was proposed to the HGSC by a group of dedicated insect biologists, headed by Gene Robinson. Following a workshop at the HGSC and a honey bee white paper, the HGSC began the project in 2002. A 6-fold coverage WGS, BAC sequence from pooled arrays, and an initial genome assembly (Amel_v1.0) were released beginning in 2003. This has been a challenging project with difficulty in recovering AT-rich regions. The WGS data had lower coverage in AT-rich regions and BAC data from clones showed evidence of internal deletions. Additional reads from AT enriched DNA addressed these underrepresented regions. The current assembly Amel_4.0 was produced with Atlas and includes 2.7 million reads (1.8 Gb) or 7.5x coverage of the (clonable) genome. About 97% of STSs, 98% of ESTs, and 96% of cDNAs are represented in the 231 Mb assembly. About 2,500 reads were also produced from a strain of Africanized honey bee and SNPs were extracted. These were released in dbSNP and the NCBI Trace Archive. Analysis of the genome by a consortium of 20 labs has been completed. This produced a gene list derived from five different methods melded through the GLEAN software. Publications include a main paper in Nature and up to forty companion papers in Genome Research and Insect Molecular Biology. Sponsors: Sequencing of the honey bee is jointly funded by National Human Genome Resea…

GenScript
type: Organization
type: NamedIndividual
has db xref: nlx_152374
synonym: GenScript USA
synonym: GenScript USA Inc
IAO_0000115: Commercial organization which provides life science services and products to researchers. They specialize in gene synthesis, peptide, protein, antibody and preclinical drug development service.

Wasserman Lab Online Software Tools
type: Resource
type: NamedIndividual
has db xref: nif-0000-25613
synonym: Wasserman Software
IAO_0000115: This portal leads to the numerous Wasserman Lab online software tools available for use. The following are list of active Software tools available: - ConSite: Transcription factor binding site detection using phylogenetic footprinting - dbMTN: Multiple Tissue Northern Blot Comparison Tool - Gene Set Builder: A tool for collation, curation and distribution of sets of genes - The Gene Characterization Index: a bioinformatics method for scoring the extent to which a protein-encoding gene is functionally described - JASPAR: Transcription Factor Binding Profile Database - MSCAN: Algorithm that detects clusters of transcription factor binding sites in genomic sequences - NHRscan: A computational predictor of nuclear hormone receptor binding sites - oPOSSUM: Web-based analysis of over-represented transcription factor binding sites - ORCA: Transcription factor binding site detection using phylogenetic footprinting (alternative to ConSite) - OrthoSeq: Alignment of DNA sequences - PAZAR: An open-access system for the collection and dissemination of regulatory sequence annotation - Phylofoot: Tools for phylogenetic footprinting - RAVEN: Regulatory analysis of Variation in ENhancers - SAGE2Splice: A tool that uses unmapped SAGE tags to predict novel splice junctions in the genome - TFBS: Perl modules for transcription factor binding site detection and analysis - TFCat: TFCat is a catalog of mouse and human TFs based on a reliable core collection of annotations obtained by expert review of the scientific literature. - TFe: An online encyclopedic collection of well-studied transcription factor proteins in the human, mouse, and rat genomes - Ulysses: Protein Interactions Conserved Across Evolution

HIV Molecular Immunology Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02965
synonym: Human Immunodeficiency Virus Molecular Immunology Database
IAO_0000115: An annotated, searchable collection of HIV-1 cytotoxic and helper T-cell epitopes and antibody binding sites, plus related tools and information. The goal of this database is to provide a comprehensive listing of defined HIV epitopes. These data are also printed in the HIV Molecular Immunology compendium, which is updated yearly and provided free of charge to scientific researchers, both by online download and as a printed copy. The data included in this database are extracted from the HIV immunology literature. HIV-specific B-cell and T-cell responses are summarized and annotated. Immunological responses are divided into three sections, CTL (CD8+), T helper (CD4+), and antibody. Within these sections, defined epitopes are organized by protein and binding sites within each protein, moving from left to right through the coding regions spanning the HIV genome. We include human responses to natural HIV infections, as well as vaccine studies in a range of animal models and human trials. Responses that are not specifically defined, such as responses to whole proteins or monoclonal antibody responses to discontinuous epitopes, are summarized at the end of each protein sub-section. Studies describing general HIV responses to the virus, but not to any specific protein, are included at the end of each section. The annotation includes information such as cross-reactivity, escape mutations, antibody sequence, TCR usage, functional domains that overlap with an epitope, immune response associations with rates of progression and therapy, and how specific epitopes were experimentally defined. Basic information such as HLA specificities for T-cell epitopes, isotypes of monoclonal antibodies, and epitope sequences are included whenever possible. All studies that we can find that incorporate the use of a specific monoclonal antibody are included in the entry for that antibody. A single T-cell epitope can have multiple entries, generally one entry per study. Finally, tables and maps o…

Neuroscience Information Framework
type: Resource
type: NamedIndividual
has db xref: biotools:neuroscinfframework
has db xref: nif-0000-25673
has db xref: OMICS_01190
has db xref: r3d100010106
synonym: neuinfo
synonym: neuinfo.org
synonym: NIF
IAO_0000115: Framework for identifying, locating, relating, accessing, integrating, and analyzing information from neuroscience research. Users can search for and add neuroscience-related resources at NIF portal and receive and RRID to track and cite resources within scientific manuscripts.

Addiction Research GPCR Assay Bank
type: Resource
type: NamedIndividual
has db xref: nif-0000-25722
synonym: GPCR Assay Bank
IAO_0000115: Describes data from and access to permanent cell lines containing beta-arrestin fluorescent protein biosensors. This assay Bank provides plasmids, cells lines, and resulting data to the NIDA/NIH funded research community in order to better understand and combat addiction.

ORNIS
type: Resource
type: NamedIndividual
has db xref: nif-0000-25776
IAO_0000115: ORNIS is a database of bird specimens as well as a portal to connect the academic and museum communities involved with studying birds. This project expands on existing infrastructure developed for distributed mammal (MaNIS), amphibian and reptile (HerpNet), and fish (FishNet) databases. Over 5 million bird specimens are housed in North American collections, documenting the composition, distribution, ecology, and systematics of the world's estimated 10,000-16,000 bird species. Millions of additional observational records are held in diverse data sets. ORNIS addresses the urgent call for increased access to these data in an open and collaborative manner, and involves development of a suite of online software tools for data analysis and error-checking. This project expands on existing infrastructure developed for distributed mammal (MaNIS), amphibian and reptile (HerpNet), and fish (FishNet) databases. Improved access to avian data sets will allow predictive uses to reveal patterns and processes of evolutionary and ecological phenomena that have not been apparent heretofore. Along with similar infrastructures for other vertebrate groups, it also will enable detailed and synthetic knowledge of the earth's biodiversity for tracking climate change, emerging diseases (e.g., West Nile Virus), and other conservation challenges for species in the 21st century.

Neuroscience Education Resources Virtual Encycloportal
type: Resource
type: NamedIndividual
has db xref: nif-0000-25827
abbrev: NERVE
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. Society for Neuroscience (SfN) provides this Web site, Neuroscience Education Resources Virtual Encycloportal (NERVE), to advance neuroscience teaching and educational efforts. SfN is a nonprofit association of more than 38,000 researchers and professionals, believes K-12 educators and vital partners for engaging the next generation of researchers. NERVE gives access to information and tools for teaching about the nervous system and related health issues. The goal of NERVE is to provide a gateway to credible information from government, nonprofit and other respected sources. Society scientists and educators have reviewed information for appropriateness but responsibility for content remains that of the originating author or organizations. NERVE gives access to information and tools for teaching about the nervous system and related health issues.

CODEHOP
type: Resource
type: NamedIndividual
has db xref: biotools:codehop
has db xref: OMICS_02339
synonym: CODEHOP: COnsensus-DEgenerate Hybrid Oligonucleotide Primers
synonym: COnsensus-DEgenerate Hybrid Oligonucleotide Primers
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.Service to design PCR primers from protein multiple sequence alignments. NOTICE: This version of CODEHOP is no longer maintained.

Schizophrenia Research Forum
type: Resource
type: NamedIndividual
has db xref: nif-0000-00154
synonym: Schziophrenia Research Forum - A Catalyst for Creative Thinking
abbrev: SRF
IAO_0000115: The mission of the SRF is to help in the search for causes, treatments, and understanding of the devastating disease of schizophrenia. Our goal is to foster collaboration among researchers by providing an international online forum where ideas, research news, and data can be presented and discussed. The website is intended to bring together scientists working specifically on schizophrenia, scientists researching related diseases, and basic scientists whose work can shed light on these diseases. In this way, we hope that the Schizophrenia Research Forum will be a catalyst for creative thinking in the quest to understand a deeply complex disease. It is our goal to create and maintain up-to-date content of the highest quality. The website is free of charge to users, independent of industry sponsorship, and open to the public. Though geared toward researchers, we welcome other visitorspeople with mental illnesses, families, the media, and others who need accurate information on research into schizophrenia. We do, however, require that users who wish to post comments and other materials be registered members. All such materials are subject to approval by the editorial team. As a forum, we encourage participation and welcome feedback from the community.

Development of a Specific-Pathogen-Free Baboon Colony
type: Resource
type: NamedIndividual
has db xref: nif-0000-25871
abbrev: Development of a SPF Baboon Colony
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Program developing a self-sustaining colony of baboons free of all known herpesviruses, four retroviruses, and SV40 for research. When the program is fully developed, they will provide healthy, behaviorally normal, SPF baboons that are free of all known herpes viruses, four retroviruses, and SV40. To accomplish this goal, the center has established in collaboration with co-investigators and consultants serological and PCR tests for each of the 11 target viruses. These baboon viruses include six herpesviruses (analogs of human HSV, VZV, CMV, HHV6, EBV, and HHV8), four retroviruses (simian foamy virus, SRV/D, SIV, and STLV), and SV40. Twenty-four infant baboons are being recruited into the SPF program in each of the first five years, for a final total of at least 66 SPF baboons. All infants will be repeatedly tested for each of the target viruses. At one month of age, larger social groups of 4-6 SPF animals are formed. Beginning at 2-3 years of age, SPF animals will be integrated into larger socially compatible groups. These groups will eventually mature into breeding harems of SPF animals. This approach provides infants with age-matched companions for socialization during their early period of development, minimizes opportunities for transmission of viruses to the infants from adult animals, and allows for the simultaneous elimination of many different viruses from SPF animals.

CNVassoc
type: Resource
type: NamedIndividual
has db xref: OMICS_02609
synonym: CNVassoc: Association analysis of CNV data
IAO_0000115: Software package that carries out association analysis of common copy number variants in population-based studies. It includes functions for analysing association under a series of study designs (case-control, cohort, etc), using several dependent variables (class status, censored data, counts) as response, adjusting for covariates and considering various inheritance models. It also includes functions for inferring copy number (CNV genotype calling). Various classes and methods for generic functions (print, summary, plot, anova, ... ) have been created to facilitate the analysis.

PRO
type: Resource
type: NamedIndividual
has db xref: OMICS_06200
synonym: Protein Ontology
IAO_0000115: An ontological representation of protein-related entities, explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. PRO encompasses three sub-ontologies: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp).

University of Cologne; Cologne; Germany
type: Organization
type: NamedIndividual
has db xref: grid.6190.e
has db xref: ISNI:0000 0000 8580 3777
has db xref: nlx_14953
has db xref: Wikidata:Q54096
synonym: Universitat zu Koln
synonym: University of Cologne
abbrev: UoC
IAO_0000115: Public university in Germany that offers degrees in law, management and business, the arts and humanities, and human sciences.

HIV Resistance Mutation Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02963
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.The HIV Resistance Mutation Database is a resource that allows users to download HIV sequences and information on HIV drug resistance and mutations. Users must download the data from either of two files available on the site, as the online portion of the database is no longer available. The system requires Mac OS9 to work. The DATABASES folder contains the current versions of 2 databases copied from resdb: BestDefined, and resistrelated. The BestDefined database is a list of the Brander epitopes. The resistrelated database is a compilation of HIV drug resistance mutations. The Bib and biblio files are the associated references for these databases. The RESIST_HTML folder contains the html files used by the resistance database web site.

British Heart Foundation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100000274
has db xref: grid.452924.c
has db xref: ISNI: 0000 0001 0540 7035
has db xref: nlx_82345
has db xref: Wikidata: Q4970039
abbrev: BHF
IAO_0000115: British charity and fundraiser for cardiovascular research.

HIV Sequence Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02967
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. HIV Sequence Database is a database of annotated HIV sequences, plus a variety of tools and information for researchers studying HIV and SIV. The main aim of this website is to provide easy access to our sequence database, alignments, and the tools and interfaces we have produced. The HIV Sequence Database focuses on five primary goals: * Collecting HIV and SIV sequence data (all sequences since 1987) * Curating and annotating this data, and making it available to the scientific community * Computer analysis of HIV and related sequences * Production of software for the analysis of (sequence) data * The data and analyses on this site and published in a yearly printed publication, the HIV sequence Compendium, which is available free of charge.

Lowes Syndrome Mutation Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-00155
synonym: Lowe Syndrome Mutation Database
IAO_0000115: The Lowe Syndrome Mutation Database is now being maintained by the National Center for Biotechnology Information (NCBI) at the National Institutes of Health. A database of mutations causing Lowe syndrome. Information on new mutations may be submitted online. Lowe oculocerebrorenal syndrome is an X-linked disorder caused by mutations in the OCRL1 gene, which encodes a 105-kDa Golgi protein with phosphatidylinositol (4,5) bisphosphate 5-phosphatase activity. genetics

International Spinal Cord Society
type: Resource
type: NamedIndividual
has db xref: nif-0000-30009
synonym: ISCoS
IAO_0000115: ISCoS promotes the highest standard of care in the practice of spinal cord injury for men, women and children throughout the world. Through its medical and multi disciplinary team of Professionals ISCoS endeavours to foster education, research and clinical excellence. ISCoS has a membership of over 1,000 Clinicians and Scientists from 87 countries. They regularly update their knowledge at the Annual Scientific Meeting held in a different country each year. Goals of ISCoS: :- Serve as an international impartial, non-political and non-profit making association whose purpose is to study all problems relating to traumatic and non-traumatic lesions of the spinal cord. This includes causes, prevention, basic and clinical research, medical and surgical management, clinical practice, education, rehabilitation and social reintegration. This society will function in close collaboration with other national and international bodies, thereby encouraging the most efficient use of available resources. :- Provide a scientific exchange among its members and others by collecting and disseminating information through publications, correspondence, exhibits, regional and international seminars, symposia, conferences and otherwise. :- Advise, encourage, promote and when requested, assist in efforts to co-ordinate or guide research, development and evaluation activities related to spinal cord lesions throughout the world. :- Advise, encourage, guide and support the efforts of those responsible for the care of patients involved and when requested, correlate these activities throughout the world. :- Advise, encourage, guide and support the efforts of those responsible for the education and training of medical professionals and professionals allied to medicine and when requested, correlate these activities throughout the world.

Clustal W2
type: Resource
type: NamedIndividual
has db xref: nif-0000-30076
has db xref: OMICS_02562
synonym: European Bioinformatics Institute - ClustalW2
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022. Command line version of multiple sequence alignment program Clustal for DNA or proteins. Alignment is progressive and considers sequence redundancy. No longer being maintained. Please consider using Clustal Omega instead which accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/ClustalW, GCG/MSF, RSF.

University of Colorado; Colorado; USA
type: University
type: NamedIndividual
has db xref: GRID grid.266185.e; ISNI 0000000121090824; Crossref Funder ID 100010174; Wikidata Q1206658
has db xref: nlx_60266
synonym: CU System
synonym: University of Colorado
synonym: University of Colorado System
abbrev: CU
IAO_0000115: University of Colorado is a four-campus system that includes the University of Colorado Boulder, the University of Colorado Colorado Springs, the University of Colorado Denver and the University of Colorado Anschutz Medical Campus.

University of Florida Labs and Facilities
type: Organization
type: NamedIndividual
has db xref: SciEx_929
synonym: Science Exchange University of Florida Labs and Facilities
synonym: UF Labs and Facilities
IAO_0000115: Portal that lists and provides information on core facilities located at the University of Florida.

Human Mitochondrial Protein Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02969
abbrev: HMPDb
IAO_0000115: Database of mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function. This database consolidates information from SwissProt, LocusLink, Protein Data Bank (PDB), GenBank, Genome Database (GDB), Online Mendelian Inheritance in Man (OMIM), Human Mitochondrial Genome Database (mtDB), MITOMAP, Neuromuscular Disease Center and Human 2-D PAGE Databases. The mitochondrion plays a central role in cellular metabolism, and evidence of mitochondrial involvement in a number of different human diseases is increasing. This database is intended as a tool not only to aid in studying the mitochondrion but in studying the associated diseases. Mitochondrial DNA Sequence: A graphical tool was developed to visualize the human mitochondrial DNA sequences that highlight coding regions for RNAs and proteins. Disease susceptible mutations are also noted in the sequence. Mitochondrial DNA Polymorphism: Human mitochondrial sequences of different ethnic groups were obtained from the Human Mitochondrial Genome Database. A DNA sequence analysis tool was developed to compare polymorphisms of different human mitochondrial DNA sequences. This tool allows the user to select mitochondrial sequences from any two human populations and compare them for sequences variations. Mitochondrial proteins related diseases: Malfunction of mitochondrial proteins affect many cells from brain, heart, liver, skeletal muscles, kidney, and the endocrine and the respiratory systems which lead to many diseases. Relevant information for mitochondrial related diseases from OMIM, the Neuromuscular Disease Center and MITOMAP are gathered, and mitochondrion-associated diseases are grouped, categorized, and linked to OMIM. 3-D Structures of Mitochondrial proteins: The available 3D structures for mitochondrial proteins are presented through a custom-made interface. A concise HTML page is generated for reporting the structural details and the associated information obtained from relevant …

LEAD-DBS
type: Resource
type: NamedIndividual
has db xref: SciRes_000188
synonym: LEAD DBS
synonym: Lead DBS
synonym: Lead-DBS
IAO_0000115: MATLAB toolbox for deep-brain-stimulation (DBS) electrode reconstructions and visualizations based on postoperative MRI and computed tomography (CT) imaging. The toolbox also facilitates visualization of localization results in 2D/3D, analysis of DBS-electrode placement's effects on clinical results, simulation of DBS stimulations, diffusion tensor imaging (DTI) based connectivity estimates, and fiber-tracking from the VAT to other brain regions (connectomic surgery).

Neural Open Simulation
type: Resource
type: NamedIndividual
has db xref: nif-0000-00161
synonym: NEOSIM - Neural Open Simulation
abbrev: NEOSIM
IAO_0000115: Simulation software that includes a parallel discrete event simulation kernel for running models of spiking neurons on a cluster of workstations. Models are specified using NeuroML, and visualized using Java2D. Simulation components are distributed across a parallel machine or network and communicate using timestamped events. The successor NEOSIM2 project under the NeuroGems umbrella at Edinburgh University (http://www.neurogems.org) continues to distribute the software, http://www.neurogems.org/neosim2/ The NEOSIM project includes: * a parallel discrete event simulation kernel for running models of spiking neural networks on clusters of machines. * a modules kit for extending the behavior of neurons and connectivity patterns. * a user interface for building and running simulations. OS: Linux, MS-Windows

ATGC: Montpellier bioinformatics platform
type: Resource
type: NamedIndividual
has db xref: nif-0000-30044
synonym: ATGC - South of France bioinformatics platform
abbrev: ATGC
IAO_0000115: A bioinformatics platform that is a joint project of several South of France laboratories with available services based on their expertise, issued from their research activities which involve phylogenetics, population genetics, molecular evolution, genome dynamics, comparative and functional genomics, and transcriptome analysis. Most of the software and databases on ATGC are (co)authored by researchers from South of France teams. Some are widely used and highly cited. South of France laboratories: * CRBM (transcriptomes and stem cells). * IBC (computational biology). * MiVEGEC (evolution and phylogeny). * LGDP (plant genomics). * LIRMM (computer science). * South Green (plant genomics).

CVXOPT - Python Software for Convex Optimization
type: Resource
type: NamedIndividual
has db xref: nif-0000-30018
abbrev: CVXOPT
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Software package for convex optimization based on the Python programming language. It can be used with the interactive Python interpreter, on the command line by executing Python scripts, or integrated in other software via Python extension modules. Its main purpose is to make the development of software for convex optimization applications straightforward by building on Pythons extensive standard library and on the strengths of Python as a high-level programming language. Current version includes the following features: * efficient Python classes for dense and sparse matrices (real and complex), with Python indexing and slicing and overloaded operations for matrix arithmetic * an interface to most of the double-precision real and complex BLAS * an interface to LAPACK routines for solving linear equations and least-squares problems, matrix factorizations (LU, Cholesky, LDLT and QR), symmetric eigenvalue and singular value decomposition, and Schur factorization * an interface to the fast Fourier transform routines from FFTW * interfaces to the sparse LU and Cholesky solvers from UMFPACK and CHOLMOD * routines for linear, second-order cone, and semidefinite programming problems * routines for nonlinear convex optimization * interfaces to the linear programming solver in GLPK, the semidefinite programming solver in DSDP5, and the linear, quadratic and second-order cone programming solvers in MOSEK * a modeling tool for specifying convex piecewise-linear optimization problems. A platform-independent source package and a binary Windows installer are available from the Download section. CVXOPT is also available precompiled for the major platforms: * Debian Linux * Ubuntu Linux * Fedora Linux * Python(x,y) for Microsoft Windows CVXOPT is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.

Lafora Progressive Myoclonus Epilepsy Mutation and Polymorphism Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-00157
synonym: Lafora Progressive Myoclonus Epilepsy Mutation Polymorphism Database
synonym: The Lafora Progressive Myoclonus Epilepsy Mutation and Polymorphism Database
synonym: The Lafora Progressive Myoclonus Epilepsy Mutation Polymorphism Database
abbrev: Lafora Database
IAO_0000115: The Lafora database is a repository of information related to progressive myoclonus epilepsy mutation and polymorphism data. Users may view all mutations in the database(Mutations of EPM2A and NHLRC1(EPM2B)), click on individual exons for mutations, or search the database by keyword. Nucleotide and amino acids positions were assigned based on the GenBank reference sequence NM_005670 for EPM2A and NM_198586 for EPM2B. The data can be viewed using the XRT Table Browser, and where possible, links to external sources such as NCBI, PubMed are provided. At this time, the database is under development. The BioXRT (Cross-Referenced Tables) Table Browser is a highly configurable tool for viewing complex, table based information. The tables can be displayed using pre-set options, or customized to view arbitrary subsets of rows, columns or other features.

Hollywood
type: Resource
type: NamedIndividual
has db xref: nif-0000-02972
has db xref: OMICS_01889
synonym: Hollywood mRNA Alternative Splicing
synonym: Hollywood.mit.edu
synonym: Hollywood.mit.edu - Alternatively spliced mRNA
IAO_0000115: Database built upon genomic annotation of splicing patterns of known genes derived from spliced alignment of complementary DNAs (cDNAs) and expressed sequence tags for human and mouse. It links features such as splice site sequence and strength, exonic splicing enhancers and silencers, conserved and non-conserved patterns of splicing, and cDNA library information for inferred alternative exons. A query tool allows searches for sets of exons with specific splicing characteristics or splicing regulatory element composition, or gives a graphical or sequence-level summary of splicing patterns for a specific gene. A graphical representation of gene splicing patterns is provided, and these patterns can alternatively be layered onto existing information in the UCSC Genome Browser.

Assembly/Alignment/Annotation of 12 Related Drosophila Species
type: Resource
type: NamedIndividual
has db xref: nif-0000-30021
synonym: AAA: 12 Drosophila Genomes
IAO_0000115: A single source for sequences, assemblies, annotations and analyses of the genomes of members of the fruitfly genus Drosophlia. It is meant as resource for Drosophilists and other researchers interested in comparative analysis of these species and their genomes. There are pages for each species, as well as pages for different types of multi-species resources (e.g. alignments). If you have a public resource that will help this project, please consider making it available through this page by emailing multiple_at_fruitfly.org.

StreamingTrim
type: Resource
type: NamedIndividual
has db xref: OMICS_05196
IAO_0000115: A DNA reads trimming software, written in Java, with which researchers are able to analyse the quality of DNA sequences in fastq files and to search for low-quality zones in a very conservative way.

pLabel
type: Resource
type: NamedIndividual
has db xref: OMICS_02469
IAO_0000115: Mass spectral peak labeling software developed for proteomics research., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

HomoloGene
type: Resource
type: NamedIndividual
has db xref: nif-0000-02975
has db xref: OMICS_01544
has db xref: r3d100010781
synonym: NCBI HomoloGene
IAO_0000115: Automated system for constructing putative homology groups from complete gene sets of wide range of eukaryotic species. Databse that provides system for automatic detection of homologs, including paralogs and orthologs, among annotated genes of sequenced eukaryotic genomes. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences. Reports include homology and phenotype information drawn from Online Mendelian Inheritance in Man, Mouse Genome Informatics, Zebrafish Information Network, Saccharomyces Genome Database and FlyBase.

Mind Research Network
type: Organization
type: NamedIndividual
has db xref: grid.280503.c
has db xref: ISNI: 0000 0004 0409 4614
has db xref: nif-0000-00474
has db xref: Wikidata: Q7751519
synonym: Mind Research Network for Neuroscience Discovery
abbrev: MRN
IAO_0000115: Non-profit organization focused on imaging technology that is dedicated to advancing the diagnosis and treatment of mental illness and brain injury. MRN consists of an interdisciplinary association of scientists located at universities, national laboratories and research centers around the world and is focused on imaging technology and its emergence as an integral element of neuroscience investigation. The MRNs initial plan called for the building of state-of-the-art magnetic resonance imaging (MRI) and magnetoencephalogram (MEG) neuroimaging systems to be applied to studies of mental illness. This important task was carried out by Minds initial collaborators: Massachusetts General Hospitals Martinos Biomedical Imaging Center (Harvard and MIT), the University of Minnesota, the University of New Mexico, and Los Alamos National Laboratory. Since both the Network and the mission have expanded beyond building neuroimaging tools, a comprehensive understanding of mental illness and more fundamental and systematic understanding of the brain, is possible. The MRN Mobile Imaging system is a custom designed one-of-a-kind facility.

Advanced Neuroscience Imaging Research Laboratory Software Packages
type: Resource
type: NamedIndividual
has db xref: nif-0000-30033
synonym: Advanced Neuroscience Imaging Research Software
synonym: ANSIR Laboratory Software Packages
abbrev: ANSIR Software
IAO_0000115: Research group based in the Department of Radiology of Wake Forest University School of Medicine devoted to the application of novel image analysis methods to research studies. The ANSIR lab also maintains a fully-automated functional and structural image processing pipeline supporting the image storage and analysis needs of a variety of scientists and imaging studies at Wake Forest. Software packages and toolkits are currently available for download from the ANSIR Laboratory, including: WFU Biological Parametric Mapping Toolbox, WFU_PickAtlas, and Adaptive Staircase Procedure for E-Prime.

aCGH.Spline
type: Resource
type: NamedIndividual
has db xref: OMICS_02607
IAO_0000115: An R package for array comparative genomic hybridization (aCGH) dye bias normalization.

National Postdoctoral Association
type: Organization
type: NamedIndividual
has db xref: grid.436397.c
has db xref: nif-0000-00476
abbrev: NPA
IAO_0000115: Representative organization for postdoctoral scholars in the United States. It is member-driven and non-profit.

pBuild
type: Resource
type: NamedIndividual
has db xref: OMICS_02468
IAO_0000115: A software tool that can compare several search engines' results and combine them together.

Genox Corpooration
type: Organization
type: NamedIndividual
has db xref: nlx_152373
IAO_0000115: Biotechnological company that produces and supplies materials to oxidative stress and aging researchers.

Charles University; Prague; Czech Republic
type: Organization
type: NamedIndividual
has db xref: Crossref Funder ID 100007397
has db xref: GRID grid.4491.8
has db xref: ISNI 0000 0004 1937 116X
has db xref: nlx_87455
has db xref: Wikidata Q31519
synonym: Charles University
synonym: Charles University in Prague
synonym: Univerzita Karlova
abbrev: CU
IAO_0000115: Research university located in Prague, Czech Republic.

American FactFinder
type: Resource
type: NamedIndividual
has db xref: nif-0000-30094
has db xref: r3d100010768
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE.Documented on September 2, 2025. Database that provides access to population, housing, economic, and geographic data from several censuses and surveys about the United States, Puerto Rico and the Island Areas. Census data may be compiled into tables, maps and downloadable files, which can be viewed or printed. A large selection of pre-made tables and maps satisfies many information requests. By law, no one is permitted to reveal information from these censuses and surveys that could identify any person, household, or business. The following data are available: * American Community Survey * ACS Content Review * American Housing Survey * Annual Economic Surveys * Annual Surveys of Governments * Census of Governments * Decennial Census * Economic Census * Equal Employment Opportunity (EEO) Tabulation * Population Estimates Program * Puerto Rico Community Survey

National Ataxia Foundation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100002243
has db xref: grid.453757.7
has db xref: ISNI: 0000 0001 0739 8769
has db xref: nif-0000-00478
abbrev: NAF
IAO_0000115: Membership supported, nonprofit organization established dedicated to improving the lives of persons affected by ataxia through support, education, and research. The Foundation's primary purpose is to support promising ataxia research and to provide vital programs and services for ataxia families. The Foundation first began direct funding of ataxia research through the NAF Research Seed-Money Program. Since that time, the Foundation has established additional research programs which have included programs such as the NAF Young Investigator Award, the NAF Fellowship Award and other research initiatives. NAF research programs continue to fund promising ataxia research studies throughout the world. The Foundation supports research in dominant ataxia (including SCAs), recessive ataxia (including Friedreich's) and sporadic ataxia. The Foundation has developed an extensive library of NAF brochures, fact sheets, books, and videos on ataxia. Also available to its members is the Foundation's quarterly news publication, Generations. This 48 page ataxia news magazine provides the latest information on ataxia research, articles on living with ataxia, personal accounts from ataxia families throughout the United States, and much more.

Office of Intramural Training and Education
type: Resource
type: NamedIndividual
has db xref: nif-0000-00485
synonym: NIH Office of Intramural Training and Education
synonym: NIH Office of Intramural Training and Education (OITE)
abbrev: OITE
IAO_0000115: Division of the Office of Intramural Research (OIR), Office of the Director (OD) which provides services to current trainees in programs in the NIH Intramural Research Program, potential applicants to training programs at the NIH, investigators and staff at the NIH, and trainees and investigators outside the NIH.

Time-series RNA-seq Analysis Package
type: Resource
type: NamedIndividual
has db xref: OMICS_02590
abbrev: TRAP
IAO_0000115: A comprehensive software package integrating all necessary tasks such as mapping short reads, measuring gene expression levels, finding differentially expressed genes (DEGs), clustering and pathway analysis for time-series data in a single environment.

CGHnormaliter
type: Resource
type: NamedIndividual
has db xref: OMICS_02572
synonym: CGHnormaliter - Normalization of array CGH data with imbalanced aberrations.
IAO_0000115: Software for normalization and centralization of array comparative genomic hybridization (aCGH) data with imbalanced aberrations. The algorithm uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs).

ATandT Labs Research - Software Tools
type: Resource
type: NamedIndividual
has db xref: nif-0000-30042
synonym: AT&T Labs Research - software tools: labs research
abbrev: AT&T Labs Research - Software Tools
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE.Documented on January 4,2023.Software tools that have been developed by AT&T Labs researchers. In addition to the software tools available through Open Source and Non-Commercial licenses as listed on this page, AT&T has additional software and technology solutions available for licensing. Please reference the individual project web pages for specific license agreements. If an available license agreement does not meet your needs, please contact attip (at) att.com for assistance with a customized license. Open Source Licenses * AST: Advanced Software Technologies Open Source Collection * Cdt: Container Data Types Library * ECharts: A state machine-based programming language * GGobi: Data visualization for high-dimensional data * GSDjVu/DjVuDigital: Ghostscript driver to convert PS and PDF files to DjVu files * Graphviz: Tools for viewing and interacting with graph diagrams * PADS: Processing Arbitrary Data Streams * Sfio: Portable library for performing I/O * UWIN: Unix on Windows 95 and NT Machines * Vcodex: Software package for data transformation * WSP: Web Scraping Proxy * Yoix: The Yoix Scripting Language and Interpreter * iPlots: Interactive graphics for data analysis in R * vmalloc: Region Memory Allocator Non-Commercial Binary Licenses * BoosTexter: A general purpose machine-learning program * Hancock: A language for processing large-scale data Non-Commercial Source Licenses * ASDT: The AT&T Statistical Dialog Toolkit (ASDT) * Hancock: A language for processing large-scale data

Human Potential Tumor Associated Antigen database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02987
synonym: HPtaa Database
IAO_0000115: To accelerate the process of tumor antigen discovery, we generated a publicly available Human Potential Tumor Associated Antigen database (HPtaa) with pTAAs identified by insilico computing. 3518 potential targets have been included in the database, which is freely available to academic users. It successfully screened out 41 of 82 known Cancer-Testis antigens, 6 of 18 differentiation antigen, 2 of 2 oncofetal antigen, and 7 of 12 FDA approved cancer markers that have Gene ID, therefore will provide a good platform for identification of cancer target genes. This database utilizes expression data from various expression platforms, including carefully chosen publicly available microarray expression data, GEO SAGE data, Unigene expression data. In addition, other relevant databases required for TAA discovery such as CGAP, CCDS, gene ontology database etc, were also incorporated. In order to integrate different expression platforms together, various strategies and algorithms have been developed. Known tumor antigens are gathered from literature and serve as training sets. A total tumor specificity penalty was computed from positive clue penalty for differential expression in human cancers, the corresponding differential ratio, and normal tissue restriction penalty for each gene. We hope this database will help with the process of cancer immunome identification, thus help with improving the diagnosis and treatment of human carcinomas.

HS3D - Homo Sapiens Splice Sites Dataset
type: Resource
type: NamedIndividual
has db xref: nif-0000-02988
synonym: Homo Sapiens Splice Sites Dataset
synonym: HS3D (Homo Sapiens Splice Sites Dataset)
abbrev: HS3D
IAO_0000115: Data set of Homo Sapiens Exons, Introns and Splice regions extracted from GenBank Rel.123 with an aim of giving standardized material to train and to assess the prediction accuracy of computational approaches for gene identification and characterization. From the complete GenBank (Primate Sequences Division) Rel.123 (162,557 entries), entries of Human Nuclear DNA including Complete CDS and more than one Exon have been selected, and 4523 exons and 3802 introns have been extracted from these entries. Details about extracted exons and introns are reported (Locus, number, Start and End position in the entry, sequence, length, G+C content, presence of not AGCT data (nucleotide scan check)). Statistics are also reported (overall nucleotides, average G+C content, nucleotide scan check results, number of not GT starting / AG ending introns, minimum / maximum / average length, length standard deviation). 3799+3799 donor and acceptor sites, as windows of 140 nucleotides around each splice site have been extracted. After discarding sequences not including canonical GTAG junctions (65+74), including insufficient data (not enough material for a 140 nucleotide window) (686+589), including not AGCT bases (29+30), and redundant (218+226) there are 2796+ 2880 windows. Finally, there are 271,937 + 332,296 windows of false splice sites, selected by searching canonical GTAG pairs in not splicing positions. The false sites in a range of +/- 60 from a true splice site are marked as proximal.

Ablynx
type: Commercial Organization
type: NamedIndividual
has db xref: nif-0000-30052
IAO_0000115: A biopharmaceutical company engaged in the discovery and development of Nanobodies, a novel class of antibody-derived therapeutic proteins based on single-domain antibody fragments, for a range of serious life-threatening human diseases including inflammation, hematology, oncology and pulmonary disease.

Type-III-Secretion-System related database
type: Resource
type: NamedIndividual
has db xref: OMICS_05160
synonym: T3SS-related Database
abbrev: T3DB
IAO_0000115: Database aimed to annotate all bacterial Type III Secretion System (T3SS) related structure, effector, regulator, and auxiliary genes.

SMRT-Analysis
type: Resource
type: NamedIndividual
has db xref: OMICS_05142
synonym: SMRT Analysis
IAO_0000115: Open-source bioinformatics software suite for analyzing single molecule, real-time DNA sequencing data. Users can choose from a variety of analysis protocols that utilize PacBio and third-party tools. Analysis protocols include de novo genome assembly, cDNA mapping, DNA base-modification detection, and long-amplicon analysis to determine phased consensus sequences.

National Center for Toxicological Research
type: Organization
type: NamedIndividual
has db xref: grid.483504.e
has db xref: ISNI: 0000 0001 2158 7187
has db xref: nif-0000-30057
has db xref: Wikidata: Q6971380
synonym: National Center for Toxicological Research (NCTR)
abbrev: NCTR
IAO_0000115: The National Center for Toxicological Research (NCTR), FDA's internationally recognized research center, plays a critical role in FDA's mission. The unique scientific expertise of NCTR is critical in supporting FDA product centers and their regulatory roles. The NCTR is an important research component of the FDA that plays a critical role in the missions of FDA and DHHS to promote and protect public health. * NCTRin partnership with researchers from government, academia, and industrydevelops, refines, and applies current and emerging technologies to improve safety evaluations of FDA-regulated products. * NCTR fosters national and international collaborations to improve and protect public health and enhance the quality of life for the American people. Through the training of scientists from around the world, as well as FDA staff, NCTR researchers spread the principles of regulatory science globally. * NCTR conducts FDA research with the goal to develop a scientifically sound basis for regulatory decisions and reduce risks associated with FDA-regulated products. NCTR represents the FDA on key committees of the National Toxicology Program (NTP), a program that evaluates the effects of chemicals on health. Over the past 30 years, the NTP and NCTR have conducted studies on FDA-nominated compounds, providing data to support science-based regulatory decisions.

CPTRA
type: Resource
type: NamedIndividual
has db xref: biotools:cptra
has db xref: OMICS_01303
synonym: Cross Platform Transcriptome Analysis
synonym: Cross Platform Transcriptome Analysis (CPTRA)
IAO_0000115: Software package for analyzing transcriptome sequencing data from different sequencing platforms.

mtDB - Human Mitochondrial Genome Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-02994
has db xref: OMICS_01642
synonym: Human Mitochondrial Genome Database
abbrev: mtDB
IAO_0000115: A database of human mitochondrial genomes containing mtDNA sequences, polymorphic sites, and the ability to search for specific variants. It contains 1865 complete sequences and 839 coding region sequences.

Pennington Biomedical Research Center
type: Organization
type: NamedIndividual
has db xref: grid.250514.7
has db xref: ISNI: 0000 0001 2159 6024
has db xref: nif-0000-30066
has db xref: Wikidata: Q7163465
synonym: Pennington Center
abbrev: PBRC
IAO_0000115: Research institute which investigates chronic disease and its triggers.

Neal's DNA Mutation Site
type: Resource
type: NamedIndividual
has db xref: nif-0000-02995
synonym: Human p53 Human hprt Rodent lacI and Rodent lacZ Databases
synonym: Human p53 Human hprt Rodent lacI and Rodent lacZ Databases and Software
synonym: Human p53 Human hprt Rodent lacI Rodent lacZ Databases
IAO_0000115: This site provides access to mutation databases and software including the human hprt database, Human p53 database, Transgenic lacZ database, and Transgenic lacI database. Other avaialble programs include Mutational spectra comparison and relational database data entry. The most recent hprt database contains information on over 2,300 mutations found in vivo and in vitro in the human hprt gene and runs under Windows. The version for evaluation on this homepage has fewer mutations and is a DOS program. The database contains information on the mutagen, dose, spontaneous and induced mutant fraction, base position, amino acid position, amino acid change, local DNA sequence, cell type, citation, and other items. In addition, information regarding the cause and effect of mutations affecting splicing is given. Routines have been developed for the analysis of single base substitutions. The p53 database contains information on nearly 5,867 mutations found in the human p53 gene. The database itself has been updated in April of 1997. The database contains information on the cancer type, loss of heterozygosity, base position, amino acid position, amino acid change, local DNA sequence,citation, and other items. Routines have been developed for the analysis of single base substitutions. The Transgenic lacZ database contains information on 405 mutations found in vivo in the transgenic lacZ gene. It has last been updated in January of 1998. It provides information on the mutagen, dose, organ, mutant fraction, base position, amino acid position, amino acid change, local DNA sequence, citation, and other items. The Transgenic lacI database contains information on over 1700 mutations found in vivo in the transgenic lacI gene and on nearly 8000 mutations in the lacI gene in native E. coli. The database was updated in January 1998. The database contains information on the mutagen, dose, organ, mutant fraction, base position, amino acid position, amino acid change, local DNA sequence, cit…

Human Proteinpedia
type: Resource
type: NamedIndividual
has db xref: nif-0000-02999
has db xref: r3d100010985
IAO_0000115: A community portal for sharing and integration of human protein data that allows research laboratories to contribute and maintain protein annotations. The Human Protein Reference Database (HPRD) integrates data that is deposited along with the existing literature curated information in the context of an individual protein. Data pertaining to post-translational modifications, protein-protein interactions, tissue expression, expression in cell lines, subcellular localization and enzyme substrate relationships can be submitted.

Interrupted CoDing Sequence Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-03036
abbrev: ICDS Database
IAO_0000115: Database of interrupted coding sequences detected by a similarity-based approach in complete prokaryotic genomes. The definition of each interrupted gene is provided as well as the ICDS genomic localization with the surrounding sequence. To facilitate the experimental characterization of ICDS, optimized primers are proposed for re-sequencing purposes. The database is accessible by BLAST search or by genome. 118 Genomes are available in the database.

AllerHunter: Cross-reactive Allergen Prediction Home
type: Resource
type: NamedIndividual
has db xref: nif-0000-30082
synonym: AllerHunter: Cross-reactive Allergen Prediction Program
abbrev: AllerHunter
IAO_0000115: A cross-reactive allergen prediction program built on a combination of Support Vector Machine (SVM) and pairwise sequence similarity. Cross-reactivity is based on similarity of proteins to allergens. However, not all proteins with similar sequence or structure to known allergens are cross-reactive allergens. AllerHunter aims to predict allergens and non-allergens with high sensitivity and specificity, without compromising efficiency at classification of proteins with similar sequence to known allergens. There are distinct differences between prediction of allergenicity and cross-reactivity of allergens. Allergenicity is the immunogenic potential of an allergen to induce IgE antibody production, whereas cross-reactivity is the potential of a substance to bind to IgE previously induced by a known allergen. It is difficult to predict allergenicity because causes of immunogenicity of allergens are still not completely clear. However it is possible to predict cross-reactivity since it implies similarity in IgE binding sites. Please provide protein sequence in fasta format.

AltAnalyze - Alternative Splicing Analysis Tool
type: Resource
type: NamedIndividual
has db xref: biotools:altanalyze
has db xref: nif-0000-30083
has db xref: OMICS_02250
synonym: Alternative Splicing Analysis Tool
abbrev: AltAnalyze
IAO_0000115: Software application for microarry, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), it will assess alternative exon (known and novel) expression along protein isoforms, domain composition and microRNA targeting. In addition to splicing-sensitive platforms, it provides comprehensive methods for the analysis of other data (RMA summarization, batch-effect removal, QC, statistics, annotation, clustering, network creation, lineage characterization, alternative exon visualization, gene-set enrichement and more). AltAnalyze can be run through an intuitive graphical user interface or command-line and requires no advanced knowledge of bioinformatics programs or scripting. Alternative regulated exons can be subsequently visualized in the context of proteins, domains and microRNA binding sites with the Cytoscape Plugin DomainGraph.

HuRef
type: Resource
type: NamedIndividual
has db xref: nif-0000-03001
synonym: Human Reference Genome
synonym: Human Reference Genome - J. Craig Venter Institute
IAO_0000115: Database for the diploid genome sequence of J. Craig Venter as published in PLoS Biology. Its graphical interface depicts the haploid sequence with SNP and insertion/deletion DNA variants as identified by genome assembly and comparison methods, as well as represents the haplotype blocks from which diploid genome sequence can be inferred and gene annotations.

Mutant Mouse Resource and Research Center
type: Resource
type: NamedIndividual
has db xref: nif-0000-00045
synonym: Mutant Mouse Regional Resource Center
abbrev: MMRRC
IAO_0000115: National public repository system for mutant mice. Archives and distributes scientifically valuable spontaneous and induced mutant mouse strains and ES cell lines for use by biomedical research community. Includes breeding/distribution facilities and information coordinating center. Mice strains are cryopreserved, unless live colony must be established. Live mice are supplied from production colony, from colony recovered from cryopreservation, or via micro-injection of cell line into host blastocysts. MMRRC member facilities also develop technologies to improve handling of mutant mice, including advances in assisted reproductive techniques, cryobiology, genetic analysis, phenotyping and infectious disease diagnostics.

HvrBase++- an mtDNA database
type: Resource
type: NamedIndividual
has db xref: nif-0000-03003
synonym: HvrBase++
IAO_0000115: HvrBase++ is the improved and extended version of HvrBase. Extensions are made by adding more population-based sequence samples from all primates including humans. The current collection comprises 13,873 hypervariable region I (HVRI) sequences and 4940 hypervariable region II (HVRII) sequences. In addition, we included 1376 complete mitochondrial genomes, 205 sequences from X-chromosomal loci and 202 sequences from autosomal chromosomes 1, 8, 11 and 16. In order to reduce the introduction of erroneous data into HvrBase++, we have developed a procedure that monitors GenBank for new versions of the current data in HvrBase++ and automatically updates the collection if necessary. For the stored sequences, supplementary information such as geographic origin, population affiliation and language of the sequence donor can be retrieved. As a new key feature, HvrBase++ provides an interactive graphical tool to easily access data from dynamically created geographical maps.

Celgene
type: Organization
type: NamedIndividual
has db xref: nif-0000-30309
synonym: Celgene Corporation
abbrev: CELG
IAO_0000115: An American global biotechnology company that manufactures drug therapies for cancer and inflammatory disorders. The company's major products are Thalomid (thalidomide), which is approved for the acute treatment of the cutaneous manifestations of moderate to severe erythema nodosum leprosum (ENL), as well as in combination with dexamethasone for patients with newly diagnosed multiple myeloma, and Revlimid (lenalidomide), for which the company has received FDA and EMA approval in combination with dexamethasone for the treatment of multiple myeloma patients who have received at least one prior therapy. Revlimid is also approved in the United States for the treatment of patients with transfusion-dependent anemia due to Low- or Intermediate-1-risk Myelodysplastic syndromes (MDS) associated with a deletion 5q cytogenetic abnormality with or without additional cytogenetic abnormalities. Both Thalomid and Revlimid are sold through proprietary risk-management distribution programs to ensure safe and appropriate use of these pharmaceuticals. Vidaza is approved for the treatment of patients with MDS. Celgene also receives royalties from Novartis Pharma AG on sales of the entire Ritalin family of drugs, which are widely used to treat Attention Deficit Hyperactivity Disorder (ADHD). (Adapted from Wikipedia) There are numerous clinical trials at major medical centers using compounds from Celgene. Investigational compounds are being studied for patients with incurable hematological and solid tumor cancers, including multiple myeloma, myelodysplastic syndromes, chronic lymphocyte leukemia (CLL), non-Hodgkin's lymphoma (NHL), glioblastoma, and ovarian, pancreatic and prostate cancer.

Amplify
type: Resource
type: NamedIndividual
has db xref: nif-0000-30103
synonym: Amplify 3
IAO_0000115: A freeware Macintosh program for simulating and testing polymerase chain reactions (PCRs) that can also be used as a tool for designing primers by evaluating candidates. It's a program to simulate the polymerase chain reaction. You specify a target sequence and primers, and it predicts the result. It's useful for planning experiments, testing primers and teaching about PCR. Amplify draws a diagram of the predicted results showing all expected primer matches and amplified fragments. Clicking on any of these objects gives additional information about them.

I2D
type: Resource
type: NamedIndividual
has db xref: nif-0000-03005
has db xref: r3d100010675
synonym: I2D - Interologous Interaction Database
synonym: Interologous Interaction Database
synonym: OPHID
IAO_0000115: Database of known and predicted mammalian and eukaryotic protein-protein interactions, it is designed to be both a resource for the laboratory scientist to explore known and predicted protein-protein interactions, and to facilitate bioinformatics initiatives exploring protein interaction networks. It has been built by mapping high-throughput (HTP) data between species. Thus, until experimentally verified, these interactions should be considered predictions. It remains one of the most comprehensive sources of known and predicted eukaryotic PPI. It contains 490,600 Source Interactions, 370,002 Predicted Interactions, for a total of 846,116 interactions, and continues to expand as new protein-protein interaction data becomes available.

SHEsis: Analysis Tools For Random Samples
type: Resource
type: NamedIndividual
has db xref: nif-0000-30105
abbrev: SHEsis
IAO_0000115: A powerful web-based platform for analyses of linkage disequilibrium, haplotype construction, and genetic association at polymorphism loci.

Chimera
type: Resource
type: NamedIndividual
has db xref: OMICS_06335
synonym: chimera - A package for secondary analysis of fusion products
IAO_0000115: A Bioconductor package that organizes, annotates, analyses and validates fusions reported by different fusion detection tools. The current implementation can deal with output from bellerophontes, chimeraScan, deFuse, fusionCatcher, FusionFinder, FusionHunter, FusionMap, mapSplice, Rsubread, tophat-fusion, tophat-fusion-post and STAR. The core of Chimera is a fusion data structure that can store fusion events detected with any of the aforementioned tools.

Grass Foundation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100001654
has db xref: grid.479773.9
has db xref: ISNI: 0000 0004 5899 7819
has db xref: nif-0000-00500
synonym: The Grass Foundation
IAO_0000115: The Grass Foundation is a small, not-for-profit, private foundation chartered to support research and education in neuroscience. The hallmark program of The Grass Foundation is the Grass Fellowship Program at the Marine Biological Laboratory in Woods Hole, Massachusetts. This program provides a first opportunity for neuroscientists during late stages of predoctoral training or during postdoctoral years to conduct independent research for scientific discovery on their own at the MBL each summer. While sharing the Grass Laboratory, Fellows function as an intellectual and social group within the MBL community. The number of fellowships awarded varies annually. Additional programs supported by The Grass Foundation include the Robert S. Morison Fellowship, The Grass-MBL Faculty Grant Program, the Ricardo Miledi Program for Neuroscience Training, several neuroscience courses at the MBL, and yearly funding of a few lectureships and prizes. Please see our Program Grants section for more information.

centerline
type: Resource
type: NamedIndividual
has db xref: SciRes_000186
IAO_0000115: An application for the automatic segmentation and tracing of three-dimensional neuronal images.

Brainscape
type: Resource
type: NamedIndividual
has db xref: nif-0000-00501
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on May 23, 2013. Database for resting state functional connectivity studies. Functional connectivity has shown tremendous promise in mapping the intrinsic functional topography of the brain, evaluating neuroanatomical models, and investigating neurological and psychiatric disease. Brainscape includes a repository of public and private data and an analysis engine for exploring the correlation structure of spontaneous fluctuations in the fMRI BOLD signal. (DICOM data is the image format that can be uploaded.) With Brainscape you can upload, analyze, and share your own data. You can search for, download, and analyze studies in the repository of shared data. The analysis engine works by selecting one or more studies, typing in the coordinates of a brain region of interest, and the seed-region correlation engine computes the correlation structure across the whole brain. (T1, T2 and EPI data are the scan types Brainscape can process.) You decide who can access your data. You can keep it to yourself, share with select colleagues, or share it with everyone. The Brainscape database and analysis tools are open source and freely available.

NEST Simulator
type: Resource
type: NamedIndividual
has db xref: biotools:nest
has db xref: nif-0000-00162
synonym: nest
synonym: nest-simulator
synonym: NEural Simulation Tool
synonym: Neural Simulation Tool
abbrev: NEST
IAO_0000115: Software tool as simulator for spiking neural network models that focuses on dynamics, size and structure of neural systems rather than on exact morphology of individual neurons. Used for any size spiking neurons networks including models of information processing, models of network activity dynamics, models of learning and plasticity.

ArrayExpress
type: Resource
type: NamedIndividual
has db xref: nif-0000-30123
has db xref: OMICS_01023
has db xref: r3d100010222
synonym: ArrayExpress - functional genomics data
synonym: ArrayExpress Archive
IAO_0000115: International functional genomics data collection generated from microarray or next-generation sequencing (NGS) platforms. Repository of functional genomics data supporting publications. Provides genes expression data for reuse to the research community where they can be queried and downloaded. Integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments. Data collected to MIAME and MINSEQE standards. Data are submitted by users or are imported directly from the NCBI Gene Expression Omnibus.

IMG System
type: Resource
type: NamedIndividual
has db xref: biotools:img_m
has db xref: nif-0000-03010
has db xref: OMICS_01478
synonym: Integrated Microbial Genomes System
abbrev: IMG
abbrev: IMG/M
IAO_0000115: Resource for analysis and annotation of genome and metagenome datasets in comprehensive comparative context. IMG provides users with tools for analyzing publicly available genome datasets and metagenome datasets.

Journal of Visualized Experiments
type: Resource
type: NamedIndividual
has db xref: nif-0000-00536
abbrev: JoVE
IAO_0000115: A peer reviewed, PubMed indexed journal devoted to the publication of biological research in a video format.

Australian New Zealand Clinical Trials Registry
type: Resource
type: NamedIndividual
has db xref: nif-0000-30135
has db xref: r3d100011164
abbrev: ANZCTR
IAO_0000115: Register of clinical trials being undertaken in Australia, New Zealand and elsewhere including trials from the full spectrum of therapeutic areas of pharmaceuticals, surgical procedures, preventive measures, lifestyle, devices, treatment and rehabilitation strategies and complementary therapies. In 2007 the ANZCTR was one of the first three trial registries to be recognized by the World Health Organisation International Clinical Trials Registry Platform (WHO ICTRP) as a Primary Registry. WHO recognizes registries as Primary Registries if they fulfill certain criteria with respect to data content, quality and validity, accessibility, unique identification, technical capacity and administration. The ANZCTR contributes data to the WHO ICTRP, which was developed in 2007. Trials from all ICTRP Primary Registries can be searched at: www.who.int/trialsearch Studies should be registered prospectively, i.e. before the first patient is recruited. The registry records a trial's * objectives * main design features * sample size and recruitment status * treatments under investigation * outcomes being assessed * principal investigator * contact person Key points about the ANZCTR * Publicly owned, managed by a not-for-profit organization * All details of trials registered on the ANZCTR are made publicly available * Registration is voluntary, but if a registrant chooses to register a trial, certain fields are mandatory * Registration is free of charge * Responsibility for registration lies with the Sponsor

SNPHunter
type: Resource
type: NamedIndividual
has db xref: nif-0000-30137
synonym: Program for Population Genetics Software
synonym: SNPHunter - dbSNP Search & Management
IAO_0000115: A tool for SNP Search and downloading with local management. It also offers flanking sequence downloading and automatic SNP filtering. It requires Windows and .NET Framework.

Babelomics
type: Resource
type: NamedIndividual
has db xref: nif-0000-30144
has db xref: OMICS_00748
synonym: Babelomics 4
synonym: Babelomics 4: Gene Expression and Functional Profiling Analysis Suite
IAO_0000115: An integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Version 4 of Babelomics integrates primary (normalization, calls, etc.) and secondary (signatures, predictors, associations, TDTs, clustering, etc.) analysis tools within an environment that allows relating genomic data and/or interpreting them by means of different functional enrichment or gene set methods. Such interpretation is made not only using functional definitions (GO, KEGG, Biocarta, etc.) but also regulatory information (from Transfac, Jaspar, etc.) and other levels of regulation such as miRNA-mediated interference, protein-protein interactions, text-mining module definitions and the possibility of producing de novo annotations through the Blast2GO system . Babelomics has been extensively re-engineered and now it includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. In this release GEPAS and Babelomics have integrated into a unique web application with many new features and improvements: * Data input: import and quality control for the most common microarray formats * Normalization and base calling: for the most common expression, tiling and SNP microarrays (Affymetrix and Agilent). * Transcriptomics: diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and time-series analysis. * Genotyping: stratification analysis, association, TDT. * Functional profiling: functional enrichment and gene set enrichment analysis with functional terms (GO, KEGG, Biocarta, etc.), regulatory (Transfac, Jaspar, miRNAs, etc.), text-mining, derived bioentities, protein-protein interaction analysis. * Integrative analysis: Different variables can be related to each other (e.g. gene expression to gnomic copy number) and the results subjected to functional anal…

University of Bergen Computational Biology Unit
type: Organization
type: NamedIndividual
has db xref: nif-0000-30147
synonym: UiB Computational Biology Unit
abbrev: UiB CBU
IAO_0000115: An inter-department center that conducts bioinformatics research and expands the interface between bioinformatics and experimental biological and biomedical research. The unit is closely associated with the the Bioinformatics group at the Department of Informatics (II) and has tight links with the Sars Centre for Marine Molecular biology (SARS) and the Department of Molecular Biology (MBI). Six research groups are currently associated with CBU with projects that include sequence and structure analysis, molecular evolution, genome annotation and genomics data analysis. CBU also provides services and contributes to bioinformatics education primarily through training courses.

IMGT/HLA
type: Resource
type: NamedIndividual
has db xref: biotools:ipd-imgt_hla
has db xref: nif-0000-03014
has db xref: r3d100010804
synonym: IMGT HLA
synonym: IMGT/HLA Database
synonym: IMGT/HLA DB
synonym: International ImMunoGeneTics/Human Leukocyte Antigen Database
IAO_0000115: Database for sequences of the human major histocompatibility complex (HLA) and includes the official sequences for the WHO Nomenclature Committee For Factors of the HLA System. It currently contains 9,310 allele sequences (2013) along with detailed information concerning the material from which the sequence was derived and data on the validation of the sequences. It is established procedure for authors to submit the sequences directly to the IMGT/HLA Database for checking and assignment of an official name prior to publication, this avoids the problems associated with renaming published sequences and the confusion of multiple names for the same sequence. The need for reasonably rapid publication of new HLA allele sequences has necessitated an annual meeting of the WHO Nomenclature Committee for Factors of the HLA System. Additionally they now publish monthly HLA nomenclature updates both in journals and online to provide quick and easy access to new sequence information. The IMGT/HLA Database is part of the international ImMunoGeneTics project. In collaboration with the Imperial Cancer Research Fund (ICRF) and European Bioinformatics Institute (EBI) they have developed an Oracle database to house the HLA sequences in such a way as to allow users to present complex queries about the sequence, sequence features, references, contacts and allele designations to the database via a graphical user interface over the web. The IMGT/HLA Database Submission Tool allows direct submission of sequences to the WHO HLA Nomenclature Committee for Factors of the HLA System. The IMGT/HLA Database provides an FTP site for the retrieval of sequences in a number of pre-formatted files.

MRFSEQ
type: Resource
type: NamedIndividual
has db xref: biotools:mrfseq
has db xref: OMICS_01309
IAO_0000115: Algorithm based on a Markov random field (MRF) model that uses additional gene coexpression data to enhance differential gene expression prediction power. It is able to call differentially expressed (DE) genes but also assign confidence scores to each inferred DE gene.

BMAP cDNA Resources
type: Resource
type: NamedIndividual
has db xref: nif-0000-30154
synonym: Brain Molecular Anatomy Project cDNA Resources
abbrev: BMAP Resources
IAO_0000115: As part of BMAP gene discovery efforts, mouse brain cDNA libraries and Expressed Sequence Tags (ESTs) have been generated. Through this project a BMAP mouse brain UniGene set consisting of over 24,000 non-redundant members of unique clusters has been developed from EST sequencing of more than 50,000 cDNA clones from 10 regions of adult mouse brain, spinal cord, and retina (http://brainEST.eng.uiowa.edu/). In 2001, NIMH along with NICHD, NIDDK, and NIDA, awarded a contract to the University of Iowa ( M.B. Soares, PI) to isolate full-length cDNA clones corresponding to genes expressed in the developing mouse nervous system and determine their full-coding sequences. The BMAP mouse brain EST sequences can be accessed at NCBI's dbEST database (http://www.ncbi.nlm.nih.gov/dbEST/). Arrayed sets of BMAP mouse brain UniGenes and cDNA libraries, and individual BMAP cDNA clones can be purchased from Open Biosystems, Huntsville, AL (http://www.openbiosystems.com

ms lims
type: Resource
type: NamedIndividual
has db xref: biotools:ms-lims
has db xref: OMICS_02547
synonym: mass spectrometry based proteomics information management system
synonym: ms-lims: mass spectrometry based proteomics information management system
IAO_0000115: Software that provides a lightweight, portable yet production-grade solution for managing mass spectrometry based proteomics data.

ChIPMonk
type: Resource
type: NamedIndividual
has db xref: nif-0000-30159
has db xref: OMICS_02043
IAO_0000115: Software tool to visualize and analyse ChIP-on-chip array data. Main features: * Import of data from Nimblegen arrays (other formats can be added if people send us examples) * Normalization of data (both per array and per probe) * Various data plotting options to assess data quality and the effectiveness of normalization * Creation of data groups for visualization and analysis * Visualization of data against an annotated genome. * Statistical analysis of data to find probes of interest * Creation of reports containing probes, data and genome annotation Note: This project is no longer being developed, but critical bug fixes will still be provided

Penn Induced Pluripotent Stem Cell Core Facility
type: Resource
type: NamedIndividual
has db xref: nlx_156484
abbrev: iPSC Core
abbrev: iPSC Core Facility
IAO_0000115: Core facility that provides the following services: Induced pluripotent stem cell derivation, Characterization of induced pluripotent stem cells, Hands-on training course for embryonic / induced pluripotent stem cell culture. Additionally, the Core has several established human iPS cell lines for purchase for research purposes by non-profit institutions. Please contact the director for available cell lines. The goals of the Core are: * to facilitate derivation of induced pluripotent stem (iPS) cells from somatic cells; * to provide expertise and training to researchers in embryonic stem (ES)/iPS cell culture; * and to serve as a resource for sharing iPS cell lines and iPSC technology within the UPenn and the broader scientific community.

Gel2DE
type: Resource
type: NamedIndividual
has db xref: OMICS_02546
synonym: gel2de - Correlation analysis of gel electrophoresis data
IAO_0000115: Software application for performing pixel-by-pixel correlation analysis on a set of gel images from two-dimensional gel electrophoresis and a set of clinical parameters for a population. The application is written in C++, and has been tested on Windows, although it in principle should compile cross platform using CMake.

Allen Mouse Brain Reference Atlas
type: Resource
type: NamedIndividual
has db xref: nif-0000-00508
has db xref: nlx_21010
synonym: ABA Adult Mouse Brain
synonym: Allen Reference Atlases
synonym: ARA ontology
abbrev: ABA
abbrev: ABA Mouse Brain
abbrev: ARA
IAO_0000115: Allen Mouse Brain Atlas includes full color, high resolution anatomic reference atlas accompanied by systematic, hierarchically organized taxonomy of mouse brain structures. Enables interactive online exploration of atlas and to provide deeper level of 3D annotation for informatics analysis and viewing in Brain Explorer 3D viewer.

EONS
type: Resource
type: NamedIndividual
has db xref: nif-0000-00504
synonym: Elementary Objects of the Nervous System
synonym: EONS (Elementary Objects of the Nervous System)
synonym: EONS-The integrated synaptic modeling platform
IAO_0000115: Modeling platform to study the basic interactions between synaptic elements that allows the user to study qualitatively, and also quantitatively the relative contributions of diverse mechanisms underlying synaptic efficacy: the relevance of each and every element that comprises a synapse, the interactions between these components and their subcellular distribution, as well as the influence of synaptic geometry (presynaptic terminal, cleft and postsynaptic density). This platform consists of a graphical interface in which elements that comprise a single glutamatergic synapse (both pre- and post-synaptically), their behavior as well as the underlying synaptic geometry can be modified. For example, EONS offers the ability to study the effect of voltage-gated calcium channels density and distribution, the number and location of receptors and more. EONS is a parametric model of a generic glutamatergic synapse that takes into account pre-synaptic mechanisms, such as calcium buffering and diffusion, neurotransmitter release, diffusion and uptake in the cleft, and postsynaptic elements, such as ionotropic AMPA and NMDA receptors, their distribution and synaptic geometry, as well as metabotropic glutamate receptors. There are no complicated equations to write: all the models are predefined. This version is a great tool for first time users and students interested in learning about synapses, as well as for studying geometry and distribution hypotheses in a 2D rectangular geometry. System Requirements: EONS V1.2 is a Windows program but can be also successfully installed and run on Mac and Linux.

BiSearch: Primer Design and Search Tool
type: Resource
type: NamedIndividual
has db xref: nif-0000-30170
abbrev: BiSearch
IAO_0000115: BiSearch is a primer-design algorithm for DNA sequences. It may be used for both bisulfite converted as well as for original not modified sequences. You can search various genomes with the designed primers to avoid non-specific PCR products by our fast ePCR method. This is especially recommended when primers are designed to amplify the highly redundant bisulfite treated sequences. It has the unique property of analyzing the primer pairs for mispriming sites on the bisulfite-treated genome and determines potential non-specific amplification products with a new search algorithm. The options of primer-design and analysis for mispriming sites can be used sequentially or separately, both on bisulfite-treated and untreated sequences. In silico and in vitro tests of the software suggest that new PCR strategies may increase the efficiency of the amplification.

eMouseAtlas
type: Resource
type: NamedIndividual
has db xref: biotools:emap
has db xref: biotools:ma
has db xref: nif-0000-00038
has db xref: nif-0000-00505
synonym: e-Mouse Atlas
synonym: e-mouse Atlas
synonym: Edinburgh Mouse Atlas of Gene Expression
synonym: EMA
synonym: EMA Anatomy Atlas of Mouse Development
synonym: EMAGE Gene Expression Database
synonym: emouseatlas
abbrev: EMAGE
abbrev: EMAP
abbrev: MAP
abbrev: MAP2.0
IAO_0000115: Detailed multidimensional digital multimodal atlas of C57BL/6J mouse nervous system with data and informatics pipeline that can automatically register, annotate, and visualize large scale neuroanatomical and connectivity data produced in histology, neuronal tract tracing, MR imaging, and genetic labeling. MAP2.0 interoperates with commonly used publicly available databases to bring together brain architecture, gene expression, and imaging information into single, simple interface.Resource to visualise mouse development, identify anatomical structures, determine developmental stage, and investigate gene expression in mouse embryo. eMouseAtlas portal page allows access to EMA Anatomy Atlas of Mouse Development and EMAGE database of gene expression.EMAGE is freely available, curated database of gene expression patterns generated by in situ techniques in developing mouse embryo. EMA, e-Mouse Atlas, is 3-D anatomical atlas of mouse embryo development including histology and includes EMAP ontology of anatomical structure, provides information about shape, gross anatomy and detailed histological structure of mouse, and framework into which information about gene function can be mapped.

Integrative Modeling Platform
type: Resource
type: NamedIndividual
has db xref: SciRes_000187
synonym: IMP - the Integrative Modeling Platform
synonym: IMP the Integrative Modeling Platform
synonym: Integrative Modeling Platform (IMP)
abbrev: IMP
IAO_0000115: An open source C++ and Python toolbox for solving complex modeling problems, and a number of applications for tackling some common problems in a user-friendly way. Its broad goal is to contribute to a comprehensive structural characterization of biomolecules ranging in size and complexity from small peptides to large macromolecular assemblies, by integrating data from diverse biochemical and biophysical experiments. It can also be used from the Chimera molecular modeling system, or via one of several web applications.

Allen Institute for Brain Science Sleep Study
type: Resource
type: NamedIndividual
has db xref: nif-0000-00507
synonym: Sleep Study
abbrev: Allen Sleep Study
IAO_0000115: Collection of gene expression data in mouse brain for five different conditions of sleep and wakefulness to understand sleep deprivation and dynamic changes underlying sleep and wake cycles. Platform to generate cellular resolution expression data.

Influenza Virus Resource
type: Resource
type: NamedIndividual
has db xref: nif-0000-03023
has db xref: r3d100011004
synonym: NCBI Influenza Virus Resource
IAO_0000115: Database of data obtained from the NIAID Influenza Genome Sequencing Project as well as from GenBank, combined with tools for flu sequence analysis and annotation. In addition, it provides links to other resources that contain flu sequences, publications and general information about flu viruses. Users can search the Flu database, build queries, retrieve sequences, and apply analysis tools. This includes selecting influenza sequences by virus, subtype, host, and other criteria, finding complete genome sets, aligning sequence and others in the database (up to 1000 sequences), viewing clustering and phylogenetic trees, BLAST searching a flu sequence against the database, and more.

UCSF Spot
type: Resource
type: NamedIndividual
has db xref: OMICS_00849
IAO_0000115: Automatic software program for microarray image quantification.

BioImage Suite
type: Resource
type: NamedIndividual
has db xref: nif-0000-30179
synonym: Bioimagesuite Web
IAO_0000115: Web applications for analysis of multimodal/multispecies neuroimaging data. Image analysis software package. Has facilities for DTI and fMRI processing. Capabilities for both neuro/cardiac and abdominal image analysis and visualization. Many packages are extensible, and provide functionality for image visualization and registration, surface editing, cardiac 4D multi-slice editing, diffusion tensor image processing, mouse segmentation and registration, and much more. Can be intergrated with other biomedical image processing software, such as FSL, AFNI, and SPM.

BioMart Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-30184
synonym: BioMart software
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023.Platform provides free software and data services to international scientific community in order to foster scientific collaboration and facilitate scientific discovery process. Project adheres to open source philosophy that promotes collaboration and code reuse.

ProRata
type: Resource
type: NamedIndividual
has db xref: biotools:prorata
has db xref: OMICS_02502
synonym: prorata - Quantitative Proteomics Software
synonym: ProRata: A quantitative proteomics program for accurate protein abundance ratio estimation with confidence interval evaluation
IAO_0000115: A quantitative proteomics software program for accurate protein abundance ratio estimation with confidence interval evaluation.

BioPerl
type: Resource
type: NamedIndividual
has db xref: biotools:bioperl
has db xref: nif-0000-30188
has db xref: OMICS_04849
IAO_0000115: BioPerl is a community effort to produce Perl code which is useful in biology. This toolkit of perl modules is useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules in our repository. The BioPerl toolkit provides a library of hundreds of routines for processing sequence, annotation, alignment, and sequence analysis reports. It often serves as a bridge between different computational biology applications assisting the user to construct analysis pipelines. This chapter illustrates how BioPerl facilitates tasks such as writing scripts summarizing information from BLAST reports or extracting key annotation details from a GenBank sequence record. BioPerl includes modules written by Sohel Merchant of the GO Consortium for parsing and manipulating OBO ontologies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Allen Developing Mouse Brain Atlas
type: Resource
type: NamedIndividual
has db xref: nif-0000-00509
synonym: Allen Brain Atlas Developing Mouse Brain
IAO_0000115: Map of gene expression in developing mouse brain revealing gene expression patterns from embryonic through postnatal stages. Provides information about spatial and temporal regulation of gene expression with database. Feature include seven sagittal reference atlases created with a developmental ontology. These anatomic atlases may be viewed alongside in situ hybridization (ISH) data as well as by itself.

Biologic Stylus
type: Resource
type: NamedIndividual
has db xref: nif-0000-30198
synonym: biologicstylus
IAO_0000115: Biologic Stylus is Biologic Institute's Stylus simulation software suite. Programming Language: C++, Python

IntEnz- Integrated relational Enzyme database
type: Resource
type: NamedIndividual
has db xref: biotools:intenz
has db xref: nif-0000-03028
has db xref: r3d100010803
abbrev: IntEnz
IAO_0000115: IntEnz (Integrated relational Enzyme database) is a freely available resource focused on enzyme nomenclature. IntEnz is created in collaboration with the Swiss Institute of Bioinformatics (SIB). This collaboration is responsible for the production of the ENZYME resource. IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions.

neuromice
type: Resource
type: NamedIndividual
has db xref: nif-0000-00046
synonym: neuromice.org
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 08, 2013. A consortium of three facilities whose purpose is to establish, characterize, and distribute novel mutant mouse models with neural and/or behavioral phenotypes, and distribute them to the worldwide research community. Interested scientists are able to obtain information about mouse lines at all three sites in a single unified database. GOALS * Increase genomic and genetic tools for functional gene identification * Provide mice with mutations that alter the nervous system or behavior * Build collaborations between geneticists and neuroscientists The consortium is made up of three mutagenesis and phenotypic screening facilities, focused on identifying alterations in nervous system function and behavior, and established by NIH. They are the Neurogenomics Project at Northwestern University, the Neuroscience Mutagenesis Facility at The Jackson Laboratory, and the Neuromutagenesis Project of the Tennessee Mouse Genome Consortium. The NIH Neurogenomics Project at Northwestern University is directed by Dr. Joseph S. Takahashi, who also acts as the Director of the Neuromice.org consortium. Chemical mutagenesis is used to induce mutations throughout the genome and combined with phenotypic screens to detect mice with mutations. In order to maximize the genomic coverage and recover both dominant and recessive mutations, a dominant G1 screen and a recessive G3 screen are utilized. Phenotypic screens focus on five primary domains: learning and memory, behavioral responses to stress, responses to psychostimulants, circadian rhythmicity, and vision. The Neuroscience Mutagenesis Facility at the Jackson Laboratory is directed by Dr. Wayne N. Frankel. The Neuroscience Mutagenesis Facility is using a three-generation backcross breeding scheme to produce homozygous mutants and will thus recover dominant, semidominant, and recessive mutations. In addition, some mutagenesis will be done in ES cells followed by two gene…

Blue Brain Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-30208
synonym: Bluebrain
abbrev: Blue Brain
IAO_0000115: A Swiss-led project with the aim of reverse engineering the mammalian brain and achieving a complete virtual human brain. The researchers have demonstrated the validity of their method by developing a realistic model of a rat cortical column, consisting of about 10,000 neurons. The eventual goal is to simulate systems of millions and hundreds of millions of neurons. The virtual brain will be an exceptional tool giving neuroscientists a new understanding of the brain and a better understanding of neurological diseases. In five years of work, Henry Markram's team has perfected a facility that can create realistic models of one of the brain's essential building blocks. This process is entirely data driven and essentially automatically executed on the supercomputer. Meanwhile the generated models show a behavior already observed in years of neuroscientific experiments. These models will be basic building blocks for larger scale models leading towards a complete virtual brain.

R-pbutils
type: Resource
type: NamedIndividual
has db xref: OMICS_05140
IAO_0000115: An R software package providing plotting and convenience functions.

MITOMAP - A human mitochondrial genome database
type: Resource
type: NamedIndividual
has db xref: nif-0000-00511
has db xref: OMICS_01641
abbrev: MITOMAP
IAO_0000115: Database of polymorphisms and mutations of the human mitochondrial DNA. It reports published and unpublished data on human mitochondrial DNA variation. All data is curated by hand. If you would like to submit published articles to be included in mitomap, please send them the citation and a pdf.

BRENDA
type: Resource
type: NamedIndividual
has db xref: nif-0000-30222
has db xref: r3d100010616
synonym: BRaunschweig ENzyme Database
synonym: Brenda: Enzyme Database
synonym: BRENDA: The Comprehensive Enzyme Information System
synonym: Brenda: The Comprehensive Enzyme Information System
IAO_0000115: Database for functional enzyme and ligand-related information maintained as part of the German ELIXIR Node. Provides advanced query systems, evaluation tools, and various visualization options for the detailed assessment of enzyme properties. Enzyme data in BRENDA are classified according to the Enzyme Commission (EC) nomenclature of IUBMB.

Brian Simulator
type: Resource
type: NamedIndividual
has db xref: nif-0000-30223
synonym: Brian2
synonym: Brian 2
synonym: Brian spiking neural network simulator
abbrev: Brian
IAO_0000115: Software Python package for simulating spiking neural networks. Useful for neuroscientific modelling at systems level, and for teaching computational neuroscience. Intuitive and efficient neural simulator.

Allen Institute for Brain Science Transgenic Mouse Study
type: Resource
type: NamedIndividual
has db xref: nif-0000-00512
synonym: Transgenic Mouse Study
abbrev: Allen Transgenic Study
IAO_0000115: A comprehensive characterization of expression patterns of genetically-controlled markers or tool genes in the brains of transgenic mice generated by the Allen Institute as well as the broad scientific community. Providing standardized, detailed, anatomical profiling of transgene expression throughout the brain, this dataset is intended to reveal the potential of each transgenic mouse line and help researchers choose the appropriate tools for their studies. Transgenic mice are valuable tools to label selective neuronal or non-neuronal populations, modulate gene expression in these cells or manipulate activity of these cells for the study of neural circuits and brain function. The Allen Institute has launched a project to generate a variety of transgenic mouse lines, mainly using the Cre/lox system, to express fluorescent probes or neuronal activity manipulating tools in a variety of cell types in the brain. At the same time, utilizing Allen Institute's unique high-throughput capability, a pipeline is set up to characterize the ability in directing cell type specific expression in the brains of various transgenic mice generated by the Allen Institute as well as the broad scientific community. Through standardized, detailed, anatomical profiling of the transgene expression in the entire mouse brain, this dataset is intended to provide a comprehensive evaluation of the potential of each transgenic mouse line and help researchers choose the appropriate transgenic tools to study the function of different regions and/or cell types of the brain. This data release adds additional data to the existing set of new Cre-reporter lines generated at the Allen Institute that have stronger expression than other commonly used reporter lines are used to characterize approximately a dozen Cre-driver lines. The types of characterization data include digitized images (of sections sampling the entire brain) of colorimetric in situ hybridization (CISH), double fluorescent in situ hybridiza…

C. elegans Gene Knockout Consortium
type: Resource
type: NamedIndividual
has db xref: nif-0000-30230
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The mission of the C. elegans Gene Knockout Consortium is to facilitate genetic research of this important model system through the production of deletion alleles at specified gene targets. We choose targets based on investigator requests. Strains produced by the consortium are freely available with no restrictions to any investigator. At one time, our capacity dictated that we restrict requests to five per lab. This restriction no longer holds. Investigators are encouraged especially to register requests for functionally related groups of genes. Consortium strains are distributed by the C. elegans Genetic Center (CGC). In most cases, when you use the Consortium web site to request an existing allele, your request is forwarded automatically to the CGC. However, if you indicate that an existing allele is not satisfactory for your research, (for whatever reason), you may request that we generate another allele for the same target. Any information generated by the Consortium is entered into the official C. elegans data repository, WormBase.

Cambridge Cognition
type: Organization
type: NamedIndividual
has db xref: grid.450548.8
has db xref: ISNI: 0000 0004 0447 0405
has db xref: nif-0000-30232
synonym: Cambridge Cognition Ltd
synonym: Cambridge Cognition: Neuropsychological Cognitive Testing
synonym: Cantab
synonym: CantabConnect
IAO_0000115: Global commercial provider of cognitive assessment software for clinical trials, academic research and healthcare provision.

NOISeq
type: Resource
type: NamedIndividual
has db xref: OMICS_01311
IAO_0000115: Software used for the identification of differentially expressed genes from count data or previously normalized count data. It empirically models the noise distribution of count changes by contrasting fold-change differences (M) and absolute expression differences (D) for all the features in samples within the same condition. This reference distribution is then used to assess whether the M-D values computed between two conditions for a given gene is likely to be part of the noise or represent a true differential expression.

Coddle-Codons Optimized to Discover Deleterious LEsions
type: Resource
type: NamedIndividual
has db xref: nif-0000-30262
synonym: Choosing codons to Optimize Discovery of Deleterious Lesions
synonym: Codons Optimized to Discover Deleterious LEsions
abbrev: CODDLE
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Web-accessible program that identifies the region(s) of a user-selected gene and of its coding sequence (CDS) where the anticipated point mutations are most likely to result in deleterious effects on the gene's function. CODDLe separately handles 1) the prediction of changes which should truncate the protein and destabilize the RNA - nonsense changes and splice junction changes, and 2) the prediction of missense changes which should alter function of the gene product - those in conserved amino acid blocks in the CDS. Because the region(s) identified will be PCR amplified by the user and that amplicon will be used for polymorphism discovery, the application delivers primer pairs selected by Primer3 (Steve Rozen, Helen J. Skaletsky (1996,1997,1998)Primer3.) After selecting a primer pair, CODDLe returns a window with the selected amplicon and tabulates the effects of all possible polymorphisms which could be detected in that amplicon. CODDLe will not identify the regions of a gene where polymorphisms are most likely to be discovered. Others have shown that naturally occurring SNPs are found more often in the untranslated regions of a gene.

IPD - Immuno Polymorphism Database
type: Resource
type: NamedIndividual
has db xref: biotools:ipd
has db xref: nif-0000-03038
has db xref: r3d100010797
synonym: IPD - The Immuno Polymorphism Database
synonym: IPD-The Immuno Polymorphism Database
abbrev: IPD
IAO_0000115: A set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: * IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors, * IPD-MHC, is a database of sequences of the Major Histocompatibility Complex of different species; * IPD-human platelet antigens, alloantigens expressed only on platelets and * IPD-ESTDAB, which provides access to the European Searchable Tumour cell-line database, a cell bank of immunologically characterized melanoma cell lines.

CRAN
type: Resource
type: NamedIndividual
has db xref: nif-0000-30270
synonym: Comprehensive R Archive Network
synonym: The Comprehensive R Archive Network
synonym: the Comprehensive R Archive Network
IAO_0000115: Network of ftp and web servers around world that store identical, up to date, versions of code and documentation for R. Package archive network for R programming language.

Genetic Analysis Package
type: Resource
type: NamedIndividual
has db xref: nif-0000-30271
synonym: GAP
IAO_0000115: GAP is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, classic twin models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates.

ADNI - Alzheimer's Disease Neuroimaging Initiative
type: Resource
type: NamedIndividual
has db xref: nif-0000-00516
has db xref: SciRes_000144
synonym: Alzheimer's Disease Neuroimaging Initiative
synonym: Alzheimer's Disease Neuroimaging Initiative (ADNI)
synonym: Alzheimers Disease Neuroimaging Initiative
abbrev: ADNI
IAO_0000115: Database of the results of the ADNI study. ADNI is an initiative to develop biomarker-based methods to detect and track the progression of Alzheimer's disease (AD) that provides access to qualified scientists to their database of imaging, clinical, genomic, and biomarker data.

Dpos
type: Resource
type: NamedIndividual
has db xref: OMICS_00502
synonym: DANPOS
IAO_0000115: Peak-calling algorithm which analyzes changes in the location, fuzziness, and occupancy at each nucleosome or protein binding position.

Gene Weaver
type: Resource
type: NamedIndividual
has db xref: nif-0000-00517
has db xref: OMICS_02232
has db xref: r3d100012464
synonym: GeneWeaver
synonym: GeneWeaver - A system for the integration of functional genomics experiments
synonym: GeneWeaver.org
synonym: Ontological Discovery Environment
IAO_0000115: Freely accessible phenotype-centered database with integrated analysis and visualization tools. It combines diverse data sets from multiple species and experiment types, and allows data sharing across collaborative groups or to public users. It was conceived of as a tool for the integration of biological functions based on the molecular processes that subserved them. From these data, an empirically derived ontology may one day be inferred. Users have found the system valuable for a wide range of applications in the arena of functional genomic data integration.

Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes
type: Resource
type: NamedIndividual
has db xref: nif-0000-30292
synonym: Cancer Genomics Publication
IAO_0000115: Data set of a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, researchers analyzed mRNA expression levels corresponding to 12,600 transcript sequences in 186 lung tumor samples, including 139 adenocarcinomas resected from the lung. Hierarchical and probabilistic clustering of expression data defined distinct sub-classes of lung adenocarcinoma. Among these were tumors with high relative expression of neuroendocrine genes and of type II pneumocyte genes, respectively. Retrospective analysis revealed a less favorable outcome for the adenocarcinomas with neuroendocrine gene expression. The diagnostic potential of expression profiling is emphasized by its ability to discriminate primary lung adenocarcinomas from metastases of extra-pulmonary origin. These results suggest that integration of expression profile data with clinical parameters could aid in diagnosis of lung cancer patients.

pFind
type: Resource
type: NamedIndividual
has db xref: OMICS_02467
IAO_0000115: A search engine system for automated peptide and protein identification from tandem mass spectra.

IPI
type: Resource
type: NamedIndividual
has db xref: biotools:ipi
has db xref: nif-0000-03043
synonym: International Protein Index
synonym: IPI - International Protein Index
IAO_0000115: IPI provides a top level guide to the main databases (UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, RefSeq, Ensembl, TAIR, H-InvDB, Vega) that describe the proteomes of higher eukaryotic organisms. IPI: :1. effectively maintains a database of cross references between the primary data sources :2. provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) :3. maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. IPI is updated monthly in accordance with the latest data released by the primary data sources. As previously announced, the closure of IPI has been proposed for some time. Replacement data sets are now available through UniProt for human and mouse; sets for the other species contained within IPI are expected to be included as part of the UniProt release 2011_07. To allow users time to transition to using the new UniProt data sets, IPI releases will continue to be produced throughout the summer. The final release will be made in September 2011. Thereafter, the IPI website will cease to be maintained, although previous releases of the dataset will continue to be available from the FTP site. We would like to thank our users for their support and interest in this service.

Canadian College of Medical Geneticists
type: Organization
type: NamedIndividual
has db xref: OMICS_06305
abbrev: CCMG
IAO_0000115: National voluntary specialty organization that serves its members, governments and public by Certifying individuals who provide medical genetics services, Establishing professional and ethical standards of medical genetics services, Establishing standards of medical genetics training, Providing professional and public education, Informing public policy.

CBU Imaging Wiki
type: Resource
type: NamedIndividual
has db xref: nif-0000-30307
synonym: CBUImaging
synonym: Cognition and Brain Sciences Unit Imaging Wiki
synonym: MRC CBU Imaging Wiki
synonym: MRC Cognition and Brain Sciences Unit Imaging Wiki
IAO_0000115: Portal where neuroimaging studies are carried out using a Siemens 3T Tim Trio Magnetic Resonance Imaging (or MRI) scanner that is wholly dedicated to studies in Cognitive Neuroscience. From emotions and memories to language and learning, functional neuroimaging is being applied in many different areas of Cognitive Neuroscience. In many cases, this research relies upon support from healthy volunteers although neuroimaging studies are also being conducted in various clinical populations, including depression, anxiety, Parkinson's disease and Alzheimer's disease.

GenePaint
type: Resource
type: NamedIndividual
has db xref: nif-0000-00009
has db xref: SCR_017526
synonym: Atlas of Gene Expression Patterns in Mouse Embryo
abbrev: GenePaint.org
IAO_0000115: Digital atlas of gene expression patterns in developing and adult mouse. Several reference atlases are also available through this site. Expression patterns are determined by non-radioactive in situ hybridization on serial tissue sections. Sections are available from several developmental ages: E10.5, E14.5 (whole embryos), E15.5, P7 and P56 (brains only). To retrieve expression patterns, search by gene name, site of expression, GenBank accession number or sequence homology. For viewing expression patterns, GenePaint.org features virtual microscope tool that enables zooming into images down to cellular resolution.

CERAD - Consortium to Establish a Registry for Alzheimer's Disease
type: Resource
type: NamedIndividual
has db xref: nif-0000-00523
synonym: Consortium to Establish a Registry for Alzheimer's Disease
abbrev: CERAD
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023.Consortium that developed brief, standardized and reliable procedures for the evaluation and diagnosis of patients with Alzheimer's disease (AD) and other dementias of the elderly. These procedures included data forms, flipbooks, guidebooks, brochures, instruction manuals and demonstration tapes, which are now available for purchase. The CERAD assessment material can be used for research purposes as well as for patient care. CERAD has developed several basic standardized instruments, each consisting of brief forms designed to gather data on normal persons as well as on cognitively impaired or behaviorally disturbed individuals. Such data permit the identification of dementia based on clinical, neuropsychological, behavioral or neuropathological criteria. Staff at participating CERAD sites were trained and certified to administer the assessment instruments and to evaluate the subjects enrolled in the study. Cases and controls were evaluated at entry and annually thereafter including (when possible) autopsy examination of the brain to track the natural progression of AD and to obtain neuropathological confirmation of the clinical diagnosis. The CERAD database has become a major resource for research in Alzheimer's disease. It contains longitudinal data for periods as long as seven years on the natural progression of the disorder as well as information on clinical and neuropsychological changes and neuropathological manifestations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

AlzSWAN Knowledge Base
type: Resource
type: NamedIndividual
has db xref: nif-0000-00524
abbrev: AlzSWAN
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A community-driven knowledgebase of Alzheimer disease, in which researchers can annotate scientific claims, data, and information, putting these into the context of testable hypotheses and treatment discovery. This SWAN project adds a collection of hand-curated hypotheses to a research paper, which are then related through a set of discourse relationships. They can be browsed and relations between claims, as well as support networks for a specific claim, are made and visualized. AlzSWAN is where you explore scientific knowledge about Alzheimer disease and share your own ideas, comments and questions in a semantically structured system. AlzSWAN is enabled by Semantic Web technology, a new standard for knowledge organization and transfer on the Web. AlzSWAN organizes and manages knowledge using formal knowledge descriptions called ontologies. Using these formal knowledge descriptions, they can tie statements made in scientific publications or on the Web to scientific evidence, biological terminologies, and knowledgebases, and to claims and counterclaims made by other researchers.

BRAIN
type: Resource
type: NamedIndividual
has db xref: biotools:brain
has db xref: OMICS_02410
synonym: Baffling Recursive Algorithm for Isotope distributioN
synonym: Baffling Recursive Algorithm for Isotopic distributioN calculations
IAO_0000115: Software package for calculating aggregated isotopic distribution and exact center-masses for chemical substances (in this version composed of C, H, N, O and S).

MindSeer
type: Resource
type: NamedIndividual
has db xref: nif-0000-00525
IAO_0000115: A cross-platform application for 3D brain visualization for multi-modality neuroimaging data written in Java/Java3D, that runs in both standalone and client-server mode. It supports basic data management capabilities, visualization of 3D surfaces (SPM's output or OFF files), volumes (Analyze, NIFTI or Minc) and label sets. MindSeer has 2 different modes: # Client/Server is designed to allow users to visualize data that is stored centrally and enhance collaboration. # Standalone mode is available to view local data and is built for more performance than Client/Server Both modes have the same interface and support the same features. It has a modular architecture and is designed to be extensible. Requirements: # Java 5.0 or above. # Java Web Start. # Java3D (installed automatically by Web Start).

ISFinder
type: Resource
type: NamedIndividual
has db xref: biotools:isfinder
has db xref: nif-0000-03050
synonym: IS Finder
synonym: Isfinder
IAO_0000115: Database of a list of insertion sequences isolated from eubacteria and archaea. It is organized into individual files containing their general features (name, size, origin, family.....) as well as their DNA and potential protein sequences. Although most of the entries have been identified as individual elements, a growing number are included from their description in sequenced bacterial genomes. The search engine permits the retrieval and display of individual and groups of ISs based on a combination of their general features. Two levels of search are available. The simple search option enables the user to sort elements using a limited number of basic items whereas the extensive search offers an additional set of possibilities such as comparisons of the sequences of terminal inverted repeats and a variety of different layout displays. Built in links are provided to: the EMBL sequence database, the NCBI taxonomy database and to the ESF plasmid database. At present, only individual sequences can be downloaded one by one for comparison. An on-line BLAST facility is available and in future versions direct access to additional analytical tools will be provided on line. Direct submission of ISs is encouraged using the on-line form provided.

JAX Neuroscience Mutagenesis Facility Protocols
type: Resource
type: NamedIndividual
has db xref: nif-0000-00527
synonym: JAX NMF Protocols
synonym: JAX Protocols
synonym: Protocols of the Neuroscience Mutagenesis Facility
synonym: Protocols of the NMF
abbrev: NMF Protocols
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. The Neuroscience Mutagenesis Facility of the Jackson Laboratory (NMF) was established to produce new neurological mouse models that could serve as experimental models for the exploration of basic neurobiological mechanisms and diseases. The protocols are available. The impetus for the program resulted from the recognition that * the value of genomic data would remain limited unless more information about the functionality of its individual components became available, and * the task of linking genes to specific behavior would best be accomplished by employing a combination of different approaches. In an effort to complement already existing programs, the Neuroscience Mutagenesis Facility decided to use: a random, genome-wide approach to mutagenesis, i.e. N-ethyl-N-nitrosourea (ENU) as the mutagen; a three-generation back-cross breeding scheme to focus on the detection of recessive mutations; behavioral screens selective for the detection of phenotypes deemed useful for the program goals. Protocols: * Genetics ** Production of Mice for a Genome-Wide ENU Mutagenesis Screen ** Production of Mice using Chemical Mutagenesis of Mouse ES Cells * Protocols ** Step by step procedures-- Mouse mutagenesis with ENU ** Step by step procedures-- ES Cell mutagenesis with EMS * Phenotyping: Overview * Protocols:(currently only screens marked * are in use) ** Acoustic startle response (ASR) ** Auditory brainstem response (ABR) ** CLAMSTM(former CCMS) ** Creatine kinase ** Developmental Screen * ** Eye and Vision * ** Gait Analysis ** Gustation ** Observation * ** Seizure threshold * ** Additional Background Information

Conceptweblog
type: Resource
type: NamedIndividual
has db xref: nif-0000-03053
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented July 6, 2016. This blog, which is maintained under the aegis of the Concept Web Alliance, is devoted to the Concept Web a dynamic, interactive fabric of concepts and their relationships. The Concept Web is constructed from, inter alia, research literature, Internet databases and other web sites together with off-line resources. The aim of creating the Concept Web is to remove both redundancy and ambiguity from available knowledge in order to help deal with information overload, to semantically "connect" concepts, and so to maximize the potential for knowledge discovery.

MicroArray and Gene Expression Markup Language
type: Resource
type: NamedIndividual
has db xref: nif-0000-30390
abbrev: MAGE-ML
IAO_0000115: A language / data exchange format designed to describe and communicate information about microarray based experiments that is based on XML and can describe microarray designs, microarray manufacturing information, microarray experiment setup and execution information, gene expression data and data analysis results. MAGE-ML has been automatically derived from Microarray Gene Expression Object Model (MAGE-OM), which is developed and described using the Unified Modelling Language (UML) -- a standard language for describing object models. Descriptions using UML have an advantage over direct XML document type definitions (DTDs), in many respects. First they use graphical representation depicting the relationships between different entities in a way which is much easier to follow than DTDs. Second, the UML diagrams are primarily meant for humans, while DTDs are meant for computers. Therefore MAGE-OM should be considered as the primary model, and MAGE-ML will be explained by providing simplified fragments of MAGE-OM, rather then XML DTD or XML Schema. (from the description by Ugis Sarkans) The field of gene expression experiments has several distinct technologies that a standard must include. These include single vs. dual channel experiments, cDNA vs. oligonucleotides. Because of these different technologies and different types of gene expression experiments, it is not expected that all aspects of the standard will be used by all organizations. Given the massive amount of data associated with a single set of experiments, it is felt that Extensible Markup Language (XML) is the best way to describe the data. The use of a Document Type Definition (DTD) allows a well-defined tag set, a vocabulary, to describe the domain of gene expression experiments. It also has the virtue of compressing very well so that files in an XML format compress to ten percent of their original size. XML is now widely accepted as a data exchange format across multiple platforms.

Nomenclature Committee of IUBMB
type: Resource
type: NamedIndividual
has db xref: nif-0000-03054
synonym: IUBMB Nomenclature Committee
synonym: Nomenclature Committee of the International Union of Biochemistry and Molecular Biology
abbrev: NC-IUBMB
IAO_0000115: Portal for Recommendations on Biochemical and Organic Nomenclature, Symbols and Terminology. NC IUBMB,established by IUPAC-IUBMB Joint Commission, publishes standards on biochemical nomenclature, including enzyme nomenclature, in some cases jointly with the International Union of Pure and Applied Chemistry (IUPAC).

Isopat
type: Resource
type: NamedIndividual
has db xref: OMICS_02409
synonym: isopat: Calculation of isotopic pattern for a given molecular formula
IAO_0000115: Software function that calculates the isotopic pattern (fine structures) for a given chemical formula.

R-pbh5
type: Resource
type: NamedIndividual
has db xref: OMICS_05139
IAO_0000115: Software library for accessing data in HDF5 files produced by Pacific Biosciences sequencing machines. The R package supports accessing data from: cmp.h5, bas.h5, pls.h5, and trc.h5.

pbh5tools
type: Resource
type: NamedIndividual
has db xref: OMICS_05138
IAO_0000115: Software tools for manipulating HDF5 files produced by Pacific Biosciences. Specifically, this package provides functionality for manipulating and extracting data from cmp.h5 and bas.h5 files.

Integrated X Chromosome Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-03059
synonym: The Integrated X Chromosome Database
abbrev: IXDB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 08, 2013. A repository for physical mapping data of the human X chromosome that aims at providing a global view of genomic data at a chromosomal level including an integrated physical, genetic, transcript and sequence map of the human X chromosome. This implies acquiring, understanding and formatting an enormous amount of experimental results and can only be accomplished progressively. We have chosen to start the integration process with YAC maps generated by the community. These provide the basis for future higher resolution physical maps, as well as emerging transcript and sequence maps. The current content of IXDB therefore reflects this situation, with the emphasis placed on YAC mapping data. Due to their immediate value, IXDB has also started to systematically include bacterial clone contig maps and EST data. Currently IXDB does not store sequence data, although links to nucleic sequence databases are provided.

SMRT View
type: Resource
type: NamedIndividual
has db xref: biotools:smrt_view
has db xref: OMICS_05137
synonym: SMRT-View
IAO_0000115: An open source Genome Browser that visualizes data generated by PacBio Sequencing Systems. * Users can explore and interact with all types of analysis results, including resequencing, De novo, cDNA, and barcoding. * Users can also visualize base modifications, base identification and motifs analysis results.

JASPAR
type: Resource
type: NamedIndividual
has db xref: nif-0000-03061
has db xref: OMICS_00538
has db xref: r3d100010091
synonym: JASPAR CORE
synonym: JASPAR CORE database
synonym: JASPAR database
IAO_0000115: Open source database of curated, non-redundant set of profiles derived from published collections of experimentally defined transcription factor binding sites for multicellular eukaryotes. Consists of open data access, non-redundancy and quality. JASPAR CORE is smaller set that is non-redundant and curated. Collection of transcription factor DNA-binding preferences, modeled as matrices. These can be converted into Position Weight Matrices (PWMs or PSSMs), used for scanning genomic sequences. Web interface for browsing, searching and subset selection, online sequence analysis utility and suite of programming tools for genome-wide and comparative genomic analysis of regulatory regions. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service applications programming interface for matrix retrieval.

Jenalib: Jena Library of Biological Macromolecules
type: Resource
type: NamedIndividual
has db xref: nif-0000-03062
synonym: Image library of biological macromolecules
synonym: IMB Jena Image Library of Biological Macromolecules
synonym: Jena Library of Biological Macromolecules
abbrev: JenaLib
IAO_0000115: Database aimed at disseminating information on three-dimensional biopolymer structures with an emphasis on visualization and analysis. It provides access to all structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database (NDB). In addition, basic information on the architecture of biopolymer structures is available. The JenaLib intends to fulfill both scientific and educational needs. Authors who are willing to make available images or coordinates to the scientific community via the Image Library of Biological Macromolecules are requested to contact the author. A PDB/SWISS-PROT cross-reference database combines information from both PDB and SWISS-PROT, thus providing significantly more cross-references than either PDB or SWISS-PROT. The existing brief descriptions of X-ray, NMR and FTIR methods for structure determination are supplemented by information on circular dichroism.

Cytoscape
type: Resource
type: NamedIndividual
has db xref: nif-0000-30404
synonym: Complex Network Analysis Visualization
synonym: Cytoscape 2.6
synonym: Cytoscape 3.0
IAO_0000115: Software platform for complex network analysis and visualization. Used for visualization of molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.

enviPat
type: Resource
type: NamedIndividual
has db xref: OMICS_02408
synonym: enviPat: Isotope pattern profile and centroid calculation for mass spectrometry
IAO_0000115: Software for fast and very memory-efficient calculation of isotope patterns, subsequent convolution to theoretical envelopes (profiles) plus valley detection and centroidization or intensoid calculation. Batch processing, resolution interpolation, wrapper, adduct calculations and molecular formula parsing.

bwtool
type: Resource
type: NamedIndividual
has db xref: biotools:bwtool
has db xref: OMICS_05125
IAO_0000115: A command-line utility for bigWig files designed to read bigWig files rapidly and efficiently, providing functionality for extracting data and summarizing it in several ways, globally or at specific regions. Its functionality is subdivided into subprograms that roughly fall into three categories: data extraction, analysis, and data modification, although e.g. in the case of the matrix program or the sax program, the boundary between data extraction and analysis isn't very strong. The data modification programs all have the behavior that a bigWig is inputted and a new bigWig is outputted.

DGAP
type: Resource
type: NamedIndividual
has db xref: nif-0000-30414
synonym: Diabetes Genome Anatomy Project
synonym: The Diabetes Genome Anatomy Project
abbrev: DGAP
IAO_0000115: Produce resources to unravel the interface between insulin action, insulin resistance and the genetics of type 2 diabetes including an annotated public database, standardized protocols for gene expression and proteomic analysis, and ultimately diabetes-specific and insulin action-specific DNA chips for investigators in the field. The project aims to identify the sets of the genes involved in insulin action and the predisposition to type 2 diabetes, as well as the secondary changes in gene expression that occur in response to the metabolic abnormalities present in diabetes. There are five major and one pilot project involving human and rodent tissues that are designed to: * Create a database of the genes expressed in insulin-responsive tissues, as well as accessible tissues, that are regulated by insulin, insulin resistance and diabetes. * Assess levels and patterns of gene expression in each tissue before and after insulin stimulation in normal and genetically-modified rodents; normal, insulin resistant and diabetic humans, and in cultured and freshly isolated cell models. * Correlate the level and patterns of expression at the mRNA and/or protein level with the genetic and metabolic phenotype of the animal or cell. * Generate genomic sequence from a panel of humans with type 2 diabetes focusing on the genes most highly regulated by insulin and diabetes to determine the range of sequence and expression variation in these genes and the proteins they encode, which might affect the risk of diabetes or insulin resistance. The DGAP project will define: * the normal anatomy of gene expression, i.e. basal levels of expression and response to insulin. * the morbid anatomy of gene expression, i.e., the impact of diabetes on expression patterns and the insulin response. * the extent to which genetic variability might contribute to the alterations in expression or to diabetes itself.

MoSDi
type: Resource
type: NamedIndividual
has db xref: OMICS_06271
synonym: Motif Statistics and Discovery
synonym: Motif Statistics and Discovery - Sequence analysis toolkit for bioinformatics
IAO_0000115: Sequence analysis toolkit that contains a lot of sequence analysis algorithms, including methods for 1) motif statistics, e.g. compute the exact occurrence count distribution of a motif, 2) exact motif discovery: extraction of motifs with provably optimal p-value, 3) analysis of pattern matching algorithms: compute (for given algorithm and pattern) the exact distribution of the number of character accesses caused by searching a random text, 4) statistics of fragment masses resulting from proteolytic cleavage of proteins, 5) computing the expectated read length of sequencing reads for a given dispensation order (for 454 or IonTorrent) and 6) analysing sensitivity of spaced alignment seeds.

tweeDEseq
type: Resource
type: NamedIndividual
has db xref: biotools:tweedeseq
has db xref: OMICS_02406
synonym: tweeDEseq: RNA-seq data analysis using the Poisson-Tweedie family of distributions
IAO_0000115: Software for differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions.

DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins
type: Resource
type: NamedIndividual
has db xref: nif-0000-30426
abbrev: DP-Bind
IAO_0000115: This web-server takes a user-supplied sequence of a DNA-binding protein and predicts residue positions involved in interactions with DNA. Prediction can be performed using a profile of evolutionary conservation of the input sequence automatically generated by the web-server or the input sequence alone. Three prediction methods are run for each input sequence and consensus prediction is generated.

Dana-Farber Cancer Institute
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100007886
has db xref: grid.65499.37
has db xref: ISNI: 0000 0001 2106 9910
has db xref: nif-0000-30432
has db xref: Wikidata: Q1159198
synonym: Dana Farber Cancer Institute
synonym: Dana-Farber
abbrev: DFCI
IAO_0000115: Cancer institute that provides expert, compassionate care to children and adults with cancer while advancing the understanding, diagnosis, treatment, cure, and prevention of cancer and related diseases. As an affiliate of Harvard Medical School and a Comprehensive Cancer Center designated by the National Cancer Institute, the Institute also provides training for new generations of physicians and scientists, designs programs that promote public health particularly among high-risk and underserved populations, and disseminates innovative patient therapies and scientific discoveries to their target community across the United States and throughout the world.

DIALIGN
type: Resource
type: NamedIndividual
has db xref: biotools:dialign-tx
has db xref: nif-0000-30417
has db xref: OMICS_00973
has db xref: OMICS_24606
synonym: DIALIGN at GOBICS
IAO_0000115: Tool for multiple sequence alignment using various sources of external information that is particularly useful to detect local homologies in sequences with low overall similarity. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies. Several versions of DIALIGN are available online at GOBICS, http://dialign.gobics.de/

Brain Pharmacological Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-00168
synonym: Brain Pharmacology Database
synonym: BrainPharm
IAO_0000115: A database to support research on drugs for the treatment of different neurological disorders. It contains agents that act on neuronal receptors and signal transduction pathways in the normal brain and in nervous disorders. It enables searches for drug actions at the level of key molecular constituents, cell compartments and individual cells, with links to models of these actions.

Coriell Institute for Medical Research
type: Resource
type: NamedIndividual
has db xref: nif-0000-00169
synonym: Coriell Institute
abbrev: Coriell
IAO_0000115: Non-profit research center dedicated to the study of the human genome. Expert staff and pioneering programs in the fields of personalized medicine, cell biology, cytogenetics, genotyping, and biobanking drive our mission. The emerging field of personalized medicine draws upon a person's genomic information to tailor treatments and prescription drug dosing to optimize health outcomes. The Coriell Personalized Medicine Collaborative (CPMC) research study is seeking to understand the usefulness of genetic risk and pharmacogenomics in clinical decision-making and healthcare management. Coriell has a distinguished history in cell biology. We are building upon this expertise by playing an important role in induced pluripotent stem (iPS) cell research. These powerful cells, which can be made from skin cells or blood, are revolutionizing the way human disease is studied and how drugs are developed. The decline of neurons afflicted with Alzheimer's disease or pancreatic cells fighting diabetes can be studied in a Petri dish. By proving efficacy within the diseased environment prior to clinical trial, drugs can move through the pipeline quicker to reach patients sooner. In addition to pioneering cutting-edge research initiatives, Coriell offers custom research services including cell culture, cytogenetic analyses, and molecular biology to the scientific community. Furthermore, Coriell's Genotyping and Microarray Center is one of the nation's largest centers, with high-throughput DNA analysis systems from Illumina and Affymetrix. The Center is CLIA-certified in 48 states.

PacBioToCA
type: Resource
type: NamedIndividual
has db xref: OMICS_05093
synonym: pacBioToCA (error correction via Celera Assembler)
IAO_0000115: A module in the Celera Assembler software package that performs error correction on PacBio long reads by mapping shorter, high accuracy reads onto the long reads.

DOE Joint Genome Institute
type: Resource
type: NamedIndividual
has db xref: nif-0000-30425
synonym: Department of Energy Joint Genome Institute
synonym: DOE Joint Genome Institute - Enabling Advances in Bioenergy & Environmental Research
synonym: Joint Genome Institute
abbrev: DOE JGI
abbrev: JGI
IAO_0000115: Institute to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup. Supported by the DOE Office of Science, the DOE JGI unites the expertise at Lawrence Berkeley National Laboratory, Lawrence Livermore National Laboratory, and the HudsonAlpha Institute for Biotechnology. The facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.

DiNuP
type: Resource
type: NamedIndividual
has db xref: OMICS_00503
synonym: DiNuP - A Systematic Approach to Identify Regions of Differential Nucleosome Positioning
IAO_0000115: Software that compares the nucleosome profiles generated by high-throughput sequencing between different conditions. It provides a statistical p-value for each identified RDNP based on the difference of read distributions. DiNuP also empirically estimates the FDR as a cutoff when two samples have different sequencing depths and differentiate reliable RDNPs from the background noise.

DaliLite Pairwise comparison of protein structures
type: Resource
type: NamedIndividual
has db xref: nif-0000-30431
synonym: DaliLite - Pairwise alignment of protein structures
abbrev: DaliLite
IAO_0000115: Tool that computes optimal and suboptimal structural alignments between two protein structures. It will compare all chains in the first structure against all chains in the second (unless specific chain IDs are given). The resulting superimposed coordinate files can be downloaded or viewed interactively in Jmol. The Dali method optimizes a weighted sum of similarities of intramolecular distances. Suboptimal alignments do not overlap the optimal alignment or each other. Suboptimal alignments detected by the program are reported if the Z-score is above 2; they may be of interest if there are internal repeats in either structure. SOAP Web services are also available.

XNAT - The Extensible Neuroimaging Archive Toolkit
type: Resource
type: NamedIndividual
has db xref: nif-0000-00531
synonym: Extensible Neuroimaging Archive Toolkit
synonym: Extensible Neuroimaging Archive Toolkit (XNAT)
abbrev: XNAT
IAO_0000115: Software platform designed to facilitate common management and productivity tasks for neuroimaging and associated data.

Visiome Platform
type: Resource
type: NamedIndividual
has db xref: nif-0000-00048
abbrev: Visiome
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023.Analytical tools. Archive files may be written in any format and may include explanatory figures, program sources, readme files, and other related files. The readme file describes the purpose and usage of the archive file. This data sharing framework allows users to improve the reproducibility of simulations. Users can browse the platform contents via branch sites (A catalogue of illusions, Visitope), which introduce user friendly view of items such as basic images and original artworks of visual illusions with high resolution. The items in Visiome Platform are useful not only for reproducing the published results, but also for advancing and expanding the research in Vision Science.

Brain Operation Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-03080
synonym: BODB (Brain Operation DataBase)
abbrev: BODB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. BODB offers a way to document computational models of brain function by linking each model to Brain Operating Principles (BOPs), related brain regions, Summaries of Simulation Results (SSRs)and Summaries of Experimental Data (SEDs) used either to design or to test the model. Tools are provided to search for related models and to compare their coverage of SEDs. This allows automatic benchmarking of a model against a cluster of models addressing similar BOPs or SEDs or brain regions. Tools allow display of brain imaging results against a human brain applet; a new tool will link data to a macaque brain applet.

Gutentag
type: Resource
type: NamedIndividual
has db xref: OMICS_02396
synonym: gutentag - A genetic sequence database for labs that can be browsed using tags
IAO_0000115: An interactive, user-editable genetic sequence database tool, targeted at molecular biology research groups that can be browsed using tags. The tool is Web 2.0-flavoured, allowing users to do more than just retrieve information. Its focus on user-editability is supported by the use of tags (metadata) associated with genetic sequences. Several methods of retrieving stored data are available including tag-clouds, BLAST and keyword searches. Also, sequence tags related to HGNC gene names, conserved domains (CDD) and GO terms can be automatically generated given sequence data. The tool is constructed using the high-level Python web framework, Django, with a SQLite3 backend.

CompuCell3D
type: Resource
type: NamedIndividual
has db xref: nlx_157668
abbrev: CC3D
IAO_0000115: Open-source simulation environment for multi-cell, single-cell-based modeling of tissues, organs and organisms. It uses Cellular Potts Model to model cell behavior.

Parametric Time Warping
type: Resource
type: NamedIndividual
has db xref: OMICS_02392
synonym: ptw: Parametric Time Warping
abbrev: ptw
IAO_0000115: Software that aligns patterns, i.e. it aims to put corresponding features at the same locations. The algorithm searches for an optimal polynomial describing the warping. It is possible to align one sample to a reference, several samples to the same reference, or several samples to several references. One can choose between calculating individual warpings, or one global warping for a set of samples and one reference. Two optimization criteria are implemented: RMS (Root Mean Square error) and WCC (Weighted Cross Correlation).

SurvComp
type: Resource
type: NamedIndividual
has db xref: OMICS_02373
synonym: survcomp - Performance Assessment and Comparison for Survival Analysis
abbrev: survcomp
IAO_0000115: R package providing functions to assess and to compare the performance of risk prediction (survival) models.

Interaction Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157444
abbrev: IXNO
IAO_0000115: Ontology to enable curation of chemical-gene and chemical-protein interactions for the Comparative Toxicogenomics Database (CTD), a freely available resource that aims to promote understanding and novel hypothesis development about the effects of the environment on human health.

SASqPCR
type: Resource
type: NamedIndividual
has db xref: OMICS_02375
synonym: SASqPCR: robust and rapid analysis of RT-qPCR data in SAS
IAO_0000115: All-in-one computer program for robust and rapid analysis of quantitative reverse transcription real-time polymerase chain reaction (RT-qPCR) data in SAS. It incorporates all functions important for RT-qPCR data analysis including assessment of PCR efficiencies, validation of internal reference genes and normalizers, normalization of confounding variations across samples and statistical comparisons of target gene expression in parallel samples. The program is highly automatic in data analyses and result output. The input data have no limitations for the number of genes or cDNA samples. Users can simply change the macro variables to test various analytical strategies, optimize results and customize the analytical processes. The program is also extendable allowing advanced SAS users to develop particular statistical tests appropriate for their experimental designs. Thus users are the actual decision-makers controlling RT-qPCR data analyses. The program has to be used in SAS software; however, extensive SAS programming knowledge is not required.

Developmental Therapeutics Program
type: Resource
type: NamedIndividual
has db xref: nif-0000-30447
synonym: Developmental Therapeutics Program NCI/NIH
abbrev: DTP
IAO_0000115: Portal for preclinical information and research materials, including web-accessible data and tools, NCI-60 Tumor Cell Line Screen, compounds in vials and plates, tumor cells, animals, and bulk drugs for investigational new drug (IND)-directed studies. DTP has been involved in the discovery or development of more than 70 percent of the anticancer therapeutics on the market today, and will continue helping the academic and private sectors to overcome various therapeutic development barriers, particularly through supporting high-risk projects and therapeutic development for rare cancers. Initially DTP made its drug discovery and development services and the results from the human tumor cell line assay publicly accessible to researchers worldwide. At first, the site offered in vitro human cell line data for a few thousand compounds and in vitro anti-HIV screening data for roughly 42,000 compounds. Today, visitors can find: * Downloadable in vitro human tumor cell line data for some 43,500 compounds and 15,000 natural product extracts * Results for 60,000 compounds evaluated in the yeast assay * In vivo animal model results for 30,000 compounds * 2-D and 3-D chemical structures for more than 200,000 compounds * Molecular target data, including characterizations for at least 1,200 targets, plus data from multiple cDNA microarray projects In addition to browsing DTP's databases and downloading data, researchers can request individual samples or sets of compounds on 96-well plates for research, or they can submit their own compounds for consideration for screening via DTP's online submission form. Once a compound is submitted for screening, researchers can follow its progress and retrieve data using a secure web interface. The NCI has collected information on almost half a million chemical structures in the past 50 years. DTP has made this information accessible and useful for investigators through its 3-D database, a collection of three-dimensional structures for more than…

Distant Regulatory Elements
type: Resource
type: NamedIndividual
has db xref: biotools:dire
has db xref: nif-0000-30448
synonym: Distant Regulatory Elements of co-regulated genes
abbrev: DiRE
IAO_0000115: Web server based on the Enhancer Identification (EI) method, to determine the chromosomal location and functional characteristics of distant regulatory elements (REs) in higher eukaryotic genomes. The server uses gene co-expression data, comparative genomics, and combinatorics of transcription factor binding sites (TFBSs) to find TFBS-association signatures that can be used for discriminating specific regulatory functions. DiRE's unique feature is the detection of REs outside of proximal promoter regions, as it takes advantage of the full gene locus to conduct the search. DiRE can predict common REs for any set of input genes for which the user has prior knowledge of co-expression, co-function, or other biologically meaningful grouping. The server predicts function-specific REs consisting of clusters of specifically-associated TFBSs, and it also scores the association of individual TFs with the biological function shared by the group of input genes. Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data.

enviPick
type: Resource
type: NamedIndividual
has db xref: OMICS_05010
synonym: enviPick: Peak picking for high resolution mass spectrometry data
IAO_0000115: Software for sequential partitioning, clustering and peak detection of centroided LC-MS mass spectrometry data (.mzXML). Interactive result and raw data plot.

GeneFisher
type: Resource
type: NamedIndividual
has db xref: biotools:genefisher
has db xref: OMICS_02341
synonym: GeneFisher2 - Interactive PCR Primer Design
abbrev: GeneFisher2
IAO_0000115: A web-based program for designing degenerate primers. The procedure leads to isolation of genes in a target organism using multiple alignments of related genes from different organisms. The term gene fishing refers to the technique where PCR is used to isolate a postulated but unknown target sequence from a pool of DNA.

Triplex
type: Resource
type: NamedIndividual
has db xref: biotools:triplex
has db xref: OMICS_06259
synonym: triplex - Search and visualize intramolecular triplex-forming sequences in DNA
IAO_0000115: Software package that provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many canonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D.

LIPID MAPS Proteome Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-03085
synonym: LIPID MAPS Proteome Database (LMPD)
abbrev: LMPD
IAO_0000115: Database of lipid related proteins representing human and mouse proteins involved in lipid metabolism. Collection of lipid related genes and proteins contains data for genes and proteins from Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Caenorhabditis elegans, Escherichia coli, Macaca mulata, Drosophila melanogaster, Arabidopsis thaliana and Danio rerio.

MPprimer
type: Resource
type: NamedIndividual
has db xref: OMICS_02364
synonym: MPprimer: a program for reliable multiplex PCR primer design
IAO_0000115: A software program for reliable multiplex PCR primer design. It employs the widely used primer design program Primer3 and the primer specificity evaluation program MFEprimer to design and evaluate the candidate primers based on genomic or transcript DNA database, followed by careful examination to avoid primer dimerization. The graph-expanding algorithm derived from the greedy algorithm was used to determine the optimal primer set combinations (PSCs) for multiplex PCR. In addition, it provides a virtual electrophotogram to help users choose the best PSC. It is a valuable tool for designing specific, no dimer formation and amplicons size constrained PSCs to improve the multiplex PCR experiments.

PDP++ Software Home Page
type: Resource
type: NamedIndividual
has db xref: nif-0000-00172
synonym: Emergent
abbrev: PDP++
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The PDP++ software is a neural-network simulation system written in C++. It represents the next generation of the PDP software originally released with the McClelland and Rumelhart Explorations in Parallel Distributed Processing Handbook, MIT Press, 1987. It is easy enough for novice users, but very powerful and flexible for research use. The new version of PDP++, released 8/21/07, is now called Emergent.

MIPE
type: Resource
type: NamedIndividual
has db xref: OMICS_02358
synonym: Minimal Information for PCR Experiments
IAO_0000115: A XML format that enables genomics researchers to store critical information on PCR experiments. Accompagnying perl scripts are written to read from (dbSTS) or write to a MIPE XML file.

MFEprimer
type: Resource
type: NamedIndividual
has db xref: biotools:mfeprimer-2.0
has db xref: OMICS_02355
synonym: MFEprimer-2.0
IAO_0000115: A fast thermodynamics-based software program for checking PCR primer specificity against genomic DNA and mRNA/cDNA sequence databases.

DnaSP
type: Resource
type: NamedIndividual
has db xref: nif-0000-30461
has db xref: OMICS_01820
synonym: DNA Sequence Polymorphism
IAO_0000115: A software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters. DnaSP can also carry out several tests of neutrality: Hudson, Kreitman and Aguad (1987), Tajima (1989), McDonald and Kreitman (1991), Fu and Li (1993), and Fu (1997) tests. Additionally, DnaSP can estimate the confidence intervals of some test-statistics by the coalescent. The results of the analyses are displayed on tabular and graphic form.

FAS-DPD
type: Resource
type: NamedIndividual
has db xref: OMICS_02340
synonym: family-specific degenerate primer design
IAO_0000115: Software program to design degenerate primers for PCR.

brainmap.org
type: Resource
type: NamedIndividual
has db xref: nif-0000-00049
synonym: BrainMap Database
abbrev: BrainMap
IAO_0000115: A community database of published functional and structural neuroimaging experiments with both metadata descriptions of experimental design and activation locations in the form of stereotactic coordinates (x,y,z) in Talairach or MNI space. BrainMap provides not only data for meta-analyses and data mining, but also distributes software and concepts for quantitative integration of neuroimaging data. The goal of BrainMap is to develop software and tools to share neuroimaging results and enable meta-analysis of studies of human brain function and structure in healthy and diseased subjects. It is a tool to rapidly retrieve and understand studies in specific research domains, such as language, memory, attention, reasoning, emotion, and perception, and to perform meta-analyses of like studies. Brainmap contains the following software: # Sleuth: database searches and Talairach coordinate plotting (this application requires a username and password) # GingerALE: performs meta-analyses via the activation likelihood estimation (ALE) method; also converts coordinates between MNI and Talairach spaces using icbm2tal # Scribe: database entry of published functional neuroimaging papers with coordinate results

ImageJ
type: Resource
type: NamedIndividual
has db xref: 2012ascl.soft06013R
has db xref: ascl:1206.013
has db xref: nif-0000-30467
has db xref: Q1659584
has db xref: rid_000070
has db xref: SCR_018407
synonym: Image J
synonym: ImageJ2
synonym: ImageJ - Image Processing and Analysis in Java
IAO_0000115: Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets.

SURPI
type: Resource
type: NamedIndividual
has db xref: OMICS_04623
synonym: Sequence-based Ultra-Rapid Pathogen Identification
IAO_0000115: Software providing a computational pipeline for pathogen identification from complex metagenomic next-generation sequencing (NGS) data generated from clinical samples.

Cancer Genome Anatomy Project
type: Resource
type: NamedIndividual
has db xref: biotools:cgap
has db xref: nif-0000-30468
synonym: Cancer Genome Anatomy Project (CGAP)
abbrev: CGAP
IAO_0000115: Project to determine the gene expression profiles of normal, precancer, and cancer cells, whose generated resources are available to the cancer community. Interconnected modules provide access to all CGAP data, bioinformatic analysis tools, and biological resources allowing the user to find in silico answers to biological questions in a fraction of the time it once took in the laboratory. * Genes * Tissues * Pathways * RNAi * Chromosomes * SAGE Genie * Tools

NIH Image
type: Resource
type: NamedIndividual
has db xref: nif-0000-30469
IAO_0000115: Public image processing and analysis program for Macintosh.

NIDDK- National Institute of Diabetes and Digestive and Kidney Diseases Obesity Resources
type: Resource
type: NamedIndividual
has db xref: nif-0000-00551
synonym: NIDDKObesity Resources
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented May 23, 2017. This website contains resources for obesity researchers including: Obesity Databases, Registries and Information; Obesity Multicenter Clinical Research; Obesity Basic Research Networks; Obesity Reagents; Obesity Services; Obesity Standardization Programs; Obesity Tissues, Cells, Animals; Obesity Useful Tools.

flytrap
type: Resource
type: NamedIndividual
has db xref: nif-0000-00051
has db xref: r3d100011203
abbrev: Flytrap
IAO_0000115: Flytrap is an interactive database for displaying gene expression patterns, in particular P(GAL4) patterns, via an intuitive WWW based interface. This development consists of two components, the first being the HTML interface to the database and the second, a tool-kit for constructing and maintaining the database. The browser component of the project is entirely platform independent; based on javascript and HTML and therefore only requires a "standard" browser. This is to facilitate CD-ROM distribution and off-line browsing. Whether on-line or on CD, the basic browser structure does not reply on any server based scripts. Basic searching is now available. The search page uses javascript and will work off-line (i.e. from a CD-ROM copy). The construction tool-kit is UNIX based and requires an on-line web server. The tool-kit is used to compile the HTML browser interface from a simple database. The tool-kit part comprises a forms based HTML interface to the datasets allowing new information to b e added and updated very simply. We are also developing a java interface for the tool-kit that will enable us to edit and annotate images on-line. The basic browser interface is complete and a demonstration version can be accessed via the website. The first working version of the tool-kit is now on-line and is available for use.

Haploview
type: Resource
type: NamedIndividual
has db xref: nif-0000-30472
IAO_0000115: A Java based software tool designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses. Haploview currently allows users to examine block structures, generate haplotypes in these blocks, run association tests, and save the data in a number of formats. All functionalities are highly customizable. (entry from Genetic Analysis Software) * LD & haplotype block analysis * haplotype population frequency estimation * single SNP and haplotype association tests * permutation testing for association significance * implementation of Paul de Bakker's Tagger tag SNP selection algorithm. * automatic download of phased genotype data from HapMap * visualization and plotting of PLINK whole genome association results including advanced filtering options Haploview is fully compatible with data dumps from the HapMap project and the Perlegen Genotype Browser. It can analyze thousands of SNPs (tens of thousands in command line mode) in thousands of individuals. Note: Haploview is currently on a development and support freeze. The team is currently looking at a variety of options in order to provide support for the software. Haploview is an open source project hosted by SourceForge. The source can be downloaded at the SourceForge project site.

MAPPER - Multi-genome Analysis of Positions and Patterns of Elements of Regulation
type: Resource
type: NamedIndividual
has db xref: nif-0000-03101
has db xref: OMICS_01877
synonym: MAPPER 2 - Multi-genome Analysis of Positions and Patterns of Elements of Regulation
synonym: MAPPER database
synonym: Multi-genome Analysis of Positions and Patterns of Elements of Regulation
abbrev: MAPPER
abbrev: MAPPER 2
IAO_0000115: A platform composed of three modules: the Database, the Search Engine, and rSNPs, for the computational identification of transcription factor binding sites (TFBSs) in multiple genomes, that combines TRANSFAC and JASPAR data with the search power of profile hidden Markov models (HMMs). The Database contains putative TFBSs found in the upstream sequences of genes from the human, mouse and D.melanogaster genomes. For each gene, they scanned the region from 10,000 base pairs upstream of the transcript start to 50 base pairs downstream of the coding sequence start against all their models. Therefore, the database contains putative binding sites in the gene promoter and in the initial introns and non-coding exons. Information displayed for each putative binding site includes the transcription factor name, its position (absolute on the chromosome, or relative to the gene), the score of the prediction, and the region of the gene the site belongs to. If the selected gene has homologs in any of the other two organisms, the program optionally displays the putative TFBSs in the homologs. The Search Engine allows the identification, visualization and selection of putative TFBSs occurring in the promoter or other regions of a gene from the human, mouse, D.melanogaster, C.elegans or S.cerevisiae genomes. In addition, it allows the user to upload a sequence to query and to build a model by supplying a multiple sequence alignment of binding sites for a transcription factor of interest. rSNPs MAPPER is designed to identify Single Nucleotide Polymorphisms (SNPs) that may have an effect on the presence of one or more TFBSs.

MachiBase
type: Resource
type: NamedIndividual
has db xref: nif-0000-03092
has db xref: OMICS_01878
IAO_0000115: Database for Drosophila melanogaster transcription profiling that allows users to search the Drosophilia genome, see sequence overviews, and look at various transcripts. The data were generated in conjunction with the recently developed high-throughput genome sequencer Illumina / Solexa using a newly developed 5'-end mRNA collection method. Approximately 25 million 25-27 nucleotide (nt) 5'-end mRNA tags from the embryos, larvae, young males, young females, old males, old females, and S2 (culture cell line) of D. melanogaster were collected. By arranging this vast amount of expression tag with other annotated data, they have built a one-stop service for Drosophila melanogaster transcription profiling.

Magnaporthe comparative Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-03095
synonym: M. oryzae Database
synonym: Magnaporthe comparative genomics database
abbrev: Broad MGG
IAO_0000115: The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. As part of the Broad Fungal Genome Initiative, the Magnaporthe comparative project includes the finished M. oryzae (formerly M. grisea) genome, as well as the draft assemblies of Gaeumannomyces graminis var. tritici and M. poae. It provides users the tools to BLAST search, browse genome regions (to retrieve DNA, find clones, and graphically view sequence regions), and provides gene indexes and genome statistics. We were funded to attempt 7x sequence coverage comprising paired end reads from plasmids, Fosmids and BACs. Our strategy involves Whole Genome Shotgun (WGS) sequencing, in which sequence from the entire genome is generated and reassembled. Our specific aims are as follows: 1. Generate and assemble sequence reads yielding 7X coverage of the Magnaporthe oryzae genome through whole genome shotgun sequencing. 2. Generate and incorporate BAC and Fosmid end sequences into the genome assembly to provide a paired-end of average every 2 kb. 3. Integrate the genome sequence with existing physical and genetic map information. 4. Perform automated annotation of the sequence assembly. 5. Distribute the sequence assembly and results of our annotation and analysis through a freely accessible, public web server and by deposition of the sequence assembly in GenBank.

Dynamic Regulatory Events Miner
type: Resource
type: NamedIndividual
has db xref: nif-0000-30478
synonym: Dynamic Regulatory Events Miner (DREM)
abbrev: DREM
IAO_0000115: The Dynamic Regulatory Events Miner (DREM) allows one to model, analyze, and visualize transcriptional gene regulation dynamics. The method of DREM takes as input time series gene expression data and static transcription factor-gene interaction data (e.g. ChIP-chip data), and produces as output a dynamic regulatory map. The dynamic regulatory map highlights major bifurcation events in the time series expression data and transcription factors potentially responsible for them. DREM 2.0 was released and supports a number of new features including: * new static binding data for mouse, human, D. melanogaster, A. thaliana * a new and more flexible implementation of the IOHMM supports dynamic binding data for each time point or as a mix of static/dynamic TF input * expression levels of TFs can be used to improve the models learned by DREM * the motif finder DECOD can be used in conjuction with DREM and help find DNA motifs for unannotated splits * new features for the visualization of expressed TFs, dragging boxes in the model view, and switching between representations

Primer3Plus
type: Resource
type: NamedIndividual
has db xref: biotools:primer3plus
has db xref: OMICS_02347
synonym: Primer3Plus - pick primers from a DNA sequence
IAO_0000115: A web interface to the Primer3 primer design program as an enhanced alternative for the CGI- scripts that come with Primer3.

e-PCR
type: Resource
type: NamedIndividual
has db xref: OMICS_02345
synonym: Electronic PCR
synonym: Electronic PCR (e-PCR)
IAO_0000115: Web tool that identifies sequence tagged sites (STSs) within DNA sequences. Using e-PCR, you can search for sub-sequences that closely match the PCR primers and have the correct order, orientation, and spacing. The software may also be downloaded to run locally.

NeuroML
type: Resource
type: NamedIndividual
has db xref: nif-0000-00542
synonym: Neuro-Markup Language
IAO_0000115: A XML-based description language that provides a common data format for defining and exchanging descriptions of neuronal cell and network models. It facilitates the exchange of complex neural models, allows for greater transparency and accessibility of models, enhances interoperability between simulators and other tools, and supports the development of new software and databases. Exchange of network models will aid the investigation of structure-function relationships in neuroscience including theoretical studies relating connectivity patterns to normal and neurodegenerative network states. NeuroML is a free and open community effort developed with input from many contributors. They will need your help as the standards and tools continue to evolve.

Mammalian Mitochondrial Genomics Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-03099
abbrev: MamMiBase
IAO_0000115: Database developed to assist the phylogeneticist user in retrieving individual gene sequence alignments for genes in complete mammalian mitochondrial genomes. Data retrieval in MamMiBase requires three stages. At the first stage, the user must select the mammalian species or group that (s)he wishes to study. In the second stage, the user will select the outgroup from a list that included all species selected in the first stage plus Xenopus laevis and Gallus gallus. Finally, at the third stage, the user will select individual mitochondrial gene alignments or a phylogenetic tree that (s)he wishes to download.

Eukaryotic Linear Motif
type: Resource
type: NamedIndividual
has db xref: biotools:elm
has db xref: nif-0000-30486
synonym: Eukarotic Linear Motif resource for Functional Sites in Proteins
abbrev: ELM
IAO_0000115: Computational biology resource for investigating candidate functional sites in eukarytic proteins. Functional sites which fit to the description linear motif are currently specified as patterns using Regular Expression rules. To improve the predictive power, context-based rules and logical filters are being developed and applied to reduce the amount of false positives. The current version of the ELM server provides core functionality including filtering by cell compartment, phylogeny, globular domain clash (using the SMART/Pfam databases) and structure. In addition, both the known ELM instances and any positionally conserved matches in sequences similar to ELM instance sequences are identified and displayed (see ELM instance mapper). Although the ELM resource contains a large collection of functional site motifs, the current set of motifs is not exhaustive.

NeuroMab
type: Organization
type: NamedIndividual
has db xref: grid.482686.6
has db xref: nif-0000-00175
synonym: antibodies.inc
synonym: antibodiesinc
synonym: antibodiesinc.com
synonym: UCDavis/NIH NeuroMab Facility
IAO_0000115: A national mouse monoclonal antibody generating resource for biochemical and immunohistochemical applications in mammalian brain. NeuroMabs are generated from mice immunized with synthetic and recombinant immunogens corresponding to components of the neuronal proteome as predicted from genomic and other large-scale cloning efforts. Comprehensive biochemical and immunohistochemical analyses of human, primate and non-primate mammalian brain are incorporated into the initial NeuroMab screening procedure. This yields a subset of mouse mAbs that are optimized for use in brain (i.e. NeuroMabs): for immunocytochemical-based imaging studies of protein localization in adult, developing and pathological brain samples, for biochemical analyses of subunit composition and post-translational modifications of native brain proteins, and for proteomic analyses of native brain protein networks. The NeuroMab facility was initially funded with a five-year U24 cooperative grant from NINDS and NIMH. The initial goal of the facility for this funding period is to generate a library of novel NeuroMabs against neuronal proteins, initially focusing on membrane proteins (receptors/channels/transporters), synaptic proteins, other neuronal signaling molecules, and proteins with established links to disease states. The scope of the facility was expanded with supplements from the NIH Blueprint for Neuroscience Research to include neurodevelopmental targets, the NIH Roadmap for Medical Research to include epigenetics targets, and NIH Office of Rare Diseases Research to include rare disease targets. These NeuroMabs will then be produced on a large scale and made available to the neuroscience research community on an inexpensive basis as tissue culture supernatants or purified immunoglobulin by Antibodies Inc. The UC Davis/NIH NeuroMab Facility makes NeuroMabs available directly to end users and is unable to accommodate sales to distributors for third party distribution. Note, NeuroMab antibodies are…

European Mouse Phenotyping Resource of Standardised Screens
type: Resource
type: NamedIndividual
has db xref: nif-0000-30492
synonym: European Mouse Phenotyping Resource of Standardized Screens
abbrev: EMPReSS
IAO_0000115: Database of validated Standard Operating Procedures (SOPs) for screens to determine the phenotype of a mouse, developed by the EUMORPHIA consortium. The SOP's cover all of the main body systems including: clinical chemistry, hormonal and metabolic systems, cardiovascular, allergy and infection, renal function, sensory function, neurological and behavioral function, cancer, bone and cartilage, and respiratory function. In addition, there are generic SOPs in histology, necropsy, pathology and gene expression. EMPReSS is a platform of individual tests. These can be performed as individual tests or grouped together in sequences, recommended in the EMPReSS database, to give more information on particular phenotype. Quick List of Current Pipelines: * EUMODIC Pipeline 1 * EUMODIC Pipeline 2 * GMC Pipeline * MGP Pipeline * Additional Tests * EUMODIC Pipeline 3

MIPS Arabidopsis thaliana Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-03104
synonym: MAtDB
IAO_0000115: Repository for genome sequence data in the European Scientists Sequencing Arabidopsis (ESSA) project, part of the Arabidopsis Genome Initiative. It is moving towards becoming an integrated biological knowledge resource by integrating diverse data, tools, query and visualization capabilities. The aim is to create a comprehensive resource for Arabidopsis as a model that can then be used to transfer knowledge onto sequences from other species, including crop plants.

In-Silico PCR
type: Resource
type: NamedIndividual
has db xref: OMICS_02344
synonym: UCSC In-Silico PCR
IAO_0000115: Tool that searches a sequence database with a pair of PCR primers, using an indexing strategy for fast performance. When successful, the search returns a sequence output file in fasta format containing all sequence in the database that lie between and include the primer pair. The fasta header describes the region in the database and the primers. The fasta body is capitalized in areas where the primer sequence matches the database sequence and in lower-case elsewhere. Sources and executables to run batch jobs on your own server are available free for academic, personal, and non-profit purposes. Non-exclusive commercial licenses are also available.

Neuro Systems and Graphics Computing Laboratory
type: Resource
type: NamedIndividual
has db xref: nif-0000-00052
synonym: NeSys
IAO_0000115: This database contains axonal tracing data from the cerebro-ponto-cerebellar system in rats. Data are presented as 3-D coordinates in a common coordinate system for the pontine nuclei. It is presented through the Rodent Brain WorkBench.

JETTA
type: Resource
type: NamedIndividual
has db xref: OMICS_01334
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented July 6, 2017. Software to detect alternatively spliced exons between two conditions, for example, between two groups of treated and untreated patients in a typical clinical study.

MapViewer
type: Resource
type: NamedIndividual
has db xref: nif-0000-03103
has db xref: OMICS_00921
synonym: Entrez Map Viewer
synonym: NCBI Map Viewer
abbrev: Map Viewer
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023. Database that provides special browsing capabilities for a subset of organisms in Entrez Genomes. Map Viewer allows users to view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest. If multiple maps are available for a chromosome, it displays them aligned to each other based on shared marker and gene names, and, for the sequence maps, based on a common sequence coordinate system.

EUROpean Saccharomyces Cerevisiae ARchive for Functional Analysis
type: Resource
type: NamedIndividual
has db xref: nif-0000-30504
abbrev: EUROSCARF
IAO_0000115: Archive of yeast strains and plasmids that were generated during various yeast functional analysis projects.

Effect Size Calculator
type: Resource
type: NamedIndividual
has db xref: nif-0000-30507
abbrev: Effect Size Calculators
IAO_0000115: Calculator for a variety of functions, including Cohen's d and the effect-size correlation, rYl, using means and standard deviations or independent groups t test values and df.

Primer-BLAST
type: Resource
type: NamedIndividual
has db xref: OMICS_02343
IAO_0000115: A tool to design target-specific primers for polymerase chain reaction (PCR). It uses Primer3 to design PCR primers and then uses BLAST and global alignment algorithm to screen primers against user-selected database in order to avoid primer pairs (all combinations including forward-reverse primer pair, forward-forward as well as reverse-reverse pairs) that can cause non-specific amplifications.

National Institute of General Medical Sciences: Research Funding
type: Resource
type: NamedIndividual
has db xref: nif-0000-00547
abbrev: NIGMS: Research Funding
IAO_0000115: NIGMS places great emphasis on the support of individual, investigator-initiated grants within its scientific mission areas. Most grants are for research projects (R01), but NIGMS also funds program projects (P01) as well as some research resources. The Institute encourages research in certain scientific areas through requests for applications and program announcements. This website has information for upcoming grants, minority grants as well as training opportunities in medical research in the following disciplines: cell biology, biophysics, genetics, developmental biology, pharmacology, physiology, biological chemistry, bioinformatics, and computational biology.

3D Ribosomal Modification Maps Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-00552
abbrev: 3D rRNA modification maps
IAO_0000115: Database of maps showing the sites of modified rRNA nucleotides. Access to the rRNA sequences, secondary structures both with modification sites indicated, 3D modification maps and the supporting tables of equivalent nucleotides for rRNA from model organisms including yeast, arabidopsis, e. coli and human is provided. This database complements the Yeast snoRNA Database at UMass-Amherst and relies on linking to some content from that database, as well as to others by colleagues in related fields. Therefore, please be very cognizant as to the source when citing information obtained herein. Locations of modified rRNA nucleotides within the 3D structure of the ribosome.

WormBase
type: Resource
type: NamedIndividual
has db xref: nif-0000-00053
has db xref: OMICS_01664
has db xref: r3d100010424
synonym: WB
synonym: WB REF
synonym: Worm Base
synonym: WP
IAO_0000115: Central data repository for nematode biology including complete genomic sequence, gene predictions and orthology assignments from range of related nematodes.Data concerning genetics, genomics and biology of C. elegans and related nematodes. Derived from initial ACeDB database of C. elegans genetic and sequence information, WormBase includes genomic, anatomical and functional information of C. elegans, other Caenorhabditis species and other nematodes. Maintains public FTP site where researchers can find many commonly requested files and datasets, WormBase software and prepackaged databases.

International Classification for Nursing Practice
type: Resource
type: NamedIndividual
has db xref: nlx_157445
abbrev: ICNP
IAO_0000115: Ontology of the international classification for nursing practice.

MetaCrop
type: Resource
type: NamedIndividual
has db xref: nif-0000-03113
has db xref: r3d100010123
IAO_0000115: Database that summarizes diverse information about metabolic pathways in crop plants and allows automatic export of information for the creation of detailed metabolic models. It contains manually curated, highly detailed information about metabolic pathways in crop plants, including pathway diagrams, reactions, locations, transport processes, reaction kinetics, taxonomy and literature. It contains information about seven major crop plants with high agronomical importance and two model plants.

3D-Interologs
type: Resource
type: NamedIndividual
has db xref: nif-0000-00554
has db xref: OMICS_01896
abbrev: 3D-interologs
IAO_0000115: Database of physical protein-protein interactions across multiple genomes. Based on 3D-domain interolog mapping and a scoring function, protein-protein interactions are inferred by using three-dimensional (3D) structure heterodimers to search the UniProt database. For a query protein, the database utilizes BLAST to identify homologous proteins and the interacting partners from multiple species. Based on the scoring function and structure complexes, it provides the statistic significances, the interacting models (e.g. hydrogen bonds and conserved amino acids), and functional annotations of interacting partners of a query protein. The identification of orthologous proteins of multiple species allows the study of protein-protein evolution, protein functions, and cross-referencing of proteins.

eQtlBma
type: Resource
type: NamedIndividual
has db xref: biotools:eqtlbma
has db xref: OMICS_04875
IAO_0000115: Software package that implements Bayesian statistical methods to detect eQTLs jointly in multiple subgroups (e.g. tissues). Key features are to borrow information across subgroups, to explicitly model heterogeneity (qualitatively and quantitatively), and to borrow information across genes to estimate hyper-parameters from the data (empirical Bayes).

JuncBASE
type: Resource
type: NamedIndividual
has db xref: OMICS_01335
IAO_0000115: Software used to identify and classify alternative splicing events from RNA-Seq data. JuncBASE also uses read counts to quantify the relative expression of each isoform and identifies splice events that are significantly differentially expressed across two or more samples.

European Conditional Mouse Mutagenesis Program
type: Resource
type: NamedIndividual
has db xref: nif-0000-30531
abbrev: EUCOMM
IAO_0000115: Generate, archive, and distribute world-wide up to 12.000 conditional mutations across the mouse genome in mouse embryonic stem (ES) cells and Establish a limited number of mouse mutants from this resource. EUCOMM contributes the largest fraction of conditionally trapped and targeted genes in mouse C57BL/6N embryonic stem (ES) cells to the IKMC. EUCOMM vectors, mutant ES cells and mutant mice are distributed worldwide, enabling functional genomics research in a standardized and cost-effective manner by a much wider biomedical research community than has been possible previously. EUCOMM mutant ES cells and vectors can be obtained from the European Mouse Mutant Cell Repository (EuMMCR). EUCOMM mutant mice are archived and distributed by the European Mouse Mutant Archive (EMMA). Mutagenesis Strategies * Conditional gene trapping - random approach for expressed genes * Conditional targeted trapping - directed approach, used for expressed genes * Conditional gene targeting - directed approach, used for non-expressed genes

NeuronDB
type: Resource
type: NamedIndividual
has db xref: nif-0000-00054
synonym: Neuron DataBase
synonym: Neuron database
synonym: Neuron DB
IAO_0000115: Database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments.

City University of New York; New York; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100006462
has db xref: grid.212340.6
has db xref: ISNI:122985718
has db xref: nlx_151851
has db xref: Wikidata:Q762266
synonym: City University of New York
abbrev: CUNY
IAO_0000115: University system in New York City, New York. It is made up of 11 senior colleges, seven community colleges, The Macaulay Honors College, and five graduate and professional schools.

Pliny
type: Resource
type: NamedIndividual
has db xref: nif-0000-00556
IAO_0000115: Set of plugins for the Eclipse platform which facilities note-taking and annotation of web-based works and non-web-based works.

MethDB
type: Resource
type: NamedIndividual
has db xref: nif-0000-03119
has db xref: OMICS_01840
synonym: DNA Methylation Database
synonym: MethDB - the database for DNA methylation and environmental epigenetic effects
IAO_0000115: Database that provides a resource to store DNA methylation data and to make these data readily available to the public. Future development of the database will focus on environmental effects on DNA methylation. No restriction applies on the type of data, i.e. as well as global estimations (e.g. HPLC) as data from high resolution analysis (i.e. sequencing) can be stored. As much background information as possible should be provided by the users. This includes the origin of the sample, phenotype, expression of the related gene, etc..

pairheatmap
type: Resource
type: NamedIndividual
has db xref: biotools:pairheatmap
has db xref: OMICS_04853
synonym: pairheatmap: A tool for comparing heatmaps
IAO_0000115: A software tool to compare two heatmaps and discover patterns within and across groups. In the context of biology, group can be defined based on gene ontology.

BioConference Live
type: Resource
type: NamedIndividual
has db xref: nlx_156703
IAO_0000115: Online conferences focused on the life sciences, laboratory animal sciences and clinical diagnostics community. BioConference Live brings together research scientists, veterinarians, clinicians, medical experts, thought leaders and professionals from around the world all exclusively online. * Receive CE Credits accredited by the AACC ACCENT and PACE. * No Cost or Travel. * Watch Live Streaming Sessions by Industry Experts. * Network with peers and professionals. * Explore a virtual exhibit floor showcasing advances in life sciences and medical technologies.

Integrated Grants
type: Resource
type: NamedIndividual
has db xref: nlx_156706
synonym: Integrated Grants View
synonym: NIF Integrated Grants
IAO_0000115: Integrated Grants is a virtual database currently indexing funded research resources including NIH Research Portfolio Online Reporting Tool (RePORT) (current grants, updated monthly) and ResearchCrossroads (1970-2008, defunct as of 2009).

studyforrest.org
type: Resource
type: NamedIndividual
has db xref: nlx_156710
has db xref: r3d100011071
synonym: study forrest
synonym: studyforrest
IAO_0000115: An MRI data repository that holds a set of 7 Tesla images and behavioral metadata. Multi-faceted brain image archive with behavioral measurements. For each participant a number of different scans and auxiliary recordings have been obtained. In addition, several types of minimally preprocessed data are also provided. The full description of the data release is available in a dedicated publication. This project invites anyone to participate in a decentralized effort to explore the opportunities of open science in neuroimaging by documenting how much (scientific) value can be generated out of a single data release by publication of scientific findings derived from a dataset, algorithms and methods evaluated on this dataset, and/or extensions of this dataset by acquisition and integration of new data.

rsync
type: Resource
type: NamedIndividual
has db xref: nlx_156711
IAO_0000115: Software that provides rapid incremental file transfer.

University of Colorado Boulder; Colorado; USA
type: Organization
type: NamedIndividual
has db xref: nlx_10266
synonym: CU Boulder
synonym: CU-Boulder
synonym: UC Boulder
synonym: University of Colorado Boulder
IAO_0000115: Public university that offers degrees in the sciences, humanities, and social sciences.

SciCrunch
type: Resource
type: NamedIndividual
has db xref: nlx_156715
IAO_0000115: Community portal for researchers and content management system for data and databases. Intended to provide common source of data to research community and data about Research Resource Identifiers (RRIDs), which can be used in scientific publications. Central service where RRIDs can be searched and created. Designed to help communities of researchers create their own portals to provide access to resources, databases and tools of relevance to their research areas. Adds value to existing scientific resources by increasing their discoverability, accessibility, visibility, utility and interoperability, regardless of their current design or capabilities and without need for extensive redesign of their components or information models. Resources can be searched and discovered at multiple levels of integration, from superficial discovery based on limited description of resource at SciCrunch Registry, to deep content query at SciCrunch Data Federation.

chronopolis
type: Resource
type: NamedIndividual
has db xref: nlx_156729
abbrev: Chronopolis
IAO_0000115: Services for the long-term preservation and curation of America's digital data - data of any type or size, with minimal requirements on the data provider. It has the capacity to preserve hundreds of terabytes of digital data and comprises several partner organizations that provide a wide range of services. The project leverages high-speed networks, mass-scale storage capabilities, and the expertise of the partners in order to provide a geographically distributed, heterogeneous, and highly redundant archive system. Features of the project include: * Three geographically distributed copies of the data * Curatorial audit reporting * Development of best practices for data packaging and sharing Chronopolis is available to anyone who wants to have their data preserved. Storage is based on a yearly, per-terabyte charge. The smallest unit available is one terabyte; collections smaller than this will be charged the one terabyte rate.

Spider Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157595
abbrev: SPD
IAO_0000115: An ontology for spider comparative biology including anatomical parts (e.g. leg, claw), behavior (e.g. courtship, combing) and products (i.g. silk, web, borrow).

Japanese Genotype-phenotype Archive (JGA)
type: Resource
type: NamedIndividual
has db xref: nlx_156741
has db xref: r3d100010818
synonym: Japanese Genotype-phenotype Archive
synonym: JGA
IAO_0000115: A service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The JGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the JGA. Once processed, all data are encrypted. The JGA accepts only de-identified data approved by JST-NBDC. The JGA implements access-granting policy whereby the decisions of who will be granted access to the data resides with the JST-NBDC. After data submission the JGA team will process the data into databases and archive the original data files. The accepted data types include manufacturer-specific raw data formats from the array-based and new sequencing platforms. The processed data such as the genotype and structural variants or any summary level statistical analyses from the original study authors are stored in databases. The JGA also accepts and distributes any phenotype data associated with the samples. For other human biological data, please contact the NBDC human data ethical committee.

BioJS
type: Resource
type: NamedIndividual
has db xref: biotools:biojs
has db xref: nlx_156742
IAO_0000115: An open source JavaScript library of components for visualisation of biological data on the web.

ShARM
type: Resource
type: NamedIndividual
has db xref: nlx_156767
synonym: Shard Ageing Research Models
IAO_0000115: A not for profit organization to accelerate research into aging by sharing resources: providing access to cost and time effective, aged murine tissue through a biorepository and database of live ageing colonies, as well as promoting the networking of researchers and dissemination of knowledge through its online collaborative environment; MiCEPACE. ShARM will provide valuable resources for the scientific community while helping to reduce the number of animals used in vital research into aging. The biobank of tissue and networking facility will enable scientists to access shared research material and data. By making use of collective resources, the number of individual animals required in research experiments can be minimized. The project also has the added value of helping to reduce the costs of research by connecting scientists, pooling resource and combining knowledge. ShARM works in partnership with MRC Harwell and the Centre for Intergrated Research into Musculoskeletal Ageing (CIMA).

Biomarkers Consortium
type: NamedIndividual
has db xref: nif-0000-00559
synonym: FNIH Biomarkers Consortium
synonym: The Biomarkers Consortium
abbrev: BC
IAO_0000115: Consortium serving to develop and qualify promising biomarkers in order to help accelerate the delivery of successful new technologies, medicines and therapies for prevention, early detection, diagnosis and treatment of disease. Current core disease areas of focus include Cancer, Inflammation and Immunity, Metabolic Disorders, and Neuroscience. One of the most difficult tasks facing biomarker assessment and evaluation is harmonizing the approaches of various stakeholders--government, industry, non-profits and foundations, providers, and academic institutions. Consortium founding members and other partners recognize the critical need for a coordinated cross-sector partnership effort. The Biomarkers Consortium brings together the expertise and resources of various partners to rapidly identify, develop, and qualify potential high-impact biomarkers. Biomarkers Consortium Goals: * Facilitate the development and qualification of biomarkers using new and existing technologies; * Help qualify biomarkers for specific applications in diagnosing disease, predicting therapeutic response or improving clinical practice; * Generate information useful to inform regulatory decision making; * Make consortium project results broadly available to the entire scientific community.

BioCaster Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_156797
synonym: biocaster-ontology
abbrev: BCO
IAO_0000115: A multilingual application ontology aimed at the early detection of public health events in the media. It aims to describe the terms and relations necessary to detect and risk assess public health events in the grey literature at an early stage; and bridge the gap between the (multilingual) grey literature and existing standards in biomedicine. The BCO focuses on the usage of terms and relations within informal unstructured reports which are often made at a pre-diagnostic stage of a disease outbreak by non-medically trained reporters. This is done to provide monitoring and early warning about public health hazards from online media reports.

Biomedical Information Science and Technology Initiative
type: Resource
type: NamedIndividual
has db xref: nif-0000-00560
synonym: Biomedical Information Science & Technology Initiative
synonym: Biomedical Information Science Technology Initiative
synonym: BITSI - Biomedical Information Science and Technology Initiative
abbrev: BISTI
IAO_0000115: A consortium of representatives from each of the NIH institutes and centers. BISTI was established in May 2000 to serve as the focus of biomedical computing issues at the NIH. The mission of BISTI is to make optimal use of computer science and technology to address problems in biology and medicine by fostering new basic understandings, collaborations, and transdisciplinary initiatives between the computational and biomedical sciences. In support of this mission, the BISTI coordinates research grants, training opportunities, and scientific symposia associated with biomedical computing. Regular monthly meetings are conducted to discuss program status, future needs and directions, and topics of interest to the bioinformatics community.

MISO
type: Resource
type: NamedIndividual
has db xref: OMICS_01337
synonym: Mixture of Isoforms
synonym: Mixture of Isoforms (MISO)
IAO_0000115: Probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq and identifies differentially regulated isoforms or exons across samples.

FRAXA Research Foundation
type: Resource
type: NamedIndividual
has db xref: nif-0000-30561
synonym: FRAXA
IAO_0000115: FRAXA's mission is to accelerate progress toward effective treatments and ultimately a cure for Fragile X, by directly funding the most promising research. FRAXA also supports families affected by Fragile X and raises awareness of this important but relatively unknown disease. FRAXA was founded in 1994 by three parents of children with Fragile X, Katie Clapp, Michael Tranfaglia MD, and Kathy May, to support scientific research aimed at finding a treatment and a cure for Fragile X. Fragile X research is drastically underfunded, considering its high prevalence, prospects for a cure, and the promise that this research holds for advancing understanding of other disorders like autism, Alzheimer's disease, and X-linked mental retardation. FRAXA funds grants and fellowships at universities all over the world. We have funded more than $17 million dollars in top-notch science. FRAXA's management expenses have always been just 4% or less of income, as we have just one full-time staff, three part time staff, and hundreds of volunteer parents. Since FRAXA was founded, the Fragile X field has grown tremendously, due in large part to our grass-roots efforts. You can help us accomplish much more. FRAXA is a 501c3 tax-exempt organization; Tax ID 04-3222167

HYDEN
type: Resource
type: NamedIndividual
has db xref: biotools:hyden
has db xref: OMICS_02338
synonym: HighlY DEgeNerate primers
synonym: HYDEN - A Software for Designing Degenerate Primers
IAO_0000115: Software program for designing pairs of degenerate primers for a given set of DNA sequences. It works well for large input sets of genomic sequences (e.g., hundreds of sequences of length 1Kbp). It is a batch (i.e., command-line, as opposed to graphical interface) program, available for Windows XP (downloadable version) and Linux (upon request).

ISPS Data Archive
type: Resource
type: NamedIndividual
has db xref: nlx_156779
has db xref: r3d100010833
synonym: Yale ISPS Data Archive
synonym: Yale University Institution for Social and Policy Studies Data Archive
IAO_0000115: Data archive to assist in the sharing of research grade information pertaining to the social and economic sciences. The majority of digital content currently consists of social science research data from experiments, program files with the code for analyzing the data, requisite documentation to use and understand the data, and associated files. Access to the ISPS Data Archive is provided at no cost and is granted for scholarship and research purposes only. When possible, Data is linked to Projects and Publications, via the ISPS KnowledgeBase. ISPS operates in accordance with the prevailing standards and practices of the digital preservation community including the Open Archival Information System (OAIS) Reference Model (ISO 14721:2003) and the Data Documentation Initiative (DDI) standard. Accordingly, ISPS supports digital life-cycle management, interoperability, and preferred methods of preservation. The ISPS Data Archive is intended for use by social science researchers, policy-makers, and practitioners who are conducting or analyzing field (and other) experiments in various social science disciplines. Currently, Replication Files originate with ISPS-affiliated scholars.

mrsFAST
type: Resource
type: NamedIndividual
has db xref: biotools:mrsfast
has db xref: nlx_156780
synonym: micro-read substitution-only Fast Alignment Search Tool
synonym: mrsFAST: micro-read substitution-only Fast Alignment Search Tool
IAO_0000115: A cache-oblivious algorithm designed to map short reads to reference genome assemblies in a fast and memory-efficient manner. It optimizes cache usage to get higher performance. Currently Supported Features: * Mistmatches, No indels * Paired-end Mapping Mode * Discordant Paired-end Mapping Mode (to be used in conjuction with Variation Hunter)

Cognitive Electrophysiology Data Portal
type: Resource
type: NamedIndividual
has db xref: nlx_156800
IAO_0000115: Multiple data sets, and associated publications, of electrophysiological data from the Computational Memory Lab, University of Pennsylvania. Separate requests must be made for each dataset. A collection of behavioral testing data is also available.

University of Colorado; Colorado Springs; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100010175
has db xref: grid.266186.d
has db xref: ISNI:0000 0001 0684 1394
has db xref: nlx_143537
has db xref: Wikidata:Q2495841
synonym: University of Colorado Colorado Springs
abbrev: UCCS
IAO_0000115: Public university that offers degrees in the social sciences, humanities, and natural sciences.

NIH NeuroBioBank
type: Resource
type: NamedIndividual
has db xref: nlx_156783
synonym: National Institutes of Health NeuroBioBank
synonym: NeuroBioBank
abbrev: NBB
IAO_0000115: National resource for investigators utilizing human post-mortem brain tissue and related biospecimens for their research to understand conditions of the nervous system. Federated network of brain and tissue repositories in the United States that collects, evaluates, stores, and makes available to researchers, brain and other tissues in a way that is consistent with the highest ethical and research standards. The NeuroBioBank ensures protection of the privacy and wishes of donors. Provides information to the public about the need for tissue donation and how to register as a donor.

Strong Star
type: Resource
type: NamedIndividual
has db xref: nlx_156784
synonym: South Texas Research Organizational Network Guiding Studies on Trauma and Resilience
abbrev: STRONG STAR
IAO_0000115: A multidisciplinary and multi-institutional research consortium to develop and evaluate the most effective early interventions possible for the detection, prevention, and treatment of combatrelated posttraumatic stress disorder (PTSD) in activeduty military personnel and recently discharged veterans. Complementary investigations are focused on the root causes of PTSD, including biological factors that influence PTSD susceptibility and recovery; the influence of comorbid physical and psychological ailments; and the interaction of cognitive-behavioral therapies and pharmacologic treatments. The full cohort of STRONG STAR trials include: Treatment Studies, Biological Studies, Epidemiological Studies, and Preclinical Studies. STRONG STAR is currently conducting three clinical treatment trials at Carl R. Darnall Army Medical Center (CRDAMC). The studies are examining the effectiveness of Cognitive Processing Therapy (CPT), Prolonged Exposure Therapy (PE) and Cognitive Behavioral Therapy for Insomnia (CBTi) with active duty service members. Treatments are offered in individual, group, and online formats, and last from two to eight weeks. Study participants must be active duty service members who will remain in the Ft Hood area for at least 34 months to complete initial assessments and treatment programs. Referrals to the treatment studies can be made through a behavioral health provider or through selfreferral., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

PredictNLS
type: Resource
type: NamedIndividual
has db xref: biotools:predictnls
has db xref: nif-0000-31416
has db xref: OMICS_01633
synonym: Prediction and Analysis of Nuclear Localization Signals
IAO_0000115: Software automated tool for analysis and determination of Nuclear Localization Signals (NLS). Predicts that your protein is nuclear or finds out whether your potential NLS is found in our database. The program also compiles statistics on the number of nuclear/non-nuclear proteins in which your potential NLS is found. Finally, proteins with similar NLS motifs are reported, and the experimental paper describing the particular NLS are given.

BreakDB
type: Resource
type: NamedIndividual
has db xref: nlx_156789
synonym: Break DB
IAO_0000115: Data set developed to store, annotate and dsplay structural variant (SV) breakpoint events identified by PEMer and from other sources.

mrCaNaVaR
type: Resource
type: NamedIndividual
has db xref: biotools:mrcanavar
has db xref: nlx_156790
has db xref: OMICS_02138
synonym: micro-read Copy Number Variant Regions
synonym: mrCaNaVaR - micro-read Copy Number Variant Regions
IAO_0000115: Copy number caller that analyzes the whole-genome next-generation sequence mapping read depth to discover large segmental duplications and deletions. It also has the capability of predicting absolute copy numbers of genomic intervals.

NovelSeq
type: Resource
type: NamedIndividual
has db xref: biotools:novelseq
has db xref: nlx_156791
has db xref: OMICS_02164
synonym: NovelSeq: Novel Sequence Insertion Detection
IAO_0000115: Software pipeline to detect novel sequence insertions using high throughput paired-end whole genome sequencing data.

Stereology Resource Center
type: Organization
type: NamedIndividual
has db xref: grid.492523.b
has db xref: nlx_156794
synonym: SRC - Better Science Through Better Stereology
abbrev: SRC
IAO_0000115: A company of professionally trained stereologists, bioscientists, computer engineers, educators, and support personnel that provides comprehensive neurostereology products and services to the global bioscience community. These products and services include: stereology and image analysis software, digital imaging technology, turnkey stereologer solutions, comprehensive stereology and image analysis/image processing software, professional contract services, neurostereology workshops, basic stereology courses, and online stereology webinars. The Center also offers tissue processing (sectioning, staining, slide preparation) and stereology data collection services. Researchers may use equipment and facilities to complete projects with full confidentiality and according to Good Laboratory Practices guidelines.

PlantLoc
type: Resource
type: NamedIndividual
has db xref: OMICS_01632
synonym: PlantLoc: Plant Proteins Subcellular Localization Prediction Server
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4,2023. An accurate web server for predicting plant protein subcellular localization by substantiality motif.

Primer3
type: Resource
type: NamedIndividual
has db xref: biotools:primer3
has db xref: nlx_156833
has db xref: OMICS_02325
synonym: Primer3 - PCR primer design tool
synonym: Primer3web
synonym: Primer3web - Pick primers from a DNA sequence
IAO_0000115: Tool used to design PCR primers from DNA sequence - often in high-throughput genomics applications. It does everything from mispriming libraries to sequence quality data to the generation of internal oligos.

FastSNP
type: Resource
type: NamedIndividual
has db xref: biotools:fastsnp
has db xref: nif-0000-30566
has db xref: OMICS_00173
synonym: A Functional Analysis and Selection Tool for SNP in Large Scale Association Study
synonym: FastSNP: A Functional Analysis and Selection Tool for SNP in Large Scale Association Study
synonym: Function Analysis and Selection Tool for Single Nucleotide Polymorphisms
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 9, 2016. A web server that allows users to efficiently identify and prioritize high-risk SNPs according to their phenotypic risks and putative functional effects. A unique feature is that the functional effect information used for SNP prioritization is always up-to-date, because FASTSNP extracts the information from 11 external web servers at query time using a team of web wrapper agents. Moreover, FASTSNP is extendable by deploying more Web wrapper agents. FASTSNP provides three options for users to submit requests. If users already have some candidate SNPs on a candidate gene, they may use Query by Candidate Gene to select the specific SNPs on the gene to perform prioritization. If users have a specified SNP or a list of SNP rsid's needs to be prioritized, they can use Query by SNP option and upload the SNP list in an Excel-format file. Finally, if users have a novel SNP sequence, FASTSNP provides Novel SNP analysis. FASTSNP will generate a SNP Function Report for each SNP. Users can export SNP data to an excel file for further genotyping processes. Other features of FASTSNP include SNP quality checking and haplotype LD information.

Neuroimaging Informatics Technology Initiative
type: Resource
type: NamedIndividual
has db xref: nif-0000-00561
synonym: Neuroimaging Informatics Technology Initiative (NIfTI)
synonym: NIfTI: Neuroimaging Informatics Technology Initiative
abbrev: NIfTI
IAO_0000115: Coordinated and targeted service, training, and research to speed the development and enhance the utility of informatics tools related to neuroimaging. The initial focus will be on tools that are used in fMRI. If NIfTI proves useful in addressing informatics issues in the fMRI research community, it may be expanded to address similar issues in other areas of neuroimaging. Objectives of NIfTI * Enhancement of existing informatics tools used widely in neuroimaging research * Dissemination of neuroimaging informatics tools and information about them * Community-based approaches to solving common problems, such as lack of interoperability of tools and data * Unique training activities and research career development opportunities to those in the tool-user and tool-developer communities * Research and development of the next generation of neuroimaging informatics tools

BrainInfo
type: Resource
type: NamedIndividual
has db xref: nif-0000-00019
synonym: Brain Info
IAO_0000115: Portal to neuroanatomical information on the Web that helps you identify structures in the brain and provides a variety of information about each structure by porting you to the best of 1500 web pages at 100 other neuroscience sites. BrainInfo consists of three basic components: NeuroNames, a developing database of definitions of neuroanatomic structures in four species, their most common acronyms and their names in eight languages; NeuroMaps, a digital atlas system based on 3-D canonical stereotaxic atlases of rhesus macaque and mouse brains and programs that enable one to map data to standard surface and cross-sectional views of the brains for presentation and publication; and the NeuroMaps precursor: Template Atlas of the Primate Brain, a 2-D stereotaxic atlas of the longtailed (fascicularis) macaque brain that shows the locations of some 250 architectonic areas of macaque cortex. The NeuroMaps atlases will soon include a number of overlays showing the locations of cortical areas and other neuroscientific data in the standard frameworks of the macaque and mouse atlases. Viewers are encouraged to use NeuroNames as a stable source of unique standard terms and acronyms for brain structures in publications, illustrations and indexing systems; to use templates extracted from the NeuroMaps macaque and mouse brain atlases for presenting neuroscientific information in image format; and to use the Template Atlas for warping to MRIs or PET scans of the macaque brain to estimate the stereotaxic locations of structures.

Proteome Analyst Specialized Subcellular Localization Server
type: Resource
type: NamedIndividual
has db xref: biotools:pa-sub
has db xref: OMICS_01631
abbrev: PA-SUB
IAO_0000115: Web server specialized to predict the subcellular localization of proteins using established machine learning techniques.

NYCE
type: Resource
type: NamedIndividual
has db xref: OMICS_01630
IAO_0000115: Data analysis service that predicts subcellular location (either Nuclear, Nucleo-cytoplasmic, Cytoplasmic or Extracellular) of eukaryotic proteins using the predicted exposure value of their amino acids.

GeneCopoeia
type: Organization
type: NamedIndividual
has db xref: nlx_152370
synonym: GeneCopoeia Inc
IAO_0000115: Commercial organization which provides reagents and services for molecular biology research. Its services include clone collections, microRNA solutions, genome editing, qPCR products, and fluorescent labeling and detection.

GeneScissors
type: Resource
type: NamedIndividual
has db xref: OMICS_01232
synonym: Gene Scissors
IAO_0000115: Software for detecting and correcting spurious transcriptome inference due to RNAseq reads misalignment.

MorphBank
type: Resource
type: NamedIndividual
has db xref: nlx_156841
has db xref: r3d100010566
synonym: Morphbank : Biological Imaging
abbrev: Morphbank
IAO_0000115: An NSF supported image repository of over 374,000 high-resolution photographs of approximately 4,000 species for research and education, used largely but not exclusively in the area of biodiversity research. Images can be annotated by users and browsed by specimen, view, taxonomy, location, collection, or annotation.

Center for Magnetic Resonance Research
type: Resource
type: NamedIndividual
has db xref: nif-0000-00563
synonym: NMR Imaging and Localized Spectroscopy
abbrev: CMRR
IAO_0000115: Biomedical technology research center that focuses on development of unique magnetic resonance (MR) imaging and spectroscopy methodologies and instrumentation for the acquisition of structural, functional, and biochemical information non-invasively in humans, and utilizing this capability to investigate organ function in health and disease. The distinctive feature of this resource is the emphasis on ultrahigh magnetic fields (7 Tesla and above), which was pioneered by this BTRC. This emphasis is based on the premise that there exists significant advantages to extracting biomedical information using ultrahigh magnetic fields, provided difficulties encountered by working at high frequencies corresponding to such high field strengths can be overcome by methodological and engineering solutions. This BTRC is home to some of the most advanced MR instrumentation in the world, complemented by human resources that provide unique expertise in imaging physics, engineering, and signal processing. No single group of scientists can successfully carry out all aspects of this type of interdisciplinary biomedical research; by bringing together these multi-disciplinary capabilities in a synergistic fashion, facilitating these interdisciplinary interactions, and providing adequate and centralized support for them under a central umbrella, this BTRC amplifies the contributions of each of these groups of scientists to basic and clinical biomedical research. Collectively, the approaches and instrumentation developed in this BTRC constitute some of the most important tools used today to study system level organ function and physiology in humans for basic and translational research, and are increasingly applied world-wide. CMRR Faculty conducts research in a variety of areas including: * High field functional brain mapping in humans; methodological developments, mechanistic studies, and neuroscience applications * Metabolism, bioenergetics, and perfusion studies of human pathological state…

NIH Human Pluripotent Stem Cell Registry
type: Resource
type: NamedIndividual
has db xref: nif-0000-00565
synonym: National Institutes of Health Human Pluripotent Stem Cell Registry
synonym: NIH Human Embryonic Stem Cell Registry
IAO_0000115: A listing of human embryonic cell lines that are eligible for use in NIH funded research. Those lines that carry disease-specific mutations are noted as such under the line name. Total Eligible Lines = 200. The purpose of the Registry is to provide investigators with: # a unique NIH Code for each cell line that must be used when applying for NIH funding and # contact information to facilitate investigators' acquisition of stem cells. Before submitting a new grant application and supporting materials for consideration of a human embryonic stem cell line, scientists may wish to see what lines are already under consideration: * Human embryonic stem cell lines submitted to NIH that are being reviewed to determine if they may be used in NIH-supported research, http://grants.nih.gov/stem_cells/registry/pending.htm President George W. Bush required that the name of the registry be changed in his Executive Order #13435, issued on June 20, 2007. As a result of this Executive Order, the former National Institutes of Health Human Embryonic Stem Cell Registry will now be called the National Institutes of Health Human Pluripotent Stem Cell Registry. The registry will now include both human embryonic stem cells that were derived consistent with the President's policy of August 9, 2001 and human pluripotent stem cells derived from non-embryonic sources.

ngLOC
type: Resource
type: NamedIndividual
has db xref: biotools:ngloc
has db xref: OMICS_01629
synonym: ngLOC - A Bayesian method for predicting protein subcellular localization
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.An n-gram-based Bayesian classifier that predicts subcellular localization of proteins both in prokaryotes and eukaryotes. The downloadable version of this software with source code is freely available for academic use under the GNU General Public License.

MultiLoc
type: Resource
type: NamedIndividual
has db xref: biotools:multiloc2
has db xref: OMICS_01628
IAO_0000115: An extensive high-performance subcellular protein localization prediction system that incorporates phylogenetic profiles and Gene Ontology terms to yield higher accuracies compared to its previous version. Moreover, it outperforms other prediction systems in two benchmarks studies. A downloadable version of MultiLoc2 for local use is also available.

miRBase
type: Resource
type: NamedIndividual
has db xref: biotools:mirbase
has db xref: nif-0000-03134
has db xref: r3d100010670
has db xref: SCR_017497
synonym: microRNA database
IAO_0000115: Central online repository for microRNA nomenclature, sequence data, annotation and target prediction.Collection of published miRNA sequences and annotation.

GeneCruiser
type: Resource
type: NamedIndividual
has db xref: OMICS_00760
IAO_0000115: A web service and web application for the annotation of microarray data providing integrated access to genomic information freely available from public data sources.

MetaLocGramN
type: Resource
type: NamedIndividual
has db xref: OMICS_01626
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A tool for subcellular localization prediction of Gram-negative proteins. You can also use MetaGramLocN via SOAP. SOAP enables you to invoke our method from scripts written in your programming language of choice.

FastPCR
type: Commercial Organization
type: NamedIndividual
has db xref: OMICS_02336
IAO_0000115: Software tool for PCR primers or probe design, in silico PCR, oligonucleotide assembly and analyses, alignment and repeat searching.

miRNAMap
type: Resource
type: NamedIndividual
has db xref: nif-0000-03138
has db xref: OMICS_00408
IAO_0000115: A database of experimentally verified microRNAs and miRNA target genes in human, mouse, rat, and other metazoan genomes. In addition to known miRNA targets, three computational tools previously developed, such as miRanda, RNAhybrid and TargetScan, were applied for identifying miRNA targets in 3'-UTR of genes. In order to reduce the false positive prediction of miRNA targets, several criteria are supported for filtering the putative miRNA targets. Furthermore, miRNA expression profiles can provide valuable clues for investigating the properties of miRNAs, such tissue specificity and differential expression in cancer/normal cell. Therefore, we performed the Q-PCR experiments for monitoring the expression profiles of 224 human miRNAs in eighteen major normal tissues in human. The cross-reference between the miRNA expression profiles and the expression profiles of its target genes can provide effective viewpoint to understand the regulatory functions of the miRNA.

Hyperphagia
type: Resource
type: NamedIndividual
has db xref: nlx_156857
synonym: Best Idea Grants (BIG) in Hyperphagia Research
synonym: Best Idea Grants in Hyperphagia Research
IAO_0000115: Request for Applications to fund the best ideas in the field of hyperphagia research. Institutions of Higher Education, Nonprofit organizations, For-profit companies are eligible.

HUPO Proteomics Standards Initiative
type: Resource
type: NamedIndividual
has db xref: nif-0000-00568
has db xref: OMICS_01781
synonym: The HUPO Proteomics Standards Initiative
abbrev: HUPO PSI
IAO_0000115: Initiative to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification. The main organizational unit is the work group, with a Gel Electrophoresis (GEL) work group, a Mass Spectrometry (MS) work group, a Molecular Interactions (MI) work group, a Protein Modifications (MOD) work group, a Proteomics Informatics (PI) work group, and a Sample Processing (SP) work group. The Gel Electrophoresis (GEL) work group aims to develop reporting requirements that supplement the Minimum Information About a Proteomics Experiment (MIAPE) parent document, describing the minimum information that should be reported about gel-based experimental techniques used in proteomics. The group will also develop data formats for capturing MIAPE-compliant data about gel electrophoresis and informatics performed on gel images. The Mass Spectrometry Standards Working Group defines community data formats and controlled vocabulary terms facilitating data exchange and archiving in the field of proteomics mass spectrometry. A past achievement is the mzData standard, which captures mass spectrometry output data. mzData's aim is to unite the large number of current formats (pkl's, dta's, mgf's, .....) into a single format. mzData has been released but is now deprecated in favor of mzML. The Molecular Interactions workgroup is concentrating on improving the annotation and representation of molecular interaction data wherever it is published, be this in journal articles, authors web-sites or public domain databases; and improving the accessibility of molecular interaction data to the user community. By using a common standard data can be downloaded from multiple sources and easily combined using a single parser. The protein modification workgroup focuses on developing a consensus nomenclature and provide an ontology reconciling in a hierarchical representation the complementary descriptions of residue modifications. The protein modification on…

SaskPrimerFS
type: Resource
type: NamedIndividual
has db xref: OMICS_02335
IAO_0000115: Software pipeline for designing gene family specific PCR primers. It infers intronic regions of a target species and design for them by utilizing DNA sequence information from a reference organism.

International Symposium on Objective Measures in Auditory Implants
type: Resource
type: NamedIndividual
has db xref: nlx_156860
synonym: 8th International Symposium on Objective Measures in Auditory Implants
synonym: Objective Measures in Auditory Implants
abbrev: Objective Measures
IAO_0000115: International Symposium on Objective Measures in Auditory Implants to explore what unique measures help us to achieve the best hearing outcome for each person who needs an auditory prosthesis.

American Association for the History of Medicine
type: Organization
type: NamedIndividual
has db xref: grid.486311.9
has db xref: nlx_156861
abbrev: AAHM
IAO_0000115: A professional association of historians, physicians, nurses, archivists, curators, librarians, and others that promotes and encourages research, study, writing, and interest in the history of medicine and allied fields.

rDiff
type: Resource
type: NamedIndividual
has db xref: OMICS_01338
IAO_0000115: Software tool for detecting differential RNA processing from RNA-Seq data. It implements two statistical tests, rDiff.parametric and rDiff.nonparametric, to detect changes of the RNA processing between two samples.

Phoenix
type: Resource
type: NamedIndividual
has db xref: nlx_156864
synonym: Phoenix helper
synonym: Phoenix system
IAO_0000115: A second-generation retrovirus producer lines for the generation of helper free ecotropic and amphotropic retroviruses. The lines are based on the 293T cell line (a human embryonic kidney line transformed with adenovirus E1a and carrying a temperature sensitive T antigen co-selected with neomycin). The unique feature of this cell line is that it is highly transfectable with either calcium phosphate mediated transfection or lipid-based transfection protocols-- up to 50% or higher of cells can be transiently transfected. The lines were created by placing into 293T cells constructs capable of producing gag-pol, and envelope protein for ecotropic and amphotropic viruses. The lines offered advantages over previous stable systems in that virus can be produced in just a few days. Academic and non-profit laboratories may obtain the Phoenix cells from either Allele Biotechnology or the National Gene Vector Bank. The vectors may be obtained from Addgene. They are no longer distributing these reagents from the lab.

Allele Biotechnology
type: Organization
type: NamedIndividual
has db xref: nlx_156865
synonym: Allele Biotechnology and Pharmaceuticals Inc
abbrev: Allele Biotech
IAO_0000115: A private company offering a wide variety of Molecular Biology reagents, fluorescent proteins, luciferase assay substrates, genotyping kits, and various custom services. The company isalso in the RNAi field with its recent patents in Pol III promoter-driven siRNA, shRNA, and miRNA. They introduced high titer lentivirus, camelid antibodies, and cell based assays and also offer Baculovirus protein expression and Gryphon retrovirus systems.

WEBMAXC STANDARD
type: Resource
type: NamedIndividual
has db xref: nlx_156866
IAO_0000115: Data analysis service to calculate free and total metals and chelators, Kds, complexes, and ionic contribution. You can evaluate chelators by having a non-zero value for any chelators you wish to evalute and at least one metal greater than zero. Kd's and ranges will appear at end. Only valid for metal-chelator combinations where there are constants.

MiST - Microbial Signal Transduction database
type: Resource
type: NamedIndividual
has db xref: biotools:mist
has db xref: nif-0000-03140
synonym: Microbial Signal Transduction Database
synonym: Microbial Signal Transduction database (MiST)
synonym: MiST2
synonym: MiST 2.2
abbrev: MiST
IAO_0000115: Database which contains the signal transduction proteins for complete and draft bacterial and archaeal genomes. The MiST2 database identifies and catalogs the repertoire of signal transduction proteins in microbial genomes.

Database of Interacting Proteins (DIP)
type: Resource
type: NamedIndividual
has db xref: biotools:dip
has db xref: nif-0000-00569
has db xref: OMICS_01905
has db xref: r3d100010882
synonym: Database of Interacting Proteins
synonym: DIP
IAO_0000115: Database to catalog experimentally determined interactions between proteins combining information from a variety of sources to create a single, consistent set of protein-protein interactions that can be downloaded in a variety of formats. The data were curated, both, manually and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Because the reliability of experimental evidence varies widely, methods of quality assessment have been developed and utilized to identify the most reliable subset of the interactions. This CORE set can be used as a reference when evaluating the reliability of high-throughput protein-protein interaction data sets, for development of prediction methods, as well as in the studies of the properties of protein interaction networks. Tools are available to analyze, visualize and integrate user's own experimental data with the information about protein-protein interactions available in the DIP database. The DIP database lists protein pairs that are known to interact with each other. By interact they mean that two amino acid chains were experimentally identified to bind to each other. The database lists such pairs to aid those studying a particular protein-protein interaction but also those investigating entire regulatory and signaling pathways as well as those studying the organization and complexity of the protein interaction network at the cellular level. Registration is required to gain access to most of the DIP features. Registration is free to the members of the academic community. Trial accounts for the commercial users are also available.

Solas
type: Resource
type: NamedIndividual
has db xref: biotools:solas
has db xref: OMICS_01339
IAO_0000115: Software package for the statistical language R, devoted to the analysis of next generation short read data of RNA-seq transcripts. It provides predictions of alternative exons in a single condition/cell sample, predictions of differential alternative exons between two conditions/cell samples, and quantification of alternative splice forms in a single condition/cell sample.

Fungal Genome Initiative
type: Resource
type: NamedIndividual
has db xref: nif-0000-30591
abbrev: FGI
IAO_0000115: Produces and analyzes sequence data from fungal organisms that are important to medicine, agriculture and industry. The FGI is a partnership between the Broad Institute and the wider fungal research community, with the selection of target genomes governed by a steering committee of fungal scientists. Organisms are selected for sequencing as part of a cohesive strategy that considers the value of data from each organism, given their role in basic research, health, agriculture and industry, as well as their value in comparative genomics.

MAP Software
type: Commercial Organization
type: NamedIndividual
has db xref: SciRes_000185
synonym: Multichannel Acquisition Processor Software
synonym: RASPUTIN
synonym: Real-Time Acquisition System Programs for Unit Timing in Neuroscience
synonym: Real-Time Acquisition System Programs for Unit Timing in Neuroscience software
IAO_0000115: A suite of client / server programs that control spike sorting in the Multichannel Acquisition Processor (MAP) Data Acquisition System (MAP System) and provides real-time data visualization and analysis. Plexon's original program supporting multichannel data acquisition is a suite of programs referred to as the Real-Time Acquisition System Programs for Unit Timing in Neuroscience software (RASPUTIN). This combination of software and hardware enables users to view waveforms, acquire action potential waveforms around a voltage-threshold crossing, sort them in real time according to their shape, record continuous analog signals, such as field potentials, eye position, blood pressure, as well as capture external digital-event data, such as individual TTL lines or multi-bit strobed word data. RASPUTIN utilizes a client/server architecture on a Microsoft Windows operating system. The server program runs the MAP box and distributes the data among a set of cooperating client programs. The program can record analog signals and spike and digital-event data in a single data file, and supports 16, 32, 48, 64, 96 and 128 channel configurations. RASPUTIN's operation is based on two primary programs: Sort Client and MAP Server. The Sort Client is the primary control program for the MAP System hardware and may be used to adjust the MAP operating parameters (e.g., amplification, filtering) and to set the specific sorting parameters for each channel. MAP Server is the low-level interface for configuring the MAP, which transfers commands such as gain and filter changes or parameter settings from the various clients to the MAP box. MAP Server also accumulates data coming from the MAP box in a circular buffer memory. The client programs connect to MAP Server to gain access to that data. MAP Server also mediates communication between the clients, keeping them informed of commands sent to the MAP from other clients. RASPUTIN is not sold separately, but rather arrives pre-loaded on the MAP…

Pipeliner
type: Resource
type: NamedIndividual
has db xref: biotools:pipeliner
has db xref: OMICS_04844
IAO_0000115: Software for evaluating the performance of bioinformatics pipelines for Next Generation re-Sequencing.

HuGE Navigator - Human Genome Epidemiology Navigator
type: Resource
type: NamedIndividual
has db xref: nif-0000-00573
abbrev: HuGE Navigator
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. Knowledge base of genetic associations and human genome epidemiology including information on population prevalence of genetic variants, gene-disease associations, gene-gene and gene- environment interactions, and evaluation of genetic tests. This tool explores HuGENet, the Human Genome Epidemiology Network, which is a global collaboration of individuals and organizations committed to the assessment of the impact of human genome variation on population health and how genetic information can be used to improve health and prevent disease. What does HuGE Navigator offer? *HuGEpedia - an encyclopedia of human genetic variation in health and disease, includes, Phenopedia and Genopedia. Phenopedia allows you to look up gene-disease association summaries by disease, and Genopedia allows you to look up gene-disease association summaries by gene. In general, HuGEpedia is a searchable database that summarizes published articles about human disease and genetic variation, including primary studies, reviews, and meta-analyses. It provides links to Pubmed abstracts, researcher contact info, trends, and more. *HuGEtools - searching and mining the literature in human genome epidemiology, includes, HuGE Literature Finder, HuGE Investigator Browser, Gene Prospector, HuGE Watch, Variant Name Mapper, and HuGE Risk Translator. *HuGE Literature Finder finds published articles in human genome epidemiology since 2001. The search query can include genes, disease, outcome, environmental factors, author, etc. Results can be filtered by these categories. It is also possible to see all articles in the database for a particular topic, such as genotype prevalence, pharmacogenomics, or clinical trial. *HuGE Investigator Browser finds investigators in a particular field of human genome epidemiology. This info is obtained using a behind-the-scenes tool that automatically parses PubMed affiliation data. *Gene Prospector is a gatewa…

iLoc-Animal
type: Resource
type: NamedIndividual
has db xref: OMICS_01623
synonym: iLoc-Animal: Predicting subcellular localization of animal proteins with single or multiple sites
IAO_0000115: Data analysis service for predicting subcellular localization of animal proteins with single or multiple sites.

QDNAseq
type: Resource
type: NamedIndividual
has db xref: biotools:qdnaseq
has db xref: OMICS_05902
synonym: QDNAseq - Quantitative DNA sequencing for chromosomal aberrations
IAO_0000115: Software package for quantitative DNA sequencing for chromosomal aberrations providing a robust, cost-effective WGS method for DNA copy number analysis. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.

MAUDS
type: Resource
type: NamedIndividual
has db xref: nif-0000-30603
IAO_0000115: We define a simple method to detect cortical states that can be applied in real time for offline processing of large amounts of recorded data on conventional computers. Also, the online detection of up and down states will facilitate the study of cortical dynamics. An open-source MATLAB toolbox, and Spike 2-compatible version are made freely available. Intracellular recordings from different areas of the cerebral cortex were obtained from both in vitro and in vivo preparations during slow oscillations. A method that separates up and down states recorded intracellularly is defined and analyzed here. The method exploits the crossover of moving averages, such that transitions between up and down membrane regimes can be anticipated based on recent and past voltage dynamics. We demonstrate experimentally the utility and performance of this method both offline and online, the online use allowing to trigger stimulation or other events in the desired period of the rhythm. This technique is compared with a histogram-based approach that separates the states by establishing one or two discriminating membrane potential levels. The robustness of the method presented here is tested on data that departs from highly regular alternating up and down states. The neuronal cortical network generates slow (<1 Hz) spontaneous rhythmic activity that emerges from the recurrent connectivity. This activity occurs during slow wave sleep or anesthesia and also in cortical slices, consisting of alternating up (active, depolarized) and down (silent, hyperpolarized) states. The search for the underlying mechanisms and the possibility of analyzing network dynamics in vitro has been subject of numerous studies. This exposes the need for a detailed quantitative analysis of the membrane fluctuating behavior and computerized tools to automatically characterize the occurrence of up and down states.

ResponseNet
type: Resource
type: NamedIndividual
has db xref: biotools:responsenet
has db xref: OMICS_01562
IAO_0000115: WebServer that identifies high-probability signaling and regulatory paths that connect input data sets. The input includes two weighted lists of condition-related proteins and genes, such as a set of disease-associated proteins and a set of differentially expressed disease genes, and a molecular interaction network (i.e., interactome). The output is a sparse, high-probability interactome sub-network connecting the two sets that is biased toward signaling pathways. This sub-network exposes additional proteins that are potentially involved in the studied condition and their likely modes of action. Computationally, it is formulated as a minimum-cost flow optimization problem that is solved using linear programming.

GENEWIZ
type: Resource
type: NamedIndividual
has db xref: nif-0000-30606
synonym: GENEWIZ Inc
IAO_0000115: Commercial organization for research and development genomics services and technical support to researchers.

ResearchMaps
type: Resource
type: NamedIndividual
has db xref: nlx_156891
IAO_0000115: UCLA based service for research planning aimed to help users integrate and summarize large amounts of information into a searchable graphic format. The interactive features facilitates planning during writing of grants, research papers and reviews. ResearchMaps can also be used as a collaborative tool and as a catalyst for the creative process.

EPILEPSIE database
type: Resource
type: NamedIndividual
has db xref: nlx_156892
synonym: EPILEPSIAE Project Database
synonym: European Epilepsy Database
IAO_0000115: A comprehensive database for human surface and intracranial EEG data that is suitable for a broad range of applications e.g. of time series analyses of brain activity. Currently, the EU database contains annotated EEG datasets from more than 200 patients with epilepsy, 50 of them with intracranial recordings with up to 122 channels. Each dataset provides EEG data for a continuous recording time of at least 96 hours (4 days) at a sample rate of up to 2500 Hz. Clinical patient information and MR imaging data supplement the EEG data. The total duration of EEG recordings included execeeds 30000 hours. The database is composed of different modalities: Binary files with EEG recording / MR imaging data and Relational database for supplementary meta data.

SynSysNet
type: Resource
type: NamedIndividual
has db xref: nlx_156893
has db xref: OMICS_01914
synonym: SynSysNet - Synaptic Proteins Database
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. A curated database for synaptic proteins that provides adequate definitions of pre- and post-synaptic proteins, proteins present in sub-domains of the synapse, e.g. the synaptic vesicle and associated proteins, lipid rafts and postsynaptic density. In addition to data that was and will be gathered from the experiments conducted within SynSys - A European expertise Network on building the synapse, they have extracted and manually curated all relevant data on these proteins from other sources and provided an ontology for these. Novel splice forms are being identified that can be matched with proteomics data. Information on proteins, their 3D structure, binding small molecules Protein-Protein-Interactions (PPIs) and Compound-Protein-Interactions are integrated. Proteins or compounds can be searched and Interactive Networks can be visualized. The point Diseases present neurological diseases, to illustrate the role of SynSysNet in the medication.

XORRO
type: Resource
type: NamedIndividual
has db xref: OMICS_01569
synonym: XORRO: Rapid Paired-End Read Overlapper
IAO_0000115: Efficient paired-read overlap software program for use with Illumina sequencing.

GNU Image Manipulation Program
type: Resource
type: NamedIndividual
has db xref: nif-0000-30615
abbrev: GIMP
IAO_0000115: A software application for such tasks as photo retouching, image composition and image authoring. It has many capabilities such as it can be used as a simple paint program, an expert quality photo retouching program, an online batch processing system, a mass production image renderer, an image format converter, etc. GIMP is expandable and extensible and designed to be augmented with plug-ins and extensions. The advanced scripting interface allows everything from the simplest task to the most complex image manipulation procedures to be easily scripted.

GENO3D
type: Resource
type: NamedIndividual
has db xref: nif-0000-30608
IAO_0000115: An automatic web server for protein molecular modelling. Starting with a query protein sequence, the server performs the homology modelling in six successive steps: (i) identify homologous proteins with known 3D structures by using PSI-BLAST; (ii) provide the user all potential templates through a very convenient user interface for target selection; (iii) perform the alignment of both query and subject sequences; (iv) extract geometrical restraints (dihedral angles and distances) for corresponding atoms between the query and the template; (v) perform the 3D construction of the protein by using a distance geometry approach and (vi) finally send the results by e-mail to the user. The strategy used in Geno3D is comparative protein structure modelling by spatial restraints (distances and dihedral) satisfaction.

Stacks
type: Resource
type: NamedIndividual
has db xref: biotools:stacks
has db xref: OMICS_01567
IAO_0000115: A software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. It was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.

ProLinks Database of Functional Linkages
type: Resource
type: NamedIndividual
has db xref: nif-0000-00580
synonym: Prolinks
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented July 7, 2017. Collection of inference methods used to predict functional linkages between proteins. These methods include the Phylogenetic Profile method which uses the presence and absence of proteins across multiple genomes to detect functional linkages; the Gene Cluster method which uses genome proximity to predict functional linkage; Rosetta Stone which uses a gene fusion event in a second organism to infer functional relatedness; and the Gene Neighbor method which uses both gene proximity and phylogenetic distribution to infer linkage.

SECISearch3 and Seblastian
type: Resource
type: NamedIndividual
has db xref: OMICS_01566
synonym: Selenoprotein prediction server
abbrev: Seblastian
abbrev: SECISearch
abbrev: SECISearch3
IAO_0000115: Web server to predict eukaryotic selenoproteins and SECIS (SElenoCysteine Insertion Sequences) elements along nucleotide sequences. SECISearch3 replaces its predecessor SECISearch as a tool for prediction of eukaryotic SECIS elements. Seblastian is a method for selenoprotein gene detection that uses SECISearch3 and then predicts selenoprotein sequences encoded upstream of SECIS elements. Seblastian is able to both identify known selenoproteins and predict new selenoproteins.

SALT
type: Resource
type: NamedIndividual
has db xref: biotools:salt
has db xref: OMICS_01565
synonym: SALT - Protein domain classifier
IAO_0000115: Software that can accurately and sensitivity classify short reads of next-generation sequencing (NGS) into protein domain families. It is based on profile HMM and a supervised graph contribution algorithm. Compared to existing tools, it has high sensitivity and specificity in classifying short reads into their native domain families.

HyperTree
type: Resource
type: NamedIndividual
has db xref: biotools:hypertree
has db xref: OMICS_04814
IAO_0000115: Software application to visualize and navigate large trees in hyperbolic space. Features include: * visualize large trees with hundreds of nodes or more * rotate and drag the display in cartesian space * search and select nodes * copy clusters for pasting into other programs * color-code branches * label branches (eg, common family members) * zoom in and out * view phylogenetic trees and other hierarchical clusters, such as gene expression profile clusters * run on several platforms: Mac, Windows, Unix/Linux

Primer Designer
type: Resource
type: NamedIndividual
has db xref: OMICS_02327
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Software program to aid in designing of primers and creation of primer sheets. The program allows users to select a background and enter mutaions. An initial primer is then suggested. User can manipulate the selected primer to add or remove nucleotides from either 5? or 3? ends. A set of parameters reflecting the goodness of the primer is updated on the fly, as the user makes changes. Once happy with the primer, the information is saved in a primer sheet, which can then be uploaded to the BGME lab primer database on the Wiki.

Cortical connectivity data sets
type: Resource
type: NamedIndividual
has db xref: nif-0000-00584
synonym: CCDS
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. This site has a collection of cortical connectivity datasets and modeling software components that can be downloaded and used for modeling of cortical circuits. The toolbox combines Matlab functions and neuroanatomical data sets useful in the analysis of structural or functional brain networks. Several people have made contributions and if you wish to contribute yourself with a new function or set of functions please contact osporns_at_indiana.edu.The following is a collection of commonly used large scale cortical connectivity data sets compiled from tract-tracing studies. Hence nodes represent cortical areas and links represent large cortico-cortical tracts. * macaque71.mat (BD network). Macaque cortical connectivity: 71 nodes 746 links. Reference: Young (1993). Contributor: OS. Used in e.g. Sporns (2002). * fve30.mat; fve32.mat (BD networks). Two version the macaque visual cortex. fve30.mat: 30 nodes 311 links. fve32.mat: 32 nodes 320 links. Reference: Felleman and van Essen (1991). Contributor: OS. Used in e.g. Sportns et al. (2000) Sporns and Kotter (2004). * macaque47.mat (BD network). Large scale cortico-cortical connectivity matrix of the visual and sensorimotor areas in the macaque. 47 nodes; 505 links. Used in e.g. Honey et al. (2007). Contributor: RK. * cat.mat (WD networks). Connection matrices of cat cortex. CIJall contains all cortical and thalamic areas: 95 nodes 2126 links. CIJctx contains only 52 cortical areas: 52 nodes 820 links. Reference: Scannell et al. (1999). Contributor: OS. Used in e.g. Sporns and Zwi (2004) Sporns and Kotter (2004). * DSIhumanctx.mat (WU networks).

GOLEM An interactive, graphical gene-ontology visualization, navigation, and analysis tool
type: Resource
type: NamedIndividual
has db xref: nif-0000-30620
synonym: GOLEM An interactive graphical gene-ontology visualization navigation analysis tool
synonym: GOLEM An interactive graphical gene-ontology visualization navigation and analysis tool
abbrev: GOLEM
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented July 7, 2017. Welcome to the home of GOLEM: An interactive, graphical gene-ontology visualization, navigation,and analysis tool on the web. GOLEM is a useful tool which allows the viewer to navigate and explore a local portion of the Gene Ontology (GO) hierarchy. Users can also load annotations for various organisms into the ontology in order to search for particular genes, or to limit the display to show only GO terms relevant to a particular organism, or to quickly search for GO terms enriched in a set of query genes. GOLEM is implemented in Java, and is available both for use on the web as an applet, and for download as a JAR package. A brief tutorial on how to use GOLEM is available both online and in the instructions included in the program. We also have a list of links to libraries used to make GOLEM, as well as the various organizations that curate organism annotations to the ontology. GOLEM is available as a .jar package and a macintosh .app for use on- or off- line as a stand-alone package. You will need to have Java (v.1.5 or greater) installed on your system to run GOLEM. Source code (including Eclipse project files) are also available. GOLEM (Gene Ontology Local Exploration Map)is a visualization and analysis tool for focused exploration of the gene ontology graph. GOLEM allows the user to dynamically expand and focus the local graph structure of the gene ontology hierarchy in the neighborhood of any chosen term. It also supports rapid analysis of an input list of genes to find enriched gene ontology terms. The GOLEM application permits the user either to utilize local gene ontology and annotations files in the absence of an Internet connection, or to access the most recent ontology and annotation information from the gene ontology webpage. GOLEM supports global and organism-specific searches by gene ontology term name, gene ontology id and gene name. CONCLUSION: GOLEM is a useful software tool for biolog…

GOToolBox Functional Investigation of Gene Datasets
type: Resource
type: NamedIndividual
has db xref: nif-0000-30623
synonym: GOToolBox - Functional Investigation of Gene Datasets
synonym: GOToolBox : Functional Investigation of Gene Datasets
abbrev: GOToolBox
IAO_0000115: The GOToolBox web server provides a series of programs allowing the functional investigation of groups of genes, based on the Gene Ontology resource. The web version of the GOToolBox is free for non-commercial users only. Users from commercial companies are allowed to use the site during a reasonable testing period. For a regular use of the web version, a license fee should be paid. We have developed methods and tools based on the Gene Ontology (GO) resource allowing the identification of statistically over- or under-represented terms in a gene dataset; the clustering of functionally related genes within a set; and the retrieval of genes sharing annotations with a query gene. GO annotations can also be constrained to a slim hierarchy or a given level of the ontology. The source codes are available upon request, and distributed under the GPL license. Platform: Online tool

The Cancer Genome Atlas
type: Resource
type: NamedIndividual
has db xref: nlx_156913
synonym: Cancer Genome Atlas
abbrev: TCGA
IAO_0000115: Project exploring the spectrum of genomic changes involved in more than 20 types of human cancer that provides a platform for researchers to search, download, and analyze data sets generated. As a pilot project it confirmed that an atlas of changes could be created for specific cancer types. It also showed that a national network of research and technology teams working on distinct but related projects could pool the results of their efforts, create an economy of scale and develop an infrastructure for making the data publicly accessible. Its success committed resources to collect and characterize more than 20 additional tumor types. Components of the TCGA Research Network: * Biospecimen Core Resource (BCR); Tissue samples are carefully cataloged, processed, checked for quality and stored, complete with important medical information about the patient. * Genome Characterization Centers (GCCs); Several technologies will be used to analyze genomic changes involved in cancer. The genomic changes that are identified will be further studied by the Genome Sequencing Centers. * Genome Sequencing Centers (GSCs); High-throughput Genome Sequencing Centers will identify the changes in DNA sequences that are associated with specific types of cancer. * Proteome Characterization Centers (PCCs); The centers, a component of NCI's Clinical Proteomic Tumor Analysis Consortium, will ascertain and analyze the total proteomic content of a subset of TCGA samples. * Data Coordinating Center (DCC); The information that is generated by TCGA will be centrally managed at the DCC and entered into the TCGA Data Portal and Cancer Genomics Hub as it becomes available. Centralization of data facilitates data transfer between the network and the research community, and makes data analysis more efficient. The DCC manages the TCGA Data Portal. * Cancer Genomics Hub (CGHub); Lower level sequence data will be deposited into a secure repository. This database stores cancer genome sequences and alignments…

Inter-university Consortium for Political and Social Research (ICPSR)
type: Resource
type: NamedIndividual
has db xref: nif-0000-00615
synonym: Inter-university Consortium for Political Social Research (ICPSR)
synonym: Interuniversity Consortium for Political and Social Research
synonym: Interuniversity Consortium for Political Social Research
abbrev: ICPSR
IAO_0000115: Data archive of more than 500,000 files of research in the social sciences, hosting 16 specialized collections of data in education, aging, criminal justice, substance abuse, terrorism, and other fields. ICPSR comprises a consortium of about 700 academic institutions and research organizations providing training in data access, curation, and methods of analysis for the social science research community. ICPSR welcomes and encourages deposits of digital data. ICPSR's educational activities include the Summer Program in Quantitative Methods of Social Research external link, a comprehensive curriculum of intensive courses in research design, statistics, data analysis, and social methodology. ICPSR also leads several initiatives that encourage use of data in teaching, particularly for undergraduate instruction. ICPSR-sponsored research focuses on the emerging challenges of digital curation and data science. ICPSR researchers also examine substantive issues related to our collections, with an emphasis on historical demography and the environment.

Smart Assays
type: Commercial Organization
type: NamedIndividual
has db xref: SciEx_9345
IAO_0000115: Commercial organization that provides services for assay development, research histopathology, and early stage project consultation.

ARC Centre of Excellence in Vision Science
type: Resource
type: NamedIndividual
has db xref: nlx_157285
synonym: ARC Center of Excellence in Vision Science
synonym: Australian Research Council Centre of Excellence in Vision Science
abbrev: ACEVS
IAO_0000115: Centre of Excellence in Vision Science that brings together major vision research programs at the The Australian National University with cognate programs at the Universities of Queensland, Sydney and Western Australia. The research is focused on unravelling the cellular basis of visual sensing and processing; on revealing the algorithms that underlie the visual control of behavior and perception; and on discovering the cellular mechanisms that make the eye and retina stable, and whose breakdown causes blindness.

TheDataWeb and DataFerrett
type: Resource
type: NamedIndividual
has db xref: nif-0000-00616
synonym: Data Federated Electronic Research Review Extraction and Tabulation Tool
synonym: DataFerrett for TheDataWeb
synonym: TheDataWeb for the DataFerrett
synonym: TheDataWeb/DataFerrett
abbrev: DataFerrett
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 20,2025. A data analysis and extraction tool from the US Census Bureaus with recoding capabilities to customize federal, state, and local data to suit your requirements. DataFerret works with the DataWeb, a network of online data libraries and an infrastructure for intelligent browsing. TheDataweb provides easy access to data from disparate locations across the internet using DataFerrett as its interface. It brings together demographic, economic, environmental, health, and other datasets that are usually separated by geography and/or organization.Using DataFerrett, you can develop an unlimited array of customized spreadsheets that are as versatile and complex as your usage demands. For a listing/description of datasets available using the DataFerrett refer to the Datasets Available tab. DataFerrett helps you locate and retrieve the data you need across the Internet to your desktop or system, regardless of where the data resides. You can develop and customize tables and select the results to create a graph or map for a visual depiction of your data. You can also save your data in the databasket and save the table you have created for reuse. The DataFerrett tool can use a java applet through an internet browser or be installed as an application on your desktop. The DataFerrett Applet requires you to have popup windows enabled in your browser for this website to function properly.

r3Cseq
type: Resource
type: NamedIndividual
has db xref: OMICS_01560
IAO_0000115: An R/Bioconductor package to identify chromosomal interaction regions generated by chromosome conformation capture (3C) coupled to next-generation sequencing (NGS), a technique termed 3C-seq. It performs data analysis for a number of different experimental designs, as it can analyze 3C-seq data with or without a control experiment and it can be used to facilitate data analysis for experiments with multiple replicates. The r3Cseq package provides functions to perform data normalization, statistical analysis for cis/trans interactions and visualization in order to help scientists identify genomic regions that physically interact with the given viewpoints of interest. This tool greatly facilitates hypothesis generation and the interpretation of experimental results.

Gene Set Enrichment Analysis
type: Resource
type: NamedIndividual
has db xref: biotools:gsea
has db xref: nif-0000-30629
has db xref: OMICS_02279
has db xref: SCR_016882
synonym: Gene Set Enrichment Analysis (GSEA)
synonym: GSEA
IAO_0000115: Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes.

Piano
type: Resource
type: NamedIndividual
has db xref: biotools:piano
has db xref: OMICS_01558
IAO_0000115: Software R-package for running gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. The Piano package contains functions for combining the results of multiple runs of gene set analyses.

GenePattern
type: Resource
type: NamedIndividual
has db xref: biotools:genepattern
has db xref: nif-0000-30654
has db xref: OMICS_01855
IAO_0000115: A powerful genomic analysis platform that provides access to hundreds of tools for gene expression analysis, proteomics, SNP analysis, flow cytometry, RNA-seq analysis, and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research.

Gen-Probe
type: Organization
type: NamedIndividual
has db xref: grid.481838.e
has db xref: ISNI: 0000 0004 0641 3850
has db xref: nlx_152369
has db xref: Wikidata: Q30343851
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented July 7, 2017. Formerly a commercial organization for clinical diagnostics, blood screening, transplant products and research products, it had been acquired by Hologic in 2012.

Council of Scientific and Industrial Research
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100001412
has db xref: grid.418099.d
has db xref: nlx_149418
has db xref: Wikidata: Q3519967
synonym: Council of Scientific & Industrial Research
synonym: CSIR India
abbrev: CSIR
IAO_0000115: Research and development organization that hosts a knowledgebase in diverse scientific areas. It also hosts a network of national Indian laboratories, outreach centres, and innovation complexes.

PHAST
type: Resource
type: NamedIndividual
has db xref: OMICS_01557
synonym: Phylogenetic Analysis with Space/Time Models
IAO_0000115: A freely available software package for comparative and evolutionary genomics that consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations. For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. It consists of over 60,000 lines of C code.

NHGRI: Establishing a Central Resource of Data from Genome Sequencing Projects
type: Resource
type: NamedIndividual
has db xref: OMICS_01554
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2025. 2012 workshop to establish a Central Resource of Data from Genome Sequencing Projects. The workshop addressed the challenges to aggregating and analyzing data sets from genome sequencing studies, such as: * Data sets being generally hard to access. * Data residing in various databases. * Variant and exposure/phenotype data not being comparable across studies. Participants in the workshop discussed options for dealing with these challenges, along with their costs and tradeoffs. Videos and accompanying slides from the workshop are available. Also available as a video playlist on GenomeTV

Google Sidewiki
type: Resource
type: NamedIndividual
has db xref: nif-0000-30708
abbrev: Sidewiki
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented July 10, 2017. Sidewiki allows you to publish helpful information about any web page right in your browser, read insights in context from Sidewiki entries added by others, and share Sidewiki entries through Blogger, Facebook, Twitter and Google profiles. The toolbar with Sidewiki is free, installs in seconds and requires Internet Explorer 6+ or Firefox 2+; Windows XP SP2/Vista+. A Google Sidewiki extension is only available for Google Chrome 4.0+

EMDataResource.org
type: Resource
type: NamedIndividual
has db xref: nif-0000-30776
has db xref: r3d100010552
synonym: EMDataBank
synonym: EMDataBank - Unified Data Resource for 3DEM
synonym: EMDataBank.org
synonym: EMDataResource
synonym: EMDB
synonym: EMDResource
IAO_0000115: Portal for deposition and retrieval of cryo electron microscopy (3DEM) density maps, atomic models, and associated metadata. Global resource for 3 Dimensional Electron Microscopy structure data archiving and retrieval, news, events, software tools, data standards, validation methods.

NGSadmix
type: Resource
type: NamedIndividual
has db xref: OMICS_01553
IAO_0000115: A tool for finding admixture proportions from next generation sequencing (NGS) data that is based on genotype likelihoods. It is a multithreaded c/c++ program.

QGene
type: Resource
type: NamedIndividual
has db xref: biotools:qgene
has db xref: nif-0000-31383
synonym: QGene - Software for QTL data exploration
IAO_0000115: A free, open-source, computationally efficient Java program for comparative analyses of QTL mapping data and population simulation that runs on any computer operating system. (entry from Genetic Analysis Software) It is written with a plug-in architecture for ready extensibility. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. Source code is available on request.

SigmaPlot
type: Commercial Organization
type: NamedIndividual
has db xref: SciRes_000184
synonym: sigma plot
IAO_0000115: Statistical analysis and scientific graphing software for Windows OS.

Gemi
type: Resource
type: NamedIndividual
has db xref: OMICS_02332
synonym: Gemi - PCR oligos / primers design from multiple sequence alignments
IAO_0000115: Automated software tool to design polymerase chain reaction (PCR) primers. It accepts multiple aligned and long sequences with degenerated nucleotides. It can be used for quantitative/real-time PCR, conventional and Sanger sequencing. Gemi accepts DNA and RNA sequences with degenerate nucleotide (non-A/C/G/T bases). The programs are as the following: # The first program is to design PCR primers from multiple sequence alignment. # Program to convert ClustalW format (.aln), Phylip (.phy) and (.gde) formats to Fasta format. # Reverse and/or complement program is to find the reverse and complement counterpart of single or multiple sequences.

Mouse Phenome Database (MPD)
type: Resource
type: NamedIndividual
has db xref: biotools:mpd
has db xref: nif-0000-03160
has db xref: r3d100010101
synonym: Mouse Phenome Database
abbrev: MPD
IAO_0000115: Database enables integration of genomic and phenomic data by providing access to primary experimental data, data collection protocols and analysis tools. Data represent behavioral, morphological and physiological disease-related characteristics in naive mice and those exposed to drugs, environmental agents or other treatments. Collaborative standardized collection of measured data on laboratory mouse strains to characterize them in order to facilitate translational discoveries and to assist in selection of strains for experimental studies. Includes baseline phenotype data sets as well as studies of drug, diet, disease and aging effect., protocols, projects and publications, and SNP, variation and gene expression studies. Provides tools for online analysis. Data sets are voluntarily contributed by researchers from variety of institutions and settings, or retrieved by MPD staff from open public sources. MPD has three major types of strain-centric data sets: phenotype strain surveys, SNP and variation data, and gene expression strain surveys. MPD collects data on classical inbred strains as well as any fixed-genotype strains and derivatives that are openly acquirable by the research community. New panels include Collaborative Cross (CC) lines and Diversity Outbred (DO) populations. Phenotype data include measurements of behavior, hematology, bone mineral density, cholesterol levels, endocrine function, aging processes, addiction, neurosensory functions, and other biomedically relevant areas. Genotype data are primarily in the form of single-nucleotide polymorphisms (SNPs). MPD curates data into a common framework by standardizing mouse strain nomenclature, standardizing units (SI where feasible), evaluating data (completeness, statistical power, quality), categorizing phenotype data and linking to ontologies, conforming to internal style guides for titles, tags, and descriptions, and creating comprehensive protocol documentation including environmental parameters of th…

MorphoBank
type: Resource
type: NamedIndividual
has db xref: DOI:10.7934
has db xref: DOI:10.17616/R3PC7F
has db xref: DOI:10.25504/FAIRsharing.1y63n8
has db xref: nlx_156938
has db xref: r3d100010786
IAO_0000115: Web application providing online database and workspace for evolutionary research, specifically systematics (the science of determining the evolutionary relationships among species). It enables researchers to upload images and affiliate data with those images (labels, species names, etc.) and allows researchers to upload morphological data and affiliate it with phylogenetic matrices. MorphoBank is project-based, meaning a team of researchers can create a project and share the images and associated data exclusively with each other. When a paper associated with the project is published, the research team can make their data permanently available for view on MorphoBank where it is now archived.

Vertebrate Trait Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_156940
synonym: VT Ontology
abbrev: VT
IAO_0000115: A controlled vocabulary for the description of traits (measurable or observable characteristics) pertaining to the morphology, physiology, or development of vertebrate organisms.

Talking Glossary of Genetic Terms
type: Resource
type: NamedIndividual
has db xref: nlx_156942
has db xref: OMICS_01555
synonym: NHGRI Talking Glossary
synonym: NHGRI Talking Glossary of Genetic Terms
abbrev: Talking Glossary
IAO_0000115: Glossary of Genetic Terms to help everyone understand the terms and concepts used in genetic research. In addition to definitions, specialists in the field of genetics share their descriptions of terms, and many terms include images, animation and links to related terms.

Wellcome-CTC Mouse Strain SNP Genotype Set
type: Resource
type: NamedIndividual
has db xref: nlx_156947
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2025. Data set of genotypes available for 480 strains and 13370 successful SNP assays that are mapped to build34 of the mouse genome, including 107 SNPs that are mapped to random unanchored sequence 13374 SNPs are mapped onto Build 33 of the mouse genome. You can access the data relative to Build 33 or Build 34.

CrossRef
type: Resource
type: NamedIndividual
has db xref: nlx_156949
IAO_0000115: An official Digital Object Identifier (DOI) Registration Agency of the International DOI Foundation launched as a cooperative effort among publishers to enable persistent cross-publisher citation linking in online academic journals. The citation-linking network today covers over 65 million journal articles and other content items (books chapters, data, theses, technical reports) from thousands of scholarly and professional publishers around the globe. CrossRef does not aggregate full-text content but rather, it uses a system of distributed aggregation whereby full-text content is linked through a database consisting of minimal publisher metadata. Each record in the database is essentially a triplet: (metadata + URL+DOI). In addition to assigning DOIs to scholarly content, CrossRef has additional services: * Cited-By Linking * CrossRef Metadata Services * CrossCheck plagiarism screening (powered by iThenticate) * CrossMark update identification service * FundRef Funder identification service

FundRef
type: Resource
type: NamedIndividual
has db xref: nlx_156950
synonym: FundRef Registry
IAO_0000115: Funder Registry and associated funding metadata allows everyone to have transparency into research funding and its outcomes. Open registry of persistent identifiers for grant-giving organizations around the world.

dbVar
type: Resource
type: NamedIndividual
has db xref: nlx_157217
has db xref: r3d100010758
synonym: Database of Genomic Structural Variation
synonym: NCBI dbVar
IAO_0000115: Structural variation database designed to store data on variant DNA > / = 1 bp in size from all organisms. Associations of defined variants with phenotype information is also provided. Users can browse data containing number of variant cells from each study, and filter studies by organism, study type, method and genomic variant. Organisms include human, mouse, cattle and several additional animals.

Template-O-Matic Toolbox
type: Resource
type: NamedIndividual
has db xref: nlx_157256
synonym: Template-O-Matic
abbrev: TOM
abbrev: TOM Toolbox
IAO_0000115: Software toolbox for creating customized pediatric templates. It provides reference data based on imaging data from the NIH study of normal brain development. Using the general linear model, they statistically isolate the influence of external variables of interest on brain structure, allowing us to generate high-quality matched templates for any given group of subjects. The toolbox offers two options: # to create pediatric templates (T1) and tissue maps (GM, WM, and CSF) based on the objective 1 NIH data (n = 404), in the age range of 5-18 years, or # to assess a new reference population with regard to your variables of interest. Of note, this approach is generally applicable and in no way restricted to analyzing pediatric imaging data: for example, if you aim at investigating the effects of aging in elderly subjects, the toolbox will also allow you to create more appropriate reference (if your group is large enough to isolate such effects).

MINSEQE
type: Resource
type: NamedIndividual
has db xref: nlx_157258
synonym: Minimum Information about a high-throughput SEQuencing Experiment
IAO_0000115: The Minimum Information about a high-throughput nucleotide SEQuencing Experiment that is needed to enable the unambiguous interpretation and facilitate reproduction of the results of the experiment. By analogy to the MIAME guidelines for microarray experiments, adherence to the MINSEQE guidelines will improve integration of multiple experiments across different modalities, thereby maximising the value of high-throughput research. The five elements of experimental description considered essential when making data available supporting published high-throughput sequencing experiments are as follows: # The description of the biological system, samples, and the experimental variables being studied # The sequence read data for each assay # The "final" processed (or summary) data for the set of assays in the study # General information about the experiment and sample-data relationships # Essential experimental and data processing protocols

MAGE-TAB
type: Resource
type: NamedIndividual
has db xref: biotools:tab2mage
has db xref: nlx_157259
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 27,2023. A simple tab-delimited, spreadsheet-based format which will become a part of the MAGE microarray data standard that can be used for annotating and communicating microarray data in a MIAME compliant fashion. MAGE-TAB will enable laboratories without bioinformatics experience or support to manage, exchange and submit well-annotated microarray data in a standard format using a spreadsheet. The MAGE-TAB format is self-contained, and does not require an understanding of MAGE-ML or XML.

ResearchCompendia
type: Resource
type: NamedIndividual
has db xref: nlx_157262
has db xref: r3d100011137
synonym: Research Compendia
IAO_0000115: Tools for researchers to connect their data, code and computational methods to their published or soon to be published research in a convenient and easily citeable form. ResearchCompendia provides the tools to publish digital scholarly objects by hosting data, code, and methods in a form that is accessible, trackable, and persistent. They provide hosting and computational cloud resources for all researchers. Data and code should be citable and linked to the original publication.

resExomeDB
type: Resource
type: NamedIndividual
has db xref: nlx_157263
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. An online catalog for whole-exome sequencing (WES) results including mutations and gene-disease associations identified by WES. It is browsable and searchable by mutation, gene, study or publication. In addition, it centralizes all publications, software, platforms related to exome / whole genome sequencing.

SobekCM
type: Resource
type: NamedIndividual
has db xref: nlx_157266
synonym: SobekCM : Digital Content Management System
synonym: SobekCM Digital Repository
synonym: SobekCM Digital Repository Software
IAO_0000115: Digital repository software written in C# / ASP.net for powering digital libraries in a Windows server environment. Standards-based repository keeps all files in METS/MODS packages. Several related applications are available as well and the libraries can work independently as great digital library resources. SobekCM allows users to discover online resources via semantic and full-text searches, as well as a variety of different browse mechanisms. For each digital resource in the repository there are a plethora of display options, which may be selected by an appropriately authenticated use. This repository includes online metadata editing and online submissions in support of institutional repositories.

W3C Open Annotation Community Group
type: Resource
type: NamedIndividual
has db xref: nlx_157267
abbrev: Open Annotation Community Group
IAO_0000115: Community group working towards a common, RDF-based, specification for annotating digital resources. The effort began by trying to reconcile two proposals: the Annotation Ontology (http://code.google.com/p/annotation-ontology/) and the Open Annotation Model (http://www.openannotation.org/spec/beta/ ). Initially, editors of these proposals collaborated to devise a common draft specification that addresses requirements and use cases that were identified in the course of their respective efforts. This draft became available for public feedback and experimentation in the second quarter of 2012. The final deliverable is a specification, published under an appropriate open license, that is informed by the existing proposals, the common draft specification, and the community feedback.

Webmaker
type: Resource
type: NamedIndividual
has db xref: nlx_157268
synonym: Mozilla Webmaker
synonym: webmaker.org
IAO_0000115: A Mozilla project to teach and enable users on how to create on the web. Their tools, events and teaching guides allow webmakers to create the content that makes the web great and understand how the web works. They've built everything so you can see how it works, take it apart and remix it

Wikispaces
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_157269
synonym: Wikispaces Classroom
IAO_0000115: A social writing platform, free for education, to easily create a classroom workspace where teacher and students can communicate and work on writing projects alone or in teams. Rich assessment tools give the power to measure student contribution and engagement in real-time. Wikispaces Classroom works great on modern browsers, tablets, and phones. For a fee it is also available to non-educators including companies, organizations, universities, groups, etc.

Mobile Assay
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_157277
synonym: Mobile Diagnostic Rapid Test Reader
synonym: Mobile Diagnostic Rapid Test Strip Reader
abbrev: MobileAssay
IAO_0000115: Smart phone, tablet and mobile device software designed for highly sensitive real-time analysis and quantification of inexpensive rapid diagnostic test strips. The software allows anyone with a camera equipped device to take an image of a Rapid Diagnostic Test Strip and get back instant quantifiable results. It has the ability to run multiple tests at once and can be configured to read any lateral flow test strip.

RIKEN Arabidopsis Transposon mutants
type: Resource
type: NamedIndividual
has db xref: nif-0000-31394
IAO_0000115: RIKEN Arabidopsis Transposon mutants is a series of mutant lines which have a Ds transposon in the genome of Arabidopsis thaliana Nssen ecotype (background by Fedoroff and Smith). This web page provides information on the mutants produced in our laboratory. Each mutant line is assigned by stipulated line codes (ex. 13-4480-1). We determined the flanking sequences of Ds insertion for each independent line. Transposon insertion sites of mutants were estimated by a BLASTN homology against the genome sequence database of Arabidopsis thaliana Columbia ecotype. The closest genes (predicted by AGI) to the transposon insertion sites were picked up. The results of the BLASTP homology search against the nr database of NCBI for the closest genes have been collected for keyword searches.

WorkingWiki
type: Resource
type: NamedIndividual
has db xref: nlx_157270
IAO_0000115: Free software extension for MediaWiki that makes a wiki into an environment for collaborating on publication-quality manuscripts and software projects. It allows wiki users to work together on anything that can be done by using UNIX commands to transform textual source code into output. Researchers can use it to collaborate on programs written in R, python, C, or any other language, and there are special features to support easy work on LaTeX documents. It develops the potential of the wiki medium to serve as a combination collaborative text editor, development environment, revision control system, and publishing platform. Its potential uses are open-ended - its processing is controlled by makefiles that are straightforward to customize - and its modular design is intended to allow parts of it to be adapted to other purposes.

Overleaf
type: Commercial
type: NamedIndividual
has db xref: nlx_157271
synonym: writeLaTex
IAO_0000115: A collaboration tool which allows users to edit and publish scientific articles and papers. Overleaf utilizes the convenience of an easy-to-use WYSIWYG manuscript editor with real-time collaboration and structured, fully typeset output produced automatically. Authors can publish immediately and directly to their journal of choice while publishers can reduce their editorial and review turnaround times with powerful change tracking, commenting, and project lifecycle management features. It was formerly known as writeLaTex but changed its name to Overleaf in 2015.

Xournal
type: Resource
type: NamedIndividual
has db xref: nlx_157272
IAO_0000115: Free software application for notetaking, sketching, keeping a journal using a stylus that runs on Linux (recent distributions) and other GTK+/Gnome platforms. It is similar to Microsoft Windows Journal or to other alternatives such as Jarnal, Gournal, and NoteLab. Note: is open source and allows some annotation, but its PDF reading ability is very limited. It also uses its own format to store annotations.

Citation Style Language
type: Resource
type: NamedIndividual
has db xref: nlx_157273
synonym: Citation Styles
abbrev: CSL
IAO_0000115: An open XML-based language used to describe the formatting of citations and bibliographies. CSL has become the standard way to add citation support to software.

EnablingOpenScholarship
type: Resource
type: NamedIndividual
has db xref: nlx_157274
abbrev: EOS
IAO_0000115: An organization for universities and research institutions that is an information service and a forum for raising and discussing issues around the mission of modern universities and research institutions, particularly with regard to the creation, dissemination and preservation of research findings. Its aim is to further the opening up of scholarship and research that we are now seeing through the growing open access, open education, open science and open innovation movements. These, and other, "open" approaches to scholarship are changing the way research and learning are done and there are profound implications for universities and research institutions. EOS has been established to help guide developments and to assist others in understanding the issues and their implications. The context in which EOS has been established is that of increasing interest from governments, funders and the research community itself in opening up the way research is carried out and communicated. This interest is complemented by new research practices and processes that can work effectively only in an open, collaborative environment. Developments of relevance to the mission of EnablingOpenScholarship are reported on and news and details of forthcoming meetings, briefings and discussion sessions is provided.

JournalGuide
type: Resource
type: NamedIndividual
has db xref: nlx_157276
synonym: Journal Guide
IAO_0000115: Database of journal information that provides tools to search, sort, filter, compare, and evaluate scholarly journals. In addition to searching by journal name, category or publisher, authors can use title and abstract of paper to discover journals that have already published articles on similar topics. Data sources include major industry data sets, public resources, information submitted directly by journal editors, and real-life publishing experiences submitted by authors.

Fitzgerald Industries International
type: Organization
type: NamedIndividual
has db xref: nlx_152365
synonym: Fitzgerald
IAO_0000115: Commercial organization that supplies antibodies, proteins, ELISA kits, serum, and plasma to the research community.

Open Science Framework
type: Resource
type: NamedIndividual
has db xref: DOI:10.17605
has db xref: DOI:10.17616/R3N03T
has db xref: DOI:10.25504/FAIRsharing.g4z879
has db xref: nlx_157292
has db xref: r3d100011268
has db xref: SCR_017419
abbrev: OSF
IAO_0000115: Platform to support research and enable collaboration. Used to discover projects, data, materials, and collaborators helpful to your own research.

Center for Open Science
type: Resource
type: NamedIndividual
has db xref: nlx_157293
abbrev: COS
IAO_0000115: Non-profit organization to increase the openness, integrity, and reproducibility of scientific research. COS priorities are to (1) make the entire scientific workflow accessible, (2) increase scientists' accountability, (3) facilitate good practices by scientists, (4) increase reward for good practices, and (5) promote reproducibility of scientific findings. COS has three primary activities: * Infrastructure development to support the scientific workflow and to connect technologies that support scientific research and communication, such as the Open Science Framework * Community building on open practices among open-source developers, open science researchers, and the broader scientific community, such as the Open Science Collaboration * Metascience, research on scientific practices, such as Reproducibility Project: Psychology and our partnership with Science Exchange, Reproducibility Project: Cancer Biology.

Laura and John Arnold Foundation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100009827
has db xref: grid.480593.3
has db xref: ISNI: 0000 0004 0555 6315
has db xref: nlx_157294
has db xref: Wikidata: Q17088752
synonym: Arnold Foundation
abbrev: LJAF
IAO_0000115: Private foundation whose funding activities are primarily centered around improving life in the United States. Its mission is to produce big and lasting changes in society over the long term. Their four areas of focus (2014) are: criminal justice, K-12 education, public accountability, and research integrity.

Child Language Data Exchange System (CHILDES)
type: Resource
type: NamedIndividual
has db xref: nif-0000-00624
has db xref: r3d100010887
synonym: Child Language Data Exchange System
abbrev: CHILDES
IAO_0000115: Child language component of TalkBank system. TalkBank is system for sharing and studying conversational interactions. Includes software developed for speech recognition and analysis as well as behavior recognition. Database contains transcript and media data collected from conversations between young children and their playmates and caretakers. Conversations with older children and adults are available from TalkBank. All of data is transcribed in CHAT and CA/CHAT formats.

TalkBank
type: Resource
type: NamedIndividual
has db xref: nif-0000-00626
has db xref: r3d100010551
IAO_0000115: Databases of transcript and media data collected from conversations with adults and older children to foster fundamental research in the study of human and animal communication. Conversations with children are available from CHILDES. All of the data is transcribed in CHAT and CA/CHAT formats. Databases of the following types are included in the collection: Aphasia patient speech, Child speech, Study of Phonological Development, Conversation Analysis, and Bilingualism and Second Language Acquisition. TalkBank will use these databases to advance the development of standards and tools for creating, sharing, searching, and commenting upon primary materials via networked computers.

MUGEN Mouse Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-03171
abbrev: MMdb
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. MUGEN Mouse Database (MMdb) is a virtual and fully searchable repository of murine models of immune processes and immunological diseases. MMdb is being developed within the context of the MUGEN network of Excellence, a consortium of 21 leading research institutes and universities, and currently holds all mutant mouse models that were developed within the consortium. Its primary aim is to enable information exchange between participating institutions on mouse strain characteristics and availability. More importantly, it aims to create a mouse-centric international forum on modelling of immunological diseases and pave the way to systems biology of the mouse by correlating various genotypic and phenotypic characteristics. The basic categorization of models is based on three major research application categories: * Model of Human Disease * Model of Immune Processes * Transgenic Tool Mutant strains carry detailed information on affected gene(s), mutant alleles and genetic background (DNA origin, targeted, host and backcrossing background). Each gene/transgene index also includes IDs and direct links to Ensembl (EBI��s genome browser), ArrayExpress (providing expression profiles), Eurexpress II (for embryonic expression patterns) and NCBI��s Entrez Gene database. Phenotypic description is standardized and hierarchically structured, based on MGI��s mammalian phenotypic ontology terms, but also includes relevant images and references. Since version 2.1.0 MMdb is also utilizing PATO. Availability (in the form of live mice, cryopreserved embryos or sperm, as well as ES cells) is clearly indicated, along with handling and genotyping details (in the form of documents or hyperlinks) and all relevant contact information (including EMMA and JAX hyperlinks where available).

Coriell Cell Repositories
type: Resource
type: NamedIndividual
has db xref: nif-0000-00182
abbrev: CCR
IAO_0000115: A biorepository and biomaterial supply resource which establishes, verifies, maintains, and distributes cells, cultures and DNA derived from cell cultures to the scientific community around the world. Scientists can browse the sample catalog and request specific cell lines for their research studies. An inventory of the remaining stock of each cell line and DNA preparation is presented in real time. Coriell's significant cell biobank collections include: NIGMS Human Genetic Cell Repository, NINDS Human Genetics DNA and Cell Line Repository, NIA Aging Cell Repository, NHGRI Sample Repository for Human Genetic Research, NEI Age-Related Eye Disease Study (AREDS) Genetic Repository, HD Community BioRepository, American Diabetes Association, GENNID Study, and Autism Research Resource. The repositories are ISO 9000-2001 compliant.

Mental Functioning Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157305
synonym: mental-functioning-ontology
abbrev: MF
abbrev: MFO
IAO_0000115: An ontology for mental functioning, including mental processes such as cognition and traits such as intelligence, and related diseases and disorders. It is developed in the context of the Ontology for General Medical Science and the Basic Formal Ontology. The project is being developed in collaboration between the University of Geneva, Switzerland, and the University at Buffalo, USA. The project is being developed with full involvement of all relevant communities, following best practices laid out by the OBO Foundry. Efforts are currently underway to align with related projects including the Behaviour Ontology, the Cognitive Atlas, the Cognitive Paradigm Ontology and the Neural Electro Magnetic Ontologies.

Metabolomics Standards Initiative
type: Resource
type: NamedIndividual
has db xref: nlx_157308
abbrev: MSI
IAO_0000115: Oversight Committee appointed to monitor, coordinate and review the efforts of working groups (WG) in specialist areas (Biological context metadata WG, Chemical analysis WG, Data processing WG, Ontology WG, Exchange format WG) that will examine standardization and make recommendations.

nmrCV
type: Resource
type: NamedIndividual
has db xref: nlx_157310
IAO_0000115: Ontology for describing NMR experiments and acquisitions.

PathGuide: the pathway resource list
type: Resource
type: NamedIndividual
has db xref: nif-0000-00640
has db xref: OMICS_01701
has db xref: SciRes_000148
abbrev: Pathguide
IAO_0000115: Catalog containing information about 547 biological pathway related resources and molecular interaction related resources. Databases that are free and those supporting BioPAX, CellML, PSI-MI or SBML standards are respectively indicated.

SplicingCompass
type: Resource
type: NamedIndividual
has db xref: biotools:splicingcompass
has db xref: OMICS_01340
synonym: Splicing Compass
IAO_0000115: Software for detection of differential splicing between two different conditions using RNA-Seq data.

RIKEN BioResource Center
type: Resource
type: NamedIndividual
has db xref: nif-0000-31407
synonym: RIKEN Tsukuba Institute RIKEN BioResource Center
abbrev: BRC
abbrev: RIKEN BRC
IAO_0000115: RIKEN BRC contributes to advancement of life science research by collecting, preserving and distributing biological resources such as experimental animals, experimental plants, cultured cell lines, genetic materials (DNA), and associated bioinformatics. The RIKEN BRC develops novel bioresources to promote scientific research and new technologies to increase the value of bioresources, and also to implement effective procedures for the preservation, quality control and usage of bioresources. The RIKEN BRC is working closely with institutions in Japan and abroad.

MutDB
type: Resource
type: NamedIndividual
has db xref: biotools:mutdb
has db xref: nif-0000-03173
IAO_0000115: Database with annotations for human variation data with protein structural information and other functionally relevant information, if available. The mutations are organized by gene.

RNAhybrid
type: Resource
type: NamedIndividual
has db xref: biotools:rnahybrid
has db xref: nif-0000-31412
has db xref: OMICS_00416
IAO_0000115: Software tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, i.e., the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction.

LUMPY
type: Resource
type: NamedIndividual
has db xref: OMICS_04674
synonym: LUMPY Express
synonym: lumpy-sv
IAO_0000115: Software package as probabilistic framework for structural variant discovery. Capable of integrating any number of SV detection signals including those generated from read alignments or prior evidence. Simplified wrapper for standard analyses, LUMPY Express, can also be executed.

Ascomycete Phenotype Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157321
abbrev: APO
IAO_0000115: A structured controlled vocabulary for the phenotypes of Ascomycete fungi.

Nucleic Acid Database
type: Resource
type: NamedIndividual
has db xref: biotools:ndb
has db xref: nif-0000-03184
has db xref: r3d100010415
abbrev: NDB
IAO_0000115: A database of three-dimensional structural information about nucleic acids and their complexes. In addition to primary data, it contains derived geometric data, classifications of structures and motifs, standards for describing nucleic acid features, as well as tools and software for the analysis of nucleic acids. A variety of search capabilities are available, as are many different types of reports. NDB maintains the macromolecular Crystallographic Information File (mmCIF).

NCBI Taxonomy
type: Resource
type: NamedIndividual
has db xref: nif-0000-03179
has db xref: r3d100010776
synonym: Entrez Taxonomy Browser
synonym: NCBI Taxonomy Browser
synonym: NCBI Taxonomy Database
synonym: Taxonomy Browser
IAO_0000115: Database for a curated classification and nomenclature that contains the names of all organisms that are represented in the public sequence databases with at least one nucleotide or protein sequence. Data provided encompasses archaea, bacteria, eukaryota, viroids and viruses. The NCBI taxonomy database is not a primary source for taxonomic or phylogenetic information. Furthermore, the database does not follow a single taxonomic treatise but rather attempts to incorporate phylogenetic and taxonomic knowledge from a variety of sources, including the published literature, web-based databases, and the advice of sequence submitters and outside taxonomy experts. Consequently, the NCBI taxonomy database is not a phylogenetic or taxonomic authority and should not be cited as such.

NCBI Protein Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-03178
has db xref: r3d100011331
synonym: Entrez Protein
synonym: Entrez Protein Database
synonym: Protein Database
synonym: Protein sequence database
abbrev: NCBI GP
abbrev: NCBI Protein
abbrev: NCBI_GP
IAO_0000115: Databases of protein sequences and 3D structures of proteins. Collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.

Radiotracer Chemistry Instrumentation and Biological Imaging
type: Resource
type: NamedIndividual
has db xref: nif-0000-31420
synonym: Radiotracer Chemistry and Instrumentation for Biological Imaging
abbrev: RCIBI
IAO_0000115: Develop new scientific tools to image the movement of molecules in energy-relevant and environmentally-sensitive contexts in response to BER's call to explore the potential of radiotracer imaging in energy and environmentally-responsive contexts. Their goal is to visualize metabolic networks and regulatory systems underlying cellular communication in the living organism including plants and microbial communities. This has broad implications to DOE missions in energy and the environment and is very relevant to improvements in plant biomass for biofuel.

Beta Cell Genomics Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157324
abbrev: BCGO
abbrev: OBI BCGO
IAO_0000115: An application ontology built for the Beta Cell Genomics database aiming to support database annotation, complicated semantic queries, and automated cell type classification. The ontology is developed using Basic Formal Ontology (BFO) as upper ontology, Ontology for Biomedical Investigations (OBI) as ontology framework and integrated subsets of multiple OBO Foundry (candidate) ontologies. Current the BCGO contains 2383 classes including terms referencing to 24 various OBO Foundry ontologies including CL, CLO, UBERON, GO, PRO, UO, etc.

Gene Expression Profiling in Spinal Cord Injury
type: Resource
type: NamedIndividual
has db xref: nif-0000-00011
IAO_0000115: Database which provides on-line searching of microarray datasets generated from rat spinal cord after contusion injury. Both the primary injury site and a site 5 mm distal to the injury site were assayed. Tissue was obtained from Long Evans rats subject to spinal cord contusion injury using the MASCIS impactor (formerly known as the NYU impactor). RNA expression was assayed at the site of injury and distal to the site of injury using the Affymetrix Rat Neuro U34 chip.

Rat Gene Symbol Tracker
type: Resource
type: NamedIndividual
has db xref: nif-0000-31426
synonym: RGST (Rat Gene Symbol Tracker)
synonym: RGST - Rat Gene Symbol Tracker
abbrev: RGST
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented September 2, 2016. Database for defining official rat gene symbols. It includes rat gene symbols from three major sources: the Rat Genome Database (RGD), Ensembl, and NCBI-Gene. All rat symbols are compared with offici…

Biological Collections Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157333
abbrev: BCO
IAO_0000115: Ontology developed as an application ontology as part of the Biocode Commons project whose goal is to support the interoperability of biodiversity data, including data on museum collections, environmental and metagenomic samples, and ecological surveys. It includes consideration of the distinctions between individuals, organisms, voucher specimens, lots, and samples the relations between these entities, and processes governing the creation and use of samples. Within scope as well are properties including collector, location, time, storage environment, containers, institution, and collection identifiers.

BrainWeb - Simulated Brain Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-00020
synonym: BainWeb SBD
synonym: BrainWeb
synonym: BrainWeb Simulated Brain Database
IAO_0000115: Database of human brain images derived from a realistic phantom and generated using a sophisticated MRI simulator. Custom simulations may be generated to match a user's selected parameters. The goal is to aid validation of computer-aided quantitative analysis of medical image data. The SBD contains a set of realistic MRI data volumes produced by an MRI simulator. These data can be used by the neuroimaging community to evaluate the performance of various image analysis methods in a setting where the truth is known. The SBD contains simulated brain MRI data based on two anatomical models: normal and multiple sclerosis (MS). For both of these, full 3-dimensional data volumes have been simulated using three sequences (T1-, T2-, and proton-density- (PD-) weighted) and a variety of slice thicknesses, noise levels, and levels of intensity non-uniformity. These data are available for viewing in three orthogonal views (transversal, sagittal, and coronal), and for downloading.

Geospiza
type: Commercial Organization
type: NamedIndividual
has db xref: nif-0000-31431
has db xref: OMICS_01127
synonym: Geospiza Inc.
IAO_0000115: Developer of enterprise-class software systems for workflow management of genetic analysis. Geospiza has established itself as the life science industry's top software developer for meeting the combined laboratory, data management and analytical needs of biotechnology and pharmaceutical companies, universities, researchers, contract core and diagnostic laboratories involved in genetic testing and manufacturing bio-therapeutics. Geospiza's products are designed and built by biologists, enabling researchers to focus on the science, not the software. *GeneSifter Analysis Edition: Access easy-to-use statistical, visualization and annotation tools for Microarray and Next Generation Sequencing data. *GeneSifter Lab Edition: Manage cross-platform core lab operations from a single interface out-of-the-box.

Schramm Lab Spinal Cord Atlases
type: Resource
type: NamedIndividual
has db xref: nif-0000-00021
IAO_0000115: Serial histological sections of rat spinal cord at the lumbar and thoracic levels. Serial sections of rat spinal cord cut in the horizontal and sagittal planes. Also transverse and sagittal section series of the postnatal thoracic spinal cord immunolabeled for SMI-32.

SpliCQ
type: Resource
type: NamedIndividual
has db xref: OMICS_01341
IAO_0000115: A Java software package which allows for the identification of splicing events and differentially expressed isoforms in next generation sequencing data.

nematodes.org
type: Resource
type: NamedIndividual
has db xref: nif-0000-03187
synonym: Blaxter Lab
synonym: Nematode & Neglected Genomics
synonym: Nematode & Neglected Genomics (at) The Blaxter Lab
synonym: Nematode and Neglected Genomics
synonym: nematodes.org Nematode & Neglected Genomics (at) The Blaxter Lab
IAO_0000115: Nematode & Neglected Genomics (at) The Blaxter Lab is a nematode related portal including databases and services. Resources include genomic and transcriptomic databases for nematodes and other metazoan phyla and freely downloadable software tools for expressed sequence tag analysis, DNA barcode analysis and phylogenomics. Major categories include: * GenePool * 959 Nematode Genomes * Teaching * Research Projects * Bioinformatics Software Tools * Lab Personnel * Lab Wiki * Genomics Databases * NEMBASE4 * Tardigrada: Hypsibius dujardini * Earthworm: Lumbricus rubellus * MolluscDB * ArthropodDB * other Neglected Genomes

NESbase
type: Resource
type: NamedIndividual
has db xref: nif-0000-03188
IAO_0000115: Database of proteins in which the presence of Leucine-rich nuclear export signal (NES) has been experimentally verified. It is curated from literature. Each NESbase entry contains information of whether NES was shown to be necessary and/or sufficient for export, and whether the export was shown to be mediated by the export receptor CRM1. The compiled information was used to make a sequence logo of the Leucine-rich NESs, displaying the conservation of amino acids within a window of 25 residues. Error reports and submissions of new data are most welcome!

ORFprimer
type: Resource
type: NamedIndividual
has db xref: OMICS_02331
synonym: ORFprimer - primer design for ORFs
IAO_0000115: An extended software package for high throughput PCR primer design for biological sequences. It reads the NCBI GenBank XML sequence format and extracts open reading frames for proteins. Sequences can be requested by GI or accession number.

Jackson Laboratory Cytogenetic Models Resource
type: Resource
type: NamedIndividual
has db xref: nif-0000-01258
synonym: Cytogenetic Models Resource
synonym: Jackson Lab: Cytogenetic Models Resource
IAO_0000115: Maintains and distributes chromosome aberration stocks that provide primarily mouse models for Down syndrome. The Resource currently provides models for Down syndrome research, including: Rb(6.16)24Lub x Rb(16.17)7Bnr F1 hybrids that are used to produce Chr 16 trisomy (Ts16) embryos, which have many of the fetal developmental features of DS, and; Ts(1716)65Dn, segmental trisomy mice that survive to adulthood and have many of the features of DS. The Resource also includes stocks with selected reciprocal translocations involving Chr 16 and some Chr 16 transgenic stocks. In addition, a large number of Robertsonian chromosome stocks are held as frozen embryos in the Cryopreservation Resource. Each mouse chromosome is present in at least two different Robertsonian chromosomes in these strains so that specific trisomies for each of the 19 mouse autosomes can be produced. Breeding pairs and individual mice are provided.

Research Network in Early Experience and Brain Development
type: Resource
type: NamedIndividual
has db xref: nif-0000-31447
synonym: Research Network in Early Experience Brain Development
abbrev: Research Network on Early Experience and Brain Development
IAO_0000115: Portal on how the experiences of early childhood are incorporated into the structures of the developing brain, and how, in turn, those changes in the structures of the brain influence behavior. The network explores how knowledge of brain development can guide us in understanding of behavioral development and vice versa. It focuses specifically on sensitive periods and neural plasticity, the reciprocal phenomena whereby (a) the brain is negatively affected if certain experiences fail to occur within a certain time period, and (b) the brain is altered by experience at virtually any point in the life span. Here we consider not only how the structure of experience is incorporated into the structure of the brain, but also how this knowledge can influence the decisions we make about intervening in the lives of children. Research and other projects conducted by the Network fall into four broad categories: * Effects of early experience on brain development * New methods for studying brain-behavior relations * Comparative studies of early brain-behavioral development * Impact on public policy: Educating educators and the media RESOURCES NimStim Face Stimulus Set The Research Network on Early Experience and Brain Development has developed a battery of 646 facial expression stimuli for use in its own and other studies of face and emotion recognition. Images include the following expressions, displayed by a variety of models of various genders and races: fearful, happy, sad, angry, surprised, calm, neutral, disgusted. They are making these stimuli available to the public free of charge with registration and acceptance of the terms and conditions to use the stimulus set.

Emotion Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157396
abbrev: MFOEM
IAO_0000115: An ontology of affective phenomena such as emotions, moods, appraisals and subjective feelings, designed to support interdisciplinary research by providing unified annotations. The ontology is a domain specialization of the broader Mental Functioning Ontology.

NLSdb: a database of nuclear localization signals
type: Resource
type: NamedIndividual
has db xref: nif-0000-03191
synonym: NLSdb - a database of nuclear localization signals
abbrev: NLSdb
IAO_0000115: A database of nuclear localization signals (NLSs) and of nuclear proteins targeted to the nucleus by NLS motifs. NLSs are short stretches of residues mediating transport of nuclear proteins into the nucleus. The database contains 114 experimentally determined NLSs that were obtained through an extensive literature search. Using "in silico mutagenesis" this set was extended to 308 experimental and potential NLSs. This final set matched over 43% of all known nuclear proteins and matches no currently known non-nuclear protein. NLSdb contains over 6000 predicted nuclear proteins and their targeting signals from the PDB and SWISS-PROT/TrEMBL databases. The database also contains over 12 500 predicted nuclear proteins from six entirely sequenced eukaryotic proteomes (Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana and Saccharomyces cerevisiae). NLS motifs often co-localize with DNA-binding regions. This observation was used to also annotate over 1500 DNA-binding proteins. From this site you can: * Query NLSdb * Find out how to use NLSdb * Browse the entries in NLSdb * Find out if your protein has an NLS using PredictNLS * Predict subcellular localization of your protein using LOCtree

Madagascar
type: Resource
type: NamedIndividual
has db xref: nif-0000-01270
IAO_0000115: Software package for multidimensional data analysis and reproducible computational experiments. It aims to provide a powerful environment and a convenient technology transfer tool for researchers working with digital image and data processing in geophysics and related fields., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

JCVI Primer Designer
type: Resource
type: NamedIndividual
has db xref: OMICS_02330
IAO_0000115: High throughput PCR primer design software. Target regions defined through a rich set of descriptors, such as Ensembl accessions and arbitrary genomic coordinates, may be specified. Primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the specified target regions. As part of the tiling process, primer pairs are computationally screened to meet the criteria for success with one of two PCR amplification protocols.

CCHMC Pediatric Brain Templates
type: Resource
type: NamedIndividual
has db xref: nif-0000-01274
abbrev: Pediatric Brain Templates
IAO_0000115: Brain imaging data collected from a large population of normal, healthy children that have been used to construct pediatric brain templates, which can be used within statistical parametric mapping for spatial normalization, tissue segmentation and visualization of imaging study results. The data has been processed and compiled in various ways to accommodate a wide range of possible research approaches. The templates are made available free of charge to all interested parties for research purposes only. When processing imaging data from children, it is important to take into account the fact that the pediatric brain differs significantly from the adult brain. Therefore, optimized processing requires appropriate reference data be used because adult reference data will introduce a systematic bias into the results. We have shown that, in the in the case of spatial normalization, the amount of non-linear deformation is dramatically less when a pediatric template is used (left, see also HBM 2002; 17:48-60). We could also show that tissue composition is substantially different between adults and children, and more so the younger the children are (right, see also MRM 2003; 50:749-757). We thus believe that the use of pediatric reference data might be more appropriate.

Assembly Based ReAligner
type: Resource
type: NamedIndividual
has db xref: biotools:abra
has db xref: OMICS_04668
synonym: ABRA - Assembly Based ReAligner
abbrev: ABRA
IAO_0000115: Software that is a realigner for next generation sequencing data. It uses localized assembly and global realignment to align reads more accurately, thus improving downstream analysis (detection of indels and complex variants in particular).

Rockland Immunochemicals
type: Organization
type: NamedIndividual
has db xref: nif-0000-31467
has db xref: nlx_152452
synonym: Rockland antibodies & assays
synonym: Rockland antibodies and assays
synonym: Rockland Immunochemicals Inc.
abbrev: Rockland
IAO_0000115: A global biotechnology company manufacturing research tools, antibodies, and cGMP grade protein.

deFuse
type: Resource
type: NamedIndividual
has db xref: biotools:defuse
has db xref: OMICS_01345
IAO_0000115: Software package for gene fusion discovery using RNA-Seq data. It uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries.

Xenbase
type: Resource
type: NamedIndividual
has db xref: biotools:xenbase
has db xref: nif-0000-01286
has db xref: OMICS_01665
has db xref: r3d100010279
synonym: Xenbase: Xenopus laevis and tropicalis biology and genomics resource
abbrev: XenBase
IAO_0000115: Data collection for Xenopus laevis and Xenopus tropicalis biology and genomics.

Psychoactive Drug Screening Program Ki Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-01866
synonym: Ki Database
synonym: PDSP Ki Database
abbrev: Ki DB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. Database of information on the abilities of drugs to interact with an expanding number of molecular targets. It serves as a data warehouse for published and internally-derived Ki, or affinity, values for a large number of drugs and drug candidates at an expanding number of G-protein coupled receptors, ion channels, transporters and enzymes. The query interface is designed to let you search by any field, or combination of them to refine your search criteria. The flexible user interface also provides for customized data mining. The database is regularly updated. If you know of Ki data you would like to add, you can select Direct Ki Entry at the grey panel. If you would like, however, your own data (published or not) added, Send them a Reference at the grey panel, or send an email to Dr. Bryan Roth or Estela Lopez. Most common targets: 5-HT2A, DOPAMINE D1, DOPAMINE D2, 5-HT2C, 5-HT1A, Cholinergic, muscarinic M1, 5-HT Transporter, HISTAMINE H1, 5-HT2B, OPIOID Mu, 5-HT6, adrenergic Beta2, 5-HT7, OPIATE Delta, adrenergic Alpha1A, OPIOID Kappa, 5-HT3, m-AChR, adrenergic Beta1, adrenergic Alpha2A, 5-HT1, Acetylcholinesterase, AChE, Thromboxane A2, n-AChR, Opiate non-selective, CANNABINOID CB1, HERG, Dopamine, cocaine site, adrenergic Alpha2C, M3, Norepinephrine Uptake, Monoamine Oxidase A, Monoamine Oxidase B, 5-HT4, adrenergic Alpha1, 5-HT1E, B1 BRADYKININ, 5-HT2, 5-HT2C-INI, DOPAMINE D4, ANGIOTENSIN AT1, Neurokinin NK1, HISTAMINE H3, Sigma-1, VIP, Dopamine2-like, metabotropic glutamate 5, 5-HT2c VGI, Carbonic Anhydrase Isozymes, CA I, DOPAMINE D2 Long, adrenergic Alpha2, adrenergic Alpha2B, adrenergic Alpha2D, GABA A alpha1, CANNABINOID CB2, adrenergic Alpha1B, 5-HT5a, Melatonin, HISTAMINE H4, NMDA, 5-HT4a, Glucocorticoid, Interleukin 1-beta, Sodium Channel, Benzodiazepine central, Cholinergic, muscarinic M5, Neuropeptide Y1, GABA A alpha5, Galanin R2, Neurokinin NK3, 5-HT1B, M2, DOPAMINE D3, Angiotensi…

Pleiades Promoter Project: Genomic Resources Advancing Therapies for Brain Disorders
type: Resource
type: NamedIndividual
has db xref: nif-0000-01868
abbrev: Pleiades Promoter Project
IAO_0000115: Project to generate human DNA promoters of less than 4 kb (MiniPromoters) to drive gene expression in defined brain regions of therapeutic interest for diseases such as Alzheimer, Parkinson, Huntington, Amyotrophic Lateral Sclerosis, Multiple Sclerosis, Spinocerebellar Ataxia, Depression, Autism, and Cancer. Project develops and shares tools like human MiniPromoters that drive region- and cell-specific gene expression in the mouse brain, expression constructs, mouse embryonic stem cell lines, and knock-in mice all of which carry brain-specific MiniPromoters. Project is daughter of Genome Canada Project, Atlas of Gene Expression in Mouse Development, within which mouse brain gene expression data have already been gathered. Project team has collaborated with International BioPharma Solutions Ltd., management and communications consulting company specializing in product development and commercialization advice. Project will explore challenging interface between science and journalism with focus on genomics and gene therapy.

Yale Rudd Center for Food Policy and Obesity
type: Resource
type: NamedIndividual
has db xref: nif-0000-31473
synonym: Rudd Center for Food Policy & Obesity
abbrev: Rudd Center
IAO_0000115: A non-profit research and public policy organization devoted to improving the worlds diet, preventing obesity, and reducing weight stigma.

PoPoolation2
type: Resource
type: NamedIndividual
has db xref: OMICS_05824
IAO_0000115: Software to compare allele frequencies for SNPs between two or more populations and to identify significant differences. PoPoolation2 requires next generation sequencing data of pooled genomic DNA (Pool-Seq). It may be used for measuring differentiation between populations, for genome wide association studies and for experimental evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Nuclear Receptor Resource
type: Resource
type: NamedIndividual
has db xref: nif-0000-03205
synonym: NRR Project
synonym: Nuclear Receptor Resource (NRR) Project
synonym: Nuclear Receptor Resource Project
abbrev: NRR
IAO_0000115: Collection of individual databases on members of the steroid and thyroid hormone receptor superfamily. Although the databases are located on different servers and are managed individually, they each form a node of the NRR. The NRR itself integrates the separate databases and allows an interactive forum for the dissemination of information about the superfamily. NRR Components: Androgen receptor, Estrogen receptor, Glucocorticoid receptor, Peroxisome proliferator, Steroid receptor protein, Thyroid receptor, Vitamin D receptor.

Chemical Methods Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157363
synonym: RSC Chemical Methods Ontology
abbrev: CHMO
abbrev: RSC CMO
IAO_0000115: An ontology that describes methods used to collect data in chemical experiments, such as mass spectrometry and electron microscopy; preparing and separating material for further analysis, such as sample ionization, chromatography, and electrophoresis; and synthesizing materials, such as epitaxy and continuous vapor deposition. It also describes the instruments used in these experiments, such as mass spectrometers and chromatography columns. It is intended to be complementary to the Ontology for Biomedical Investigations (OBI).

Nuclear Receptor Signaling Atlas
type: Resource
type: NamedIndividual
has db xref: nif-0000-03208
synonym: NURSA - Nuclear Receptor Signaling Atlas
synonym: NURSA - The Nuclear Receptor Signaling Atlas
abbrev: NURSA
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE.Documented on February 25, 2022.Software tool as knowledge environment resource that accrues, develops, and communicates information that advances understanding of structure, function, and role in disease of nuclear receptors (NRs) and coregulators. It specifically seeks to elucidate roles played by NRs and coregulators in metabolism and development of metabolic disorders. Includes large validated data sets, access to reagents, new findings, library of annotated prior publications in field, and journal covering reviews and techniques.As of March 20, 2020, NURSA is succeeded by the Signaling Pathways Project (SPP).

O-GLYCBASE
type: Resource
type: NamedIndividual
has db xref: nif-0000-03209
abbrev: O-GlycBase
IAO_0000115: Revised database of O- and C-glycosylated proteins. The criteria for inclusion are at least one experimentally verified O- or C-glycosylation site. Each entry contains information about the glycan involved, the species, sequence, a literature reference and http-linked cross-references to other databases. Version 6.00 has 242 glycoprotein entries. The terminal sugar linked to serine or threonine is cited when known. The database is non-redundant in the sense that it contains no identical sequences, unless there is conflicting glycosylation data. Mucins have tandem repeat sequences, which are O-glycosylated. This result in some redundancy of the O-glycosylation sites. For prediction purposes they have also included a version of the database which contains no identical O-glycosylation sites (window=9) called O-Unique.seq. Data can no longer be retrieved by anonymous ftp. Only http is supported. New data, comments and suggestions are welcome.

Michigan State University Brain Biodiversity Bank
type: Resource
type: NamedIndividual
has db xref: nif-0000-00059
has db xref: r3d100012667
synonym: Brain Biodiversity Bank
IAO_0000115: The Brain Biodiversity Bank refers to the repository of images of and information about brain specimens contained in the collections associated with the National Museum of Health and Medicine at the Armed Forces Institute of Pathology in Washington, DC. Atlases and brain sections are available for a variety of mammals, and we are also developing a series of labeled atlases of stained sections for educators, students, and researchers. These collections include, besides the Michigan State University Collection, the Welker Collection from the University of Wisconsin, the Yakovlev-Haleem Collection from Harvard University, the Meyer Collection from the Johns Hopkins University, and the Huber-Crosby and Crosby-Lauer Collections from the University of Michigan. What we are doing currently at Michigan State is a series of demonstration projects for publicizing the contents of the collections and ways in which they can be used. For example, the images from the collection can be used for comparative brain study. We have prepared databases of the contents of the collections for presentation and use on this site, as well as for downloading by users in several formats. We are also developing a series of labeled atlases of stained sections for educators, students, and researchers. This internet site is associated with the Comparative Mammalian Brain Collections site. All of the images are in JPEG or GIF format.

Chemical Information Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157362
abbrev: CHEMINF
IAO_0000115: An ontology that aims to establish a standard in representing chemical information including chemical structure and the ability to richly describe chemical properties, whether intrinsic or computed. It includes terms for the descriptors commonly used in cheminformatics software applications and the algorithms which generate them.

Clinical Measurement Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157364
abbrev: CMO
IAO_0000115: An ontology designed to be used to standardize morphological and physiological measurement records generated from clinical and model organism research and health programs.

OmicCircos
type: Resource
type: NamedIndividual
has db xref: OMICS_04659
synonym: OmicCircos: High-quality circular visualization of omic data
IAO_0000115: An R software application and package used to generate high-quality circular plots for visualizing genomic variations, including mutation patterns, copy number variations (CNVs), expression patterns, and methylation patterns.

SEER Datasets and Software
type: Resource
type: NamedIndividual
has db xref: nif-0000-31490
synonym: SEER Datasets & Software
synonym: SEER Datasets Software
synonym: The Surveillance Epidemiology and End Results (SEER) Program
synonym: The Surveillance Epidemiology and End Results (SEER) Program of the National Cancer Institute
IAO_0000115: Portal provides SEER research data and software SEER*Stat and SEER*Prep. SEER incidence and population data associated by age, sex, race, year of diagnosis, and geographic areas can be used to examine stage at diagnosis by race/ethnicity, calculate survival by stage at diagnosis, age at diagnosis, and tumor grade or size, determine trends and incidence rates for various cancer sites over time. SEER releases new research data every Spring based on the previous November’s submission of data.

Amplicon
type: Resource
type: NamedIndividual
has db xref: OMICS_02329
IAO_0000115: Software tool for designing PCR primers on aligned groups of DNA sequences. The most important application is the design of "group-specific" PCR primer sets that amplify a DNA region from a given taxonomic group but do not amplify orthologous regions from other taxonomic groups. It is written in Python 2.3 and Tkinter 8.4. The current script was created for Windows and an executable is available. Future versions of the script should be able to run on Linux and Mac

PrimerSeq
type: Resource
type: NamedIndividual
has db xref: biotools:primerseq
has db xref: OMICS_02328
synonym: Primer Seek in RNA-Seq
IAO_0000115: Software that designs RT-PCR primers that evaluate alternative splicing events by incorporating RNA-Seq data. It is particularly advantageous for designing a large number of primers for validating alternative splicing events found in RNA-Seq data. It incorporates RNA-Seq data in the design process to weight exons by their read counts. Essentially, the RNA-Seq data allows primers to be placed using actually expressed transcripts. This could be for a particular cell line or experimental condition, rather than using annotations that incorporate transcripts that are not expressed for the data. Alternatively, you can design primers that are always on constitutive exons. PrimerSeq does not limit the use of gene annotations and can be used for a wide array of species.

Common Anatomy Reference Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157369
abbrev: CARO
IAO_0000115: An ontology developed to facilitate interoperability between existing anatomy ontologies for different species, and to provide a template for building new anatomy ontologies.

IMOD
type: Resource
type: NamedIndividual
has db xref: nif-0000-31686
synonym: IMOD - 3D Reconstruction and Analysis
IAO_0000115: A free, cross-platform set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD 4.1.8 Is Now Available for Linux, Windows, and Mac OS X

Genedata Expressionist
type: Resource
type: NamedIndividual
has db xref: OMICS_00761
synonym: Genedata Expressionist for Genomic Profiling
IAO_0000115: Software that provides data processing, analysis, management, and reporting of metabolomics, proteomics and biotherapeutics characterization studies based on mass spectrometry. It can process raw data from various MS instruments, serve MS processing, analysis and reporting needs, and ensure reproducibility and traceability of results.

Protege
type: Resource
type: NamedIndividual
has db xref: nif-0000-31708
synonym: Protege Project
synonym: Protégé
IAO_0000115: Protege is a free, open-source platform that provides a growing user community with a suite of tools to construct domain models and knowledge-based applications with ontologies. At its core, Protege implements a rich set of knowledge-modeling structures and actions that support the creation, visualization, and manipulation of ontologies in various representation formats. Protege can be customized to provide domain-friendly support for creating knowledge models and entering data. Further, Protege can be extended by way of a plug-in architecture and a Java-based Application Programming Interface (API) for building knowledge-based tools and applications. An ontology describes the concepts and relationships that are important in a particular domain, providing a vocabulary for that domain as well as a computerized specification of the meaning of terms used in the vocabulary. Ontologies range from taxonomies and classifications, database schemas, to fully axiomatized theories. In recent years, ontologies have been adopted in many business and scientific communities as a way to share, reuse and process domain knowledge. Ontologies are now central to many applications such as scientific knowledge portals, information management and integration systems, electronic commerce, and semantic web services. The Protege platform supports two main ways of modeling ontologies: * The Protege-Frames editor enables users to build and populate ontologies that are frame-based, in accordance with the Open Knowledge Base Connectivity protocol (OKBC). In this model, an ontology consists of a set of classes organized in a subsumption hierarchy to represent a domain's salient concepts, a set of slots associated to classes to describe their properties and relationships, and a set of instances of those classes - individual exemplars of the concepts that hold specific values for their properties. * The Protege-OWL editor enables users to build ontologies for the Semantic Web, in particular in the …

Audiology - Arizona School of Health Sciences
type: Resource
type: NamedIndividual
has db xref: nif-0000-01880
synonym: Audiology - ASHS
synonym: Audiology; Arizona School of Health Sciences Audiology
abbrev: Au. D.
abbrev: Au.D. at ASHS
IAO_0000115: Entry level program that teaches skills such as diagnostic, rehabilitative, habilitative, and related areas of the profession and practice of audiology. The program incorporates basic science education with clinical education through a combination of on-campus classes, clinical rotations, and computer-based education.

Cotton EST Database
type: Resource
type: NamedIndividual
has db xref: r3d100011232
IAO_0000115: Database platform for cotton expressed sequence tag (EST)-related information, covering assembled contigs, function annotation, analysis of GO and KEGG, SNP, miRNA, SSR-related marker information.

Weighted Gene Co-expression Network Analysis
type: Resource
type: NamedIndividual
has db xref: biotools:crosslinkwgcna
has db xref: nif-0000-31889
synonym: WGCNA: an R package for weighted correlation network analysis
abbrev: WGCNA
IAO_0000115: Software R package for weighted correlation network analysis. WGCNA is also available as point-and-click application. Unfortunately this application is not maintained anymore. It is known to have compatibility problems with R-2.8.x and newer, and the methods it implements are not all state of the art., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Albert Einstein College of Medicine of Yeshiva University Department of Neuroscience
type: Organization
type: NamedIndividual
has db xref: nif-0000-01885
synonym: AECOM of YU; Dept. of Neuroscience
synonym: AECOM; Dept. of Neuroscience
synonym: Albert Einstein College of Medicine of Yeshiva University; Department of Neuroscience
synonym: Albert Einstein College of Medicine; Department of Neuroscience
synonym: Yeshiva University; Albert Einstein College of Medicine; Department of Neuroscience
IAO_0000115: University department that oversees neuroscience research and graduate education.

National Center for Biomedical Ontology
type: Resource
type: NamedIndividual
has db xref: nif-0000-31891
abbrev: NCBO
IAO_0000115: Organization that provides biomedical researchers with online tools and a web portal enabling them to access, review, and integrate disparate ontological resources in all aspects of biomedical investigation and clinical practice. A major focus of the work involves the use of biomedical ontologies to aid in the management and analysis of data derived from complex experiments.

Allegheny College Neuroscience
type: Organization
type: NamedIndividual
has db xref: nif-0000-01887
synonym: Allegheny College Neuroscience Program
synonym: Allegheny Neuro
IAO_0000115: Allegheny's neuroscience major formalizes an alliance dating back 25 years between the College's well-known biology and psychology departments. The major brings faculty and students together to study the brain and the nervous system using principles from the natural and social sciences. It requires a common core of biology, chemistry, and psychology courses. Students may choose from two tracks: "cellular neurobiology" or "behavioral and cognitive neuroscience", and they have the opportunity to explore interdisciplinary topics through the Junior Seminar and the year-long Senior Research Project.

Experimental Conditions Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157401
synonym: Experimental condition ontology
abbrev: XCO
IAO_0000115: An ontology designed to represent the conditions under which physiological and morphological measurements are made both in the clinic and in studies involving humans or model organisms.

Wellcome Trust Centre for Human Genetics
type: Resource
type: NamedIndividual
has db xref: nif-0000-31897
abbrev: WTCHG
IAO_0000115: An international leader in genetics, genomics and structural biology, and research institute of the Nuffield Department of Medicine at the University of Oxford, whose objective is to extend our understanding on how genetic inheritance makes us who we are in order to gain a clearer insight into mechanisms of health and disease. Looking across all three billion letters of the human genetic code, they aim to pinpoint variant spellings and discover how they increase or decrease an individual's risk of falling ill. They collaborate with research teams across the world on a number of large-scale studies in these areas.

biobambam
type: Resource
type: NamedIndividual
has db xref: biotools:biobambam
has db xref: OMICS_04664
IAO_0000115: Software tools for read pair collation based algorithms on BAM files including * bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name * bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field * bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column * bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading. * bamsort: reads BAM and writes BAM resorted by coordinates or query name * bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name

Dictyostelium Discoideum Anatomy Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157387
synonym: Dictyostelium discoideum anatomy
abbrev: DDANAT
IAO_0000115: A structured controlled vocabulary of the anatomy of the slime-mould Dictyostelium discoideum.

RCircos
type: Resource
type: NamedIndividual
has db xref: OMICS_04661
synonym: RCircos: Circos 2D Track Plot
IAO_0000115: Software package that provides a simple and flexible way to generate Circos 2D track plot images for genomic data visualization. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics package that comes with R base installation.

Retinal Degeneration Rat Model Resource
type: Resource
type: NamedIndividual
has db xref: nif-0000-00188
synonym: NEI Retinal Degeneration Rat Model Resource
IAO_0000115: Supplier of fully penetrant rat models of the retinitis pigmentosa type of inherited retinal degeneration, including the following models: * Mutant rhodopsin transgenic rats ** P23H mutant rhodopsin transgenic rats -Three lines with different rates of photoreceptor degeneration ** S334ter mutant rhodopsin transgenic rats -Five lines with different rates of photoreceptor degeneration * RCS (Royal College of Surgeons) rats with inherited retinal dystrophy ** RCS pink-eyed inbred strain ** RCS pigmented congenic strain with slowed rate of retinal dystrophy ** RCS congenic control strains of both pigmentation types, wild-type at the retinal dystrophy (Mertk) genetic locus The resource has been supported by the National Eye Institute (NEI) for the past 19 years to produce and distribute breeding pairs of these animal models to vision scientists. Thus, the following apply: * Request for rats requires only a 1-page letter/e-mail addressing 4 questions * No charge for the animals or tissues (except for shipping costs) * No Material Transfer Agreement (MTA) required * No collaboration requirement (in most cases) The resource usually provides multiple breeding pairs of the rats to vision scientists to generate breeding stock. It can also provide extra animals to breed for immediate experimental work, animals of specific ages (depending upon availability), animals with prior exposure to different lighting conditions, eyes taken at specific ages instead of rats for pilot studies and other experiments (fresh, frozen, dissected in specific ways, or fixed with special fixatives or by different methods), or other tissues (e.g., liver, spleen, brain, testis, etc.) prepared different ways.

Datasharing.net
type: Resource
type: NamedIndividual
has db xref: nif-0000-00061
synonym: DataSharing
IAO_0000115: The U.S. National Institutes of Health Final NIH Statement on Sharing Research Data (NIH-OD-03-032) is now in effect. It specifies that all high-direct-cost NIH grant applications include plans for sharing of research data. To support and encourage collegial, enabling, and rewarding data sharing for neuroscience and beyond, the Laboratory of Neuroinformatics at Weill Medical College of Cornell University has established this site. A source of, and portal to, tools and proposals supporting the informed exchange of neuroscience data.

ggbio
type: Resource
type: NamedIndividual
has db xref: biotools:ggbio
has db xref: OMICS_04660
synonym: ggbio - Visualization tools for genomic data
IAO_0000115: An R package for extending the grammar of graphics for genomic data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.

MedScan
type: Resource
type: NamedIndividual
has db xref: nif-0000-21259
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. MedScan is a fast and flexible biomedical information extraction technology. It uses dictionaries to identify individual biomedical terms (proteins, cellular processes, small molecules, diseases, etc) referred to in literature articles, and applies advanced natural language processing techniques to detect the relationships within the article and extract these terms and the relationships; the overall process of detection, identification, extraction and assembling, is termed Information Harvesting. Information extracted by MedScan represents the multiple aspects of protein function, including protein modification, cellular localization, protein-protein interactions, gene expression regulation, molecular transport and synthesis, as well as association with diseases, and regulation of various cellular processes. This scope can be broadened by modifying information extraction rules and the dictionaries. Dictionaries can be assembled on any topic or area that is represented in the literature you wish to harvest. High-throughput data generation methodologies like microarray gene expression require new approaches for gathering information for data analysis. For the best results, computational approaches used for high-throughput data analysis require that biological information from the literature be a coherent and integrated part of the analysis software itself. Pathway Studio meets this challenge through its MedScan Technology and underlying ResNet database. All editions of Pathway Studio contain MedScan Technology to harvest information from the literature and to save this information in the Pathway Studio ResNet database ready for data analysis. MedScan is more than a web search engine. Indeed, the output of a Google search can be channeled into MedScan for example. Web searches, like Google, are excellent at finding items as a result of a query. A quick look at the output list usually locates the item…

Fission Yeast Phenotype Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157405
abbrev: FYPO
IAO_0000115: A formal ontology of phenotypes observed in fission yeast that is being developed to support the comprehensive and detailed representation of phenotypes in PomBase, the online fission yeast resource. Its scope is similar to that of the Ascomycete Phenotype Ontology (APO), but FYPO includes more detailed pre-composed terms as well as computable definitions.

Harvard Brain Tissue Resource Center
type: Resource
type: NamedIndividual
has db xref: nif-0000-00192
synonym: Harvard Brain Bank
synonym: The Brain Bank
abbrev: HBTRC
IAO_0000115: Biomaterial supply resource that acquires, processes, stores, and distributes postmortem brain specimens for brain research. Various types of brain tissue are collected, including those with neurological and psychiatric disorders, along with their parents, siblings and offspring. The HBTRC maintains an extensive collection of postmortem human brains from individuals with Huntington's chorea, Alzheimer's disease, Parkinson's disease, and other neurological disorders. In addition, the HBTRC also has a collection of normal-control specimens.

Fly Taxonomy
type: Resource
type: NamedIndividual
has db xref: nlx_157407
synonym: FlyBase Taxa
abbrev: FB-SP
abbrev: FBsp
IAO_0000115: The taxonomy of the family Drosophilidae (largely after Baechli) and of other taxa referred to in FlyBase.

FlyBase Controlled Vocabulary
type: Resource
type: NamedIndividual
has db xref: nlx_157408
abbrev: FB-CV
abbrev: FBcv
IAO_0000115: A structured controlled vocabulary used for various aspects of annotation by FlyBase. This ontology is maintained by FlyBase for various aspects of annotation not covered, or not yet covered, by other OBO ontologies. If and when community ontologies are available for the domains here covered FlyBase will use them.

DAFGA
type: Resource
type: NamedIndividual
has db xref: OMICS_04654
synonym: DAFGA: Diversity Analysis of Functional Gene Amplicons
synonym: Diversity analysis of Functional Gene Amplicons
IAO_0000115: A python script package which estimates the evolutionary rate of a particular functional gene in a standardized manner by relating its sequence divergence to that of the 16S rRNA gene. It provides gene-specific parameter sets for OTU clustering and taxonomic assignment at desired rank, and it can be implemented into the diversity measurements offered by QIIME or Mothur.

Columbia University College of Physicians and Surgeons Department of Pharmacology
type: Organization
type: NamedIndividual
has db xref: nif-0000-01915
synonym: CU College of Physicians and Surgeons Dept. of Pharmacology
IAO_0000115: The spirit of the Department of Pharmacology is one of collaborative and synergistic science. As such, interests of the members of the Department span such diverse problems as the identification of molecular signals that determine whether a cell lives or dies to the discovery of new drugs that control cardiac rhythm in inherited and non-inherited heart disease. We at Columbia in general, and within the Department of Pharmacology in particular, are proud to be an integral part of the intellectual and cultural life of New York. In many ways the diversity of scientific interests within the Department reflect the diversity of the rich scientific environment of Columbia University and, in addition, the unique cultural and urban environment of New York City. Within the Graduate Programs in Mechanisms of Health and Disease, the Department of Pharmacology offers a Pharmacology and Molecular Signaling Program leading to the Ph.D. degree. Training is focused on both classical principles of pharmacology and more modern biophysical, genetic and computational approaches to the development of new and more specific therapeutic agents to manage human disease. The interdisciplinary training program in the molecular and genetic basis of cardiac arrhythmias is designed to provide training to post doctoral fellows with either M.D. or Ph.D. degrees to enable them to become independent researchers and leaders in the field as we enter a period of post genomic medical science. The overall aim of the program is to train researchers who will be well-grounded in molecular and cellular biology, but who also are trained in cardiovascular systems physiology/pharmacology in order to integrate the cellular and subcellular mechanisms (genotype) with the basis of human disease expressed at the systems level (phenotype).

PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees
type: Resource
type: NamedIndividual
has db xref: nif-0000-03241
has db xref: r3d100010570
synonym: Protein and Associated Nucleotide Domains with Inferred Trees
abbrev: PANDIT
IAO_0000115: PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains. It contains: * the seed protein sequence alignments from the Pfam-A (curated families) database (version 17.0) * nucleotide sequence alignments derived from sequences available for the above and using the protein alignments as "templates"; * protein sequence alignments restricted to the family members for which nucleotide sequences are available * inferred phylogenetic trees for each alignment The data in PANDIT and the dataset's development have been frozen owing to a lack of funding support. The existing data, version 17.0 corresponding to Pfam 17.0, remain stable and, we hope, useful. The entire database is also available for download as a flatfile from this website.

Childhood Autism Spectrum Test
type: Resource
type: NamedIndividual
has db xref: nlx_157819
synonym: Childhood Asperger''s Syndrome Test
synonym: Childhood Autism Spectrum Test (CAST)
abbrev: CAST
IAO_0000115: Assessment test developed by the Autism Research Centre at the University of Cambridge, for assessing the severity of autism spectrum symptoms in children. This assessment is usually used with children aged from 4-11 years of age.

Cornell University Neuroscience
type: Organization
type: NamedIndividual
has db xref: nif-0000-01918
synonym: Neuroscience at Weill Cornell
synonym: Weill Medical College Neuroscience
IAO_0000115: The Weill Medical College of Cornell University has a long tradition of neuroscience research. The faculty is large, and the research programs tackle the fundamental questions in the field at all levels - from genes to cells to systems to behavior. The neuroscience community at Weill Cornell spans two campuses. The main one, containing the medical school and associated hospitals, is located on the upper east side of Manhattan, adjacent to Rockefeller University and across the street from the Memorial Sloan-Kettering Cancer Center. The second campus, with the rapidly growing Burke-Cornell Research Institute, is located in White Plains. The following graduate programs are offered: Neuroscience PhD, Tri-Institutional MD-PhD, Physiology and Biophysics, and Tri-Institutional Graduate program in Computational Biology and Medicine.

MIPgen
type: Resource
type: NamedIndividual
has db xref: biotools:mipgen
has db xref: OMICS_04657
synonym: MIPgen - One stop MIP design and analysis
IAO_0000115: Software for a fast, simple way to generate designs for MIP assays targeting hundreds or thousands of genomic loci in parallel. Packaged with MIPgen are scripts that aid in visualization of MIP designs and processing of MIP sequence reads to SAM files that can then be passed through any standard variant calling pipeline.

PAWE-3D
type: Resource
type: NamedIndividual
has db xref: nlx_154481
synonym: Power for Association With Error in 3D
IAO_0000115: Software application (entry from Genetic Analysis Software)

Brede Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-00064
abbrev: Brede
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 4th, 2023. A database of human data from functional neuroimaging scientific articles containing Talairach coordinates that provides data for novel information retrieval techniques and automated meta-analyses. Each article in this database is identified by a unique number: A WOBIB. Some of the structure of the Brede database is similar to the structure of the BrainMap database (Research Imaging Center, San Antonio). The database is inspired by the hierarchical structure of BrainMap with scientific articles (bib structures) on the highest level containing one or more experiments (exp structure, corresponding to a contrast in general linear model analyses), these in turn comprising one or more locations (loc structures). The information on the bib level (author, title, ...) is setup automatically from PubMed while the rest of the information is entered manually in a Matlab graphical user interface. On the loc level this includes the 3D stereotactic coordinates in either Talairach or MNI space, the brain area (functional, anatomical or cytoarchitectonic area) and magnitude values such as Z-score and P-value. On the exp level information such as modality, scanner and behavioral domain are recorded with external components (such as face recognition or kinetic boundaries) organized in a directed graph and marked up with Medical Subject Headings (MeSH) where possible. The database is distributed as part of the Brede neuroinformatics toolbox (hendrix.imm.dtu.dk/software/brede/) which also provides the functions to manipulate and analyze the data. The Brede Toolbox is a program package primarily written in Matlab. As of 2006/11, 186 papers with 586 experiments.

Cancer Biomedical Informatics Grid
type: Resource
type: NamedIndividual
has db xref: nif-0000-31949
synonym: caBIG
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented July 19, 2016. It has been integrated into the National Cancer Informatics Program (NCIP). The National Cancer Institute launched the cancer Biomedical Informatics Grid (caBIG) to create a virtual network of interconnected data, individuals, and organizations that worked together to redefine how cancer research is conducted. caBIG capabilities allowed researchers and clinicians to collaborate more effectively so that complex research questions might be asked and answered faster and more effectively. The mission of caBIG was to develop a truly collaborative information network that accelerated the discovery of new approaches for the detection, diagnosis, treatment, and prevention of cancer, ultimately improving patient outcomes.

Glioma Molecular Dignostic Initiatives
type: Resource
type: NamedIndividual
has db xref: nif-0000-31950
synonym: Glioma Molecular Diagnostic Initiative: Characterizing Brain Tumor Data
abbrev: GMDI
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. An initiative to develop a molecular classification schema that is both clinically and biologically meaningful, based on gene expression and genomic data from tumors (Gliomas) of patients who will be prospectively followed through natural history and treatment phase of their illness. The study will also explore gene expression profiles to determine the responsiveness of the patients and correlate with discrete chromosomal abnormalities. The initiative was designed to obtain a large amount of molecular data on DNA and RNA of freshly collected tumor samples that were collected, processed and analyzed in a standardized fashion to allow for large-scale cross sample analysis. The sample collection is accompanied by careful and prospective clinical data acquisition, allowing a variety of matched molecular and clinical data permitting a wide variety of analyses. GMDI has accrued fresh frozen tumors in the retrospective phase (all from the Henry Ford Hospital, without germline DNA) and fresh frozen tumors in the prospective phase (from a variety of institutions). In addition to characterizing the samples from patients enrolled in GMDI, the microarray group has generated genomic-scale analyses of the many human and canine glioma initiating cells/glioma stem cells (GIC/GSC) lines, as well as many canine and murine normal neural stem cell (NSC) lines produced in laboratory.

Drug Related Gene Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-37443
synonym: DRG Database
synonym: Drug Dependent Gene Database
abbrev: DRG
IAO_0000115: Gene expression data from published journal articles that test hypotheses relevant to neuroscience of addiction and addictive behavior. Data types include effects of particular drug, strain, or knock out on particular gene, in particular anatomical region. Focuses on gene expression data and exposes data from investigations using DNA microarrays, polymerase chain reaction, immunohistochemistry and in-situ hybridizations. Data are available for query through NIF interface.Data submissions are welcome.

PHI-base
type: Resource
type: NamedIndividual
has db xref: biotools:phi-base
has db xref: nif-0000-03276
has db xref: r3d100011301
synonym: Pathogen Host Interaction
synonym: Pathogen Host Interaction base
synonym: Pathogen Host Interaction-Base
IAO_0000115: Database that catalogs experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts. It is an invaluable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. In collaboration with the FRAC team, it also includes antifungal compounds and their target genes. Each entry is curated by domain experts and is supported by strong experimental evidence (gene disruption experiments, STM etc), as well as literature references in which the original experiments are described. Each gene is presented with its nucleotide and deduced amino acid sequence, as well as a detailed description of the predicted protein's function during the host infection process. To facilitate data interoperability, genes have been annotated using controlled vocabularies and links to external sources (Gene Ontology terms, EC Numbers, NCBI taxonomy, EMBL, PubMed and FRAC).

PhosPhAt
type: Resource
type: NamedIndividual
has db xref: nif-0000-03277
synonym: Arabidopsis Protein Phosphorylation Site Database
IAO_0000115: Database containing information on Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments from different research groups. Specific information on the peptide properties as well as on the experimental and analytical context is given. The PhosPhAt service has a built-in plant specific phosphorylation site predictor trained on the experimental dataset for Serine, threonine and tyrosine phosphorylation (pSer, pThr, pTyr). Protein sequences or Arabidopsis AGI gene identifier can be submitted to the predictor. Users and researchers are encouraged to assist in keeping the database current by submitting either published data or unpublished data (MS/MS data required).

Creighton University Department of Pharmacology
type: Organization
type: NamedIndividual
has db xref: nif-0000-01924
synonym: Creighton University School of Medicine Department of Pharmacology
synonym: CU Dept. of Pharmacology
synonym: CU School of Medicine Department of Pharmacology
synonym: CU School of Medicine Dept. of Pharmacology
synonym: CU SOM Department of Pharmacology
synonym: CU SOM Dept. of Pharmacology
synonym: CUSOM Department of Pharmacology
synonym: CUSOM Dept. of Pharmacology
IAO_0000115: The primary instructional mission of the Department is to provide professional students with an understanding of the pharmacological basis of therapeutics. In addition to instruction of students in the medical, dental, pharmacy and nursing programs at Creighton, faculty are actively involved in both teaching and research training of graduate students. Ten departmental faculty work with an energetic group of graduate students, postdoctoral fellows and research staff in a congenial and collaborative environment. Faculty in the Department of Pharmacology at Creighton University School of Medicine reflect the complex scope of modern pharmacological research as they apply methods of systems and cell physiology, neuroscience, biochemistry, and cellular and molecular biology to better understand drug action. Departmental faculty are engaged in diverse areas of research including, but not limited to, G protein-coupled receptor signal transduction, regulators of G-protein signaling, regulation of receptor gene expression, control of neurotransmitter release, ion channel modulation, molecular pharmacology of excitatory neurotransmission, and cardiovascular and CNS drug discovery. These studies provide insight into the mechanisms of drug action and the means by which drug action is translated into responses in the cardiovascular system, the nervous system, exocrine glands and cancer cells.

deCODE genetics
type: Organization
type: NamedIndividual
has db xref: grid.421812.c
has db xref: ISNI: 0000 0004 0618 6889
has db xref: nif-0000-31959
has db xref: Wikidata: Q493712
synonym: Islensk Erfdagreining
synonym: Islensk Erfdagreining EHF
abbrev: deCODE
IAO_0000115: A biopharmaceutical company applying its discoveries in human genetics to develop drugs and diagnostics for common diseases. They specialize in gene discovery - their population approach and resources have enabled them to isolate key genes contributing to major public health challenges from cardiovascular disease to cancer. The company's genotyping capacity is now one of the highest in the world. They have a large population-based biobank containing whole blood and DNA samples with extensive relevant phenotypic information from around 120.000 Icelanders. In the company's work in more than 50 disease projects, their statistical and informatics departments have established themselves in data processing and analysis. deCODE genetics is widely recognized as a center of excellence in genetic research.

MILD
type: Resource
type: NamedIndividual
has db xref: nlx_154480
synonym: MultIallelic Linkage Disequilibrium: a program for adjusted linkage disequilibrium (LD) calculations
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application (entry from Genetic Analysis Software).

eDoctoring
type: Resource
type: NamedIndividual
has db xref: nif-0000-31964
IAO_0000115: Online educational tool that brings challenging clinical practice to your computer, providing medical education that is engaging, challenging and interactive. While there is no substitute for real-life direct contact with patients or colleagues, research has shown that interactive online education can be a highly effective and enjoyable method of learning many components of clinical medicine, including ethics, clinical management, epidemiology and communication skills. eDoctoring offers 25 simulated clinical cases, 15 interactive tutorials and a virtual library containing numerous articles, fast facts and video clips. Their learning material is arranged in the following content areas: * Ethical, Legal and Social Implications of Genetic Testing * Palliative and End-of-Life Care * Prostate Cancer Screening and Shared Decision-Making

Drexel University Neurobiology and Anatomy
type: Organization
type: NamedIndividual
has db xref: nif-0000-01929
synonym: Drexel University College of Medicine Department of Neurobiology and Anatomy
synonym: Drexel University College of Medicine Neurobiology & Anatomy
synonym: Drexel University College of Medicine Neurobiology and Anatomy
synonym: Neurobiology & Anatomy Department at DUCOM
synonym: Neurobiology and Anatomy Department at DUCOM
IAO_0000115: The Department of Neurobiology and Anatomy at the Drexel University College of Medicine provides an outstanding academic environment for pursuing multidisciplinary training and research in neuroscience. The department offers postdoctoral training through a NIH training grants and graduate student training through the Neuroscience program for outstanding individuals preparing for a research career in the biomedical sciences. The Department is also responsible for 3 major courses given to medical students that include Medical Neuroscience, Gross Anatomy and MicroAnatomy. Training can be obtained in all aspects of advanced microscopy and imaging, tissue culture, transplantation techniques, gene therapy and sequencing, behavioral neurobiology, kinematics, intracellular recording, patch clamping, computer modeling of neurobiological processes and robotics. The Department has well equipped shared facilities for confocal microscopy, electron microscopy, image acquisition and processing, small animal surgery, behavioral analysis, biochemistry and molecular biology. Research training is also supplemented by a seminar series featuring faculty, postdoctoral fellows and outside speakers. Journal clubs and discussions of research findings are scheduled regularly and often shared among individual laboratories.

Drexel University College of Medicine Pharmacology and Physiology
type: Organization
type: NamedIndividual
has db xref: nif-0000-01931
synonym: DUCOM Pharmacology and Physiology
IAO_0000115: The Department of Pharmacology and Physiology offers graduate programs leading to the M.S. and the Ph.D. degrees. The programs require independent research under the direction of departmental faculty members who are engaged in highly active research programs involving molecular, cellular, and behavioral approaches to experimental pharmacology and physiology in a strongly collaborative environment. The disciplines of pharmacology and physiology touch on virtually every scientific discipline and clinical area within the biomedical sciences, thereby providing students with a range of opportunities into disease mechanisms and altered physiological processes, new pharmacological tools and new medications. We are unique in offering educational programs not only in the basic sciences of pharmacology and physiology but also in drug discovery and development, which provides students with a wealth of advantages in considering career opportunities within academic, biopharmaceutical, and pharmaceutical settings. Students in both the PhD and MS programs begin their coursework with a core curriculum in biomedical sciences, and immediately start laboratory rotations. Intensive graduate-level pharmacology and physiology courses round out the core programmatic courses. Specialization in ion channel physiology, smooth-muscle physiology, neuropharmacology, behavioral pharmacology, and signal transduction processes may involve the taking of several elective courses. Each program requires the defense of a thesis based on original research. For more information visit, http://www.drexel.edu/catalog/g-about/pharm.htm.

Greally Lab
type: Resource
type: NamedIndividual
has db xref: nif-0000-31979
synonym: The Greally Lab
IAO_0000115: It studies epigenetic regulation of the genome and its dysregulation in disease. This lab has a long-standing interest in gene regulatory processes that extend over large regions of the genome and give rise to human diseases. Our major projects are centred on the discovery of DNA sequence characteristics that discriminate genes undergoing genomic imprinting, using these to find new imprinted genes that are candidates for causing human disease.

Hymenoptera Anatomy Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157435
abbrev: HAO
IAO_0000115: A structured controlled vocabulary of the anatomy of the Hymenoptera (bees, wasps, sawflies and ants)

VisiGene Image Browser
type: Resource
type: NamedIndividual
has db xref: nif-0000-00198
abbrev: VisiGene
IAO_0000115: Virtual microscope for viewing in situ images that show where a gene is used in an organism, sometimes down to cellular resolution. The user can examine cell-by-cell as well as tissue-by-tissue expression patterns. Users can retrieve images that meet specific search criteria, then interactively zoom and scroll across the collection. Image set contributions are welcome. The following image collections are currently available for browsing: * High-quality high-resolution images of eight-week-old male mouse sagittal brain slices with reverse-complemented mRNA hybridization probes from the Allen Brain Atlas, courtesy of the Allen Institute for Brain Science * Mouse in situ images from the Jackson Lab Gene Expression Database (GXD) at MGI * Transcription factors in mouse embryos from the Mahoney Center for Neuro-Oncology * Mouse head and brain in situ images from NCBI' '''s Gene Expression Nervous System Atlas (GENSAT) database * Xenopus laevis in situ images from the National Institute for Basic Biology (NIBB) XDB project

Duke University, Pharmacology and Cancer Biology
type: Organization
type: NamedIndividual
has db xref: nif-0000-01935
synonym: Duke University Medical Center Pharmacology & Cancer Biology
synonym: Duke University Medical Center Pharmacology and Cancer Biology
synonym: PCB at Duke
IAO_0000115: Department of Pharmacology and Cancer Biology spans two overlapping and broad disciplines, one exploring how chemical agents impact living cells and one seeking to understand how inappropriate responses to environmental molecules and internal cellular cues can lead to development of Cancer. Occupying Levine Science Research Center, Pharmacology and Cancer Biology department is dedicated to mentoring and training of graduate students and postdoctoral fellows.Innovative undergraduate program also allows students majoring in Biology or Chemistry at Duke to complete area specialization in Pharmacology, as well as offering courses in Pharmacology and Neuropharmacology for undergraduates. Department trains also students working towards Ph.D.s in Molecular Cancer Biology. Moreover, students enter our department through several university-wide multi-disciplinary programs including the Toxicology, Cell and Molecular Biology Program and the University Program in Genetics and Genomics. Our 23 faculty members are remarkably diverse and use all of the tools available to biomedical scientists to address questions critical to fundamental biology and human health. The faculty members share the common goal of exploiting cellular signaling pathways to address a myriad of important scientific questions relevant to cancer, metabolism, nervous system function, drugs of abuse and environmental toxicants.

PicTar
type: Resource
type: NamedIndividual
has db xref: biotools:pictar
has db xref: nif-0000-31983
has db xref: OMICS_00411
IAO_0000115: An algorithm for the identification of microRNA targets. Details are provided (3' UTR alignments with predicted sites, links to various public databases etc) regarding: # microRNA target predictions in vertebrates (Krek et al, Nature Genetics 37:495-500 (2005)) # microRNA target predictions in seven Drosophila species (Grn et al, PLoS Comp. Biol. 1:e13 (2005)) # microRNA targets in three nematode species (Lall et al, Current Biology 16, 1-12 (2006)) # human microRNA targets that are not conserved but co-expressed (i.e. the microRNA and mRNA are expressed in the same tissue) (Chen and Rajewsky, Nat Genet 38, 1452-1456 (2006)) co-expressed targets

Source BioScience LifeSciences
type: Resource
type: NamedIndividual
has db xref: nif-0000-31984
synonym: imaGenes
synonym: Source BioScience imaGenes
abbrev: RZPD
IAO_0000115: Source BioScience LifeSciences are European leaders in DNA sequencing, genomic services, bioinformatic analyses and offers a comprehensive portfolio of genomic reagents and antibodies. Source BioScience LifeScience is a CPA, GLP/GCP accredited and Illumina NGS CSPro certified genomic service provider and distributes a comprehensive range of biological products to companies and institutions worldwide. Source BioScience is proud to announce that Source BioScience imaGenes has joined it's LifeSciences group. This will enable us to bring our customers one unified website with our complete range of Products, Clones and Services. We have merged our clone libraries together so that can now offer you over 20 million clones! Add to this our excellent sequencing service and our range of over 100,000 antibodies and Source BioScience LifeSciences is your ideal outsourcing partner.

Duke University Trinity College of Arts and Sciences Undergraduate Neuroscience
type: Organization
type: NamedIndividual
has db xref: nif-0000-01936
synonym: DU Trinity College of Arts and Sciences Undergraduate Neuroscience
synonym: Duke Undergraduate Neuroscience
IAO_0000115: The major and minor in Neuroscience at Duke University was approved by the Arts and Sciences Council of Trinity College of Arts and Sciences on April 9, 2009. The program offers three academic plans: Bachelor of Science (B.S.) degree in Neuroscience, Bachelor of Arts (A.B.) degree in Neuroscience, and a Minor in Neuroscience. Although Neuroscience is a new major/minor, there is a rich and long-standing tradition of excellence in undergraduate neuroscience research and education at Duke. Groups of faculty in the Department of Psychology and Neuroscience and the Department of Biology, as well as the Department of Neurobiology in the Duke University School of Medicine, have been especially engaged in teaching neuroscience in undergraduate classes and hosting independent study projects in their research laboratories. Building upon this broad foundation, the new Undergraduate Studies in Neuroscience program is a truly interdisciplinary experience reflecting the diverse sources of knowledge that advance our understanding of the brain sciences. Undergraduate Studies in Neuroscience is a unique collaboration among many Departments and Schools , with administrative support provided by Trinity College of Arts and Sciences and the Duke Institute for Brain Sciences.

Influenza Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157440
abbrev: FLU
IAO_0000115: An application ontology established by a collaborative group of influenza researchers that includes consolidated influenza sequence and surveillance terms from resources such as the BioHealthBase (BHB), a Bioinformatics Resource Center (BRC) for Biodefense and Emerging and Re-emerging Infectious Diseases, the Centers for Excellence in Influenza Research and Surveillance (CEIRS)

BlockClust
type: Resource
type: NamedIndividual
has db xref: OMICS_04641
IAO_0000115: Software for efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles.

PINdb
type: Resource
type: NamedIndividual
has db xref: nif-0000-03290
synonym: Proteins Interacting in the Nucleus Database
abbrev: PIN
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented September 2, 2016. Relational database containing the compositions of multi-protein complexes in the nucleus of budding yeast and human cells. Its content is limited to information curated from the proteomics literatur…

Lipid Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157458
abbrev: LiPrO
IAO_0000115: An ontology that describes the LIPIDMAPS nomenclature classification explicitly using description logics (OWL-DL). Lipid classes are organized hierarchically with the super-classes restricted by generic necessary conditions. More specific necessary conditions are used to define membership requirements for sub classes of lipid according to appropriate functional groups. Lipid research is increasingly integrated within systems level biology such as lipidomics where lipid classification is required before appropriate annotation of chemical functions can be applied.

East Tennessee State University, Department of Pharmacology
type: Organization
type: NamedIndividual
has db xref: nif-0000-01942
synonym: East Tennessee State University Quillen College of Medicine Department of Pharmacology
synonym: ETSU COM Dept. of Pharmacology
IAO_0000115: Faculty members of our Department are actively engaged in delivering outstanding teaching to undergraduate students, graduate students, medical students, and residents. Our Doctor of Philosophy (graduate) students matriculate to Pharmacology through the Biomedical Sciences Graduate Program at the Quillen College of Medicine. Students pursuing Master of Science and Doctor of Philosophy degrees may pursue a focus in Toxicology. Our faculty members are trained in several medical disciplines and our research applies methodological approaches that span molecular biology, cellular biology, systems biology, and human biology and pathology. Through research, our department strives to understand human disease pathology and use this understanding to develop new therapeutic entities (e.g. drugs) for the treatment of major human diseases. The primary foci of department research efforts are cardiovascular and neuropsychiatric diseases, although other areas of interest and activity exist. Our laboratories are funded by the National Institutes of Health, American Heart Association, the American Foundation for Suicide Prevention and a variety of other agencies and sources.

Emory University, Molecular and Systems Pharmacology
type: Resource
type: NamedIndividual
has db xref: nif-0000-01944
synonym: Emory Molecular and Systems Pharmacology Graduate Program
synonym: Emory MSP
synonym: Emory MSP Graduate Program
synonym: Emory University Molecular and Systems Pharmacology Graduate Program
synonym: EU MSP
IAO_0000115: The Molecular and Systems Pharmacology graduate program at Emory University offers broad training in the biomedical sciences for students interested in learning how the drugs of today work and how the novel therapeutics of tomorrow can be developed. The Program offers a specialization in toxicology. Emory University was recently rated by The Scientist magazine as the number 1 university in the world in terms of impact in pharmacology and toxicology research. Particular strengths within the MSP graduate school program at Emory include neuropharmacology, cancer biology, AIDS research, cardiovascular pharmacology, toxicology, and chemical biology. Ph.D. training in the Emory MSP program provides students with an ideal preparation for successful careers in the biotechnology and pharmaceutical industries as well as in academic research, teaching, government research, patent law and other disciplines that depend upon knowledge of fundamental pharmacological principles.

PIRSF
type: Resource
type: NamedIndividual
has db xref: biotools:pirsf
has db xref: nif-0000-03294
has db xref: OMICS_01697
synonym: PIR SuperFamily
synonym: Protein Information Resource SuperFamily
IAO_0000115: A SuperFamily classification system, with rules for functional site and protein name, to facilitate the sensible propagation and standardization of protein annotation and the systematic detection of annotation errors. The PIRSF concept is being used as a guiding principle to provide comprehensive and non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. The PIRSF classification system is based on whole proteins rather than on the component domains; therefore, it allows annotation of generic biochemical and specific biological functions, as well as classification of proteins without well-defined domains. There are different PIRSF classification levels. The primary level is the homeomorphic family, whose members are both homologous (evolved from a common ancestor) and homeomorphic (sharing full-length sequence similarity and a common domain architecture). At a lower level are the subfamilies which are clusters representing functional specialization and/or domain architecture variation within the family. Above the homeomorphic level there may be parent superfamilies that connect distantly related families and orphan proteins based on common domains. Because proteins can belong to more than one domain superfamily, the PIRSF structure is formally a network. The FTP site provides free download for PIRSF.

miR-PREFeR
type: Resource
type: NamedIndividual
has db xref: biotools:mir-prefer
has db xref: OMICS_04637
synonym: miR-PREFeR: microRNA PREdiction From small RNAseq data
synonym: miRNA PREdiction From small RNA-Seq data
IAO_0000115: An accurate, fast, and easy-to-use plant miRNA prediction software tool using small RNA-Seq data. It utilizes expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species.

Eindhoven University of Technology; North Brabant; Netherlands
type: NamedIndividual
has db xref: nlx_151954
synonym: Eindhoven University of Technology
synonym: Technische Universiteit Eindhoven
synonym: TU Eindhoven
abbrev: TU/e

Niftilib
type: Resource
type: NamedIndividual
has db xref: nif-0000-32011
synonym: Nifti Libraries
synonym: The Nifti Libraries
IAO_0000115: Niftilib is a set of i/o libraries for reading and writing files in the nifti-1 data format. nifti-1 is a binary file format for storing medical image data, e.g. magnetic resonance image (MRI) and functional MRI (fMRI) brain images. Niftilib currently has C, Java, MATLAB, and Python libraries; we plan to add some MATLAB/mex interfaces to the C library in the not too distant future. Niftilib has been developed by members of the NIFTI DFWG and volunteers in the neuroimaging community and serves as a reference implementation of the nifti-1 file format. In addition to being a reference implementation, we hope it is also a useful i/o library. Niftilib code is released into the public domain, developers are encouraged to incorporate niftilib code into their applications, and, to contribute changes and enhancements to niftilib. Please contact us if you would like to contribute additonal functionality to the i/o library.

George Washington University, Cognitive Neuroscience
type: Organization
type: NamedIndividual
has db xref: nif-0000-01951
synonym: GWU Cognitive Neuroscience Program
IAO_0000115: The Cognitive Neuroscience Program provides graduate students with an intense and focused research experience in the areas of perception, attention, and memory, with emphasis on the neural bases of these capacities. The program utilizes diverse research methods such as patient-based testing, neuro-imaging, animal modeling, and psychophysical scaling, and computational modeling. The goal of the program is to train students for careers in academic and research institutions. At the undergraduate level, the program provides both entry level and advanced courses as well as honor seminars in special topics. The program boasts a high faculty / student ratio, reflecting a strong emphasis on close collaboration between faculty and students on joint research projects. The Washington, DC research environment is outstanding, with the National Institutes of Health, Georgetown University, the University of Maryland, Johns Hopkins University, George Mason University, and other research institutions all close by. GWU's other resources for cognitive neuroscience research include a major medical school, a teaching hospital with world-class Neurology, Neurosurgery and Neuroradiology Departments, and an intensive Neuroscience Program. GWU is located in the heart of Washington, DC, a beautiful city with a wide variety of national museums, historical sites, restaurants, and cultural events. The Cognitive Neuroscience program at GW is designed to train students to become independent scientists who do basic research in an academic setting. Please note that ours is not a clinical neuropsychology program -- we provide no training in diagnosing or treating any brain or neurological disorder.

MouseNET
type: Resource
type: NamedIndividual
has db xref: nif-0000-32003
has db xref: OMICS_01550
abbrev: mouseNet
IAO_0000115: A functional network for laboratory mouse based on integration of diverse genetic and genomic data. It allows the users to accurately predict novel functional assignments and network components. MouseNET uses a probabilistic Bayesian algorithm to identify genes that are most likely to be in the same pathway/functional neighborhood as your genes of interest. It then displays biological network for the resulting genes as a graph. The nodes in the graph are genes (clicking on each node will bring up SGD page for that gene) and edges are interactions (clicking on each edge will show evidence used to predict this interaction). Most likely, the first results to load on the results page will be a list of significant Gene Ontology terms. This list is calculated for the genes in the biological network created by the mouseNET algorithm. If a gene ontology term appears on this list with a low p-value, it is statistically significantly overrepresented in this biological network. The graph may be explored further. As you move the mouse over genes in the network, interactions involving these genes are highlighted.If you click on any of the highlighted interactions graph, evidence pop-up window will appear. The Evidence pop-up lists all evidence for this interaction, with links to the papers that produced this evidence - clicking these links will bring up the relevant source citation(s) in PubMed.

George Washington University, Department of Pharmacology and Physiology
type: Organization
type: NamedIndividual
has db xref: nif-0000-01952
synonym: GWU Department of Pharmacology & Physiology
synonym: GWU Department of Pharmacology and Physiology
synonym: GWU Dept. of Pharmacology and Physiology
IAO_0000115: The Department of Pharmacology & Physiology at the George Washington University provides unique research opportunities at the predoctoral and postdoctoral levels. They also offer courses in Pharmacology and Physiology for Medical and Health Sciences students, as well as a number of graduate-level courses. Our mission is to provide the highest quality of educational opportunities to our community, and to advance scientific knowledge and improve human health through leading-edge research in the biomedical sciences.

PlantProm DB
type: Resource
type: NamedIndividual
has db xref: nif-0000-03308
has db xref: OMICS_01875
synonym: Plant Promoter Database
abbrev: PlantProm
IAO_0000115: Annotated, non-redundant database of proximal promoter sequences for RNA polymerase II with experimentally determined transcription start site(s) (TSS) from various plant species. It contains 578 unrelated entries including 151, 396 and 31 promoters with experimentally verified TSS from monocot, dicot and other plants, respectively (April 2014). This DB presents the published promoter sequences with TSS(s) determined by direct experimental approaches and therefore serves as the most accurate source for development of computational promoter prediction tools.

MAGI
type: Resource
type: NamedIndividual
has db xref: OMICS_04636
IAO_0000115: A web service for fast microRNA-Seq data analysis in a GPU infrastructure.

Kinetic Simulation Algorithm Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157456
abbrev: KISAO
IAO_0000115: An ontology that classifies algorithms available for the simulation of models in biology, their characteristics and the parameters required for their use.

PLANTTFDB
type: Resource
type: NamedIndividual
has db xref: biotools:planttfdb_2.0
has db xref: nif-0000-03311
has db xref: OMICS_00560
has db xref: r3d100010137
synonym: Plant Transcription Factor Database
synonym: PlantTFDB 2.0
abbrev: PlantTFDB
IAO_0000115: Comprehensive plant transcription factor database. Interface to allow users to search the database by IDs or free texts, to make sequence similarity search against TFs of all or individual species, and to download TF sequences for local analysis.PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors

Georgetown, Neuroscience
type: Organization
type: NamedIndividual
has db xref: nif-0000-01954
synonym: Georgetown Department of Neuroscience
synonym: Georgetown Dept. of Neuroscience
synonym: Georgetown University Medical Center; Department of Neuroscience
synonym: GUMC Department of Neuroscience
synonym: GUMC Dept. of Neuroscience
abbrev: Georgetown Neuroscience
IAO_0000115: Faculty of the Department of Neuroscience participate in the teaching of courses in the Interdisciplinary Program in Neuroscience and the School of Medicine. A Ph.D. in Neuroscience is offered through the Interdisciplinary Program in Neuroscience. Support for graduate training is offered through the Department, the research grants of individual faculty, as well as through three NIH training grants directed by Neuroscience faculty. * Training in Recovery of Function after CNS Injury. Program Director: Barbara S. Bregman, Ph.D. * Training Program in Drug Abuse. Program Director: Barbara S. Bayer, Ph.D. * Training in Neural Injury and Plasticity. Program Director: Jean R. Wrathall, Ph.D. Scientists in the Department of Neuroscience participate in a wide array of research activities with a focus on understanding both the normal and injured nervous system. The theme of neuroplasticity characterizes much of the research in the Department. We study neuroplasticity during normal development and in the adult in response to activity (e.g., learning) or drugs. Our research is also focused on studying the plasticity that ensues after traumatic (such as spinal cord injury) or ischemic damage to the nervous system and over the course of developmental or neurodegenerative diseases (such as Specific Language Impairment, autism, or Parkinson's and Alzheimer's Diseases). The specific research interests of each of the principal investigators falls under four broad subheadings: *CNS disorders ( Faden, Mocchetti, Rebeck, Riesenhuber,Ullman) *Cognitive/Computational (Riesenhuber, Ullman) *Development, Regeneration and recovery of function after injury (Bregman, Faden, Kromer, Ullman, Wrathall) *Neuroimmunology and Drugs of Abuse (Bayer, Faden, Kromer, Mocchetti) Under this common theme, a variety of diverse techniques and models are employed by the faculty. They range from molecular studies of gene function to studies on humans using Event-Related Potentials (ERPs) and functional MRI. Ex…

ALDEx2
type: Resource
type: NamedIndividual
has db xref: biotools:aldex2
has db xref: OMICS_04634
IAO_0000115: Software tool to examine compositional high-throughput sequence data with Welch's t-test. A differential relative count abundance analysis for the comparison of two conditions. For example, single-organism and meta-rna-seq high-throughput sequencing assays, or of selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected Benjamini-Hochberg false discovery rate given the biological and sampling variation using several parametric and non-parametric tests. Can to glm and Kruskal-Wallace tests on one-way ANOVA style designs.

JobTarget
type: Resource
type: NamedIndividual
has db xref: nlx_11196
IAO_0000115: JobTarget is the foundation upon which careers and companies are built. Our technology and services connect millions of job seekers to hundreds of thousands of companies through thousands of job boards. We facilitate faster, more meaningful connections by powering niche job sites that target specific audiences of talent, and providing technology and advertising solutions for employers to more quickly and cost-effectively locate the most qualified candidates for their openings. Explore our Products & Services to experience the JobTarget difference or check out Who We Serve to narrow in on the best solutions to serve you.

PLPMDB: Pyridoxal-5'-phosphate dependent enzymes Mutants Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-03316
abbrev: PLPMDB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. A searchable mutant database developed to provide access to relevant mutant information on pyridoxal-5'-phosphate dependent enzymes. All data have been extracted from publications and publicly available databases and organized to enable database searching. The database is a useful tool for planning mutant experiments and for interpretation of information from such experiments. PLPMDB includes mutation information from SWISS-PROT/TrEMBL, several web-based mutation data resources, and data extracted from the literature.

i2b2 Cross-Institutional Clinical Translational Research project
type: Resource
type: NamedIndividual
has db xref: nif-0000-33108
abbrev: i2b2-CICTR
abbrev: i2b2CICTR
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 08, 2013. A two year Clinical and Translational Science Award (CTSA) supplement that set up a SHRINE (Shared Health Research Informatics NEtwork) network to create an information exchange environment that successfully shared 4.2M deidentified patient records. The network successfully linked i2b2 sites at UW, UCSF, UC Davis and Harvard Catalyst. Recombinant Data Corporation was actively involved in this implementation. This is a collaborative information exchange pilot project to adapt and extend data discovery tools and processes to enhance research design and retrospective data study capabilities for clinical translational investigators. The novel approach of this project will be to incrementally build a common technical, semantic and appropriately secure and governed distributed system in close partnership with active researchers at three large and geographically distributed academic medical centers. This collaboration will extend the Informatics for Integrating Biology and the Bedside (i2b2) software architecture developed by the Harvard based National Center for Biomedical Computing (NCBC) to support multi-institution data query capabilities. The anticipated outcome of this two-year project is to make high-level anonymized descriptive characteristics of population-level data discoverable for research design, hypothesis generation and retrospective data studies.

Harvard University Neurobiology
type: Organization
type: NamedIndividual
has db xref: nif-0000-01956
synonym: Harvard Medical School Department of Neurobiology
synonym: Harvard Medical School Neurobiology
synonym: Harvard Neurobiology
IAO_0000115: The mission of the Department of Neurobiology is to promote research and teaching that leads to a better understanding of the normal and diseased brain. The Department faculty are committed to training leaders of the next generation of neuroscientists, including graduate and medical students. Candidates for the Ph.D. in Neurobiology are admitted to the graduate Program in Neuroscience. This interdepartmental training program links the Department of Neurobiology with faculty in the Harvard affiliated hospitals and with faculty in other basic science departments. The Program, established in 1981, now includes about 90 investigators who participate in the training of Ph.D. candidates. Approximately fifteen students are accepted each year so that the steady state enrollment is usually about 80-90. This Program in Neuroscience attracts superb students with a broad range of interests from all areas of the globe. The goals of our training are to produce scientists who have explored one area and one level of analysis in great depth, but who are familiar with the full scope of neuroscience. They should be able to move from one level to another in a critical and creative manner. We also try to develop an appreciation for translational research that bears on human brain disease. The Department of Neurobiology, established in 1966 with Stephen W. Kuffler as Chair, was the first of its kind. The intent was to bring together members of traditional departments- physiologists, biochemists, and anatomists- in order to understand the principles governing communication between cells in the nervous system. This interdisciplinary approach was revolutionary at the time, and the interdisciplinary theme has continued to permeate the evolution of the field of neuroscience ever since. The Program in Neuroscience is one of four programs administered by the Division of Medical Sciences (DMS). DMS, located at the medical school, is a division of the Faculty of Arts and Sciences of Harvard Unive…

Malaria Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157464
abbrev: IDOMAL
IAO_0000115: An application ontology to cover all aspects of malaria (clinical, epidemiological, biological, etc) as well as the intervention attempts to control it, extending the infectious disease ontology (IDO).

qBasePLUS
type: Commercial Organization
type: NamedIndividual
has db xref: OMICS_02320
abbrev: qbase+
IAO_0000115: Software program for quantitative PCR (qPCR) data analysis based on geNorm and qBase technology.

Computational Infrastructure for Geodynamics
type: Resource
type: NamedIndividual
has db xref: SciRes_000182
synonym: Computational Infrastructure for Geodynamics (CIG)
abbrev: CIG
IAO_0000115: Community-driven organization that develops and disseminates software for geophysics and related fields. They host codes in a wide range of disciplines in geodynamics and computational science including geodynamo, long-term tectonics, magma migration, mantle dynamics, seismology, and short-term crustal dynamics.

RefGenes
type: Commercial Organization
type: NamedIndividual
has db xref: OMICS_02319
IAO_0000115: Tool for the identification of reliable and condition specific reference genes for RT-qPCR data normalization. RefGenes is available within Genevestigator.

Measurement Method Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157468
abbrev: MMO
IAO_0000115: An ontology designed to represent the variety of methods used to make qualitative and quantitative clinical and phenotype measurements both in the clinic and with model organisms.

Fisher BioReagents
type: Organization
type: NamedIndividual
has db xref: nlx_152364
IAO_0000115: An Antibody supplier

HTqPCR
type: Resource
type: NamedIndividual
has db xref: biotools:htqpcr
has db xref: OMICS_02314
synonym: HTqPCR - Automated analysis of high-throughput qPCR data
IAO_0000115: Software package for the analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad Laboratories; conventional 96- or 384-well plates; or microfluidic devices such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs).

Allelic Variations of The XP Genes
type: Resource
type: NamedIndividual
has db xref: nif-0000-32042
synonym: xpmutations.org
abbrev: Allelic Variations of the XP Genes
IAO_0000115: Interactive repository of mutations and other allelic variations of the genes involved in the DNA repair disorders, Xeroderma Pigmentosum (XP), Cockayne Syndrome (CS), Trichothiodystrophy (TTD), and other UV-sensitivity disorders. Any omitted data or new data may be submitted by using the on-line data submission form. There is a message board system to support discussions amongst those interested in XP and DNA Repair. RESOURCES * Educational module of the molecular biology of Nucleotide Excision Repair * Introduction to the DNA Repair disorders (XP, CS, TTD, UVs) * Background on each of the XP genes * A searchable database of mutations and sequence variations for the XP genes * Contact point for the submission of new mutation data * Discussion Forums and a Guest Book * Web Links to Additional Resources

Syracuse University; Institute for Sensory Research
type: Resource
type: NamedIndividual
has db xref: nif-0000-01969
abbrev: ISR
IAO_0000115: The Institute for Sensory Research (ISR) defines itself as a world class research center dedicated to the discovery and application of knowledge of the sensory systems. Integration of engineering, life, and physical sciences, combining rigorous experimental methodology with mathematical analysis is stressed. Our multidisciplinary approach to bioengineering, sensory neuroscience, graduate, and undergraduate education, makes ISR a unique academic research center. At ISR, we study sensory systems, our gateways to the world. Our ears, eyes, skin, and mouth are channels through which we experience sound, light, texture, etc. These are functions that we usually take for granted until problems arise. Engineers, scientists, and students at ISR investigate both the basic sensory principles used by the brain, and also how the sensory systems can be best utilized, modified, and repaired if necessary to better communicate with our surroundings and with one another. In addition to basic research in hearing, touch, vision, and oro-facial biomechanics, recent projects include the design and testing of sensory-aid devices such as cochlear implants, hearing aids, ear protectors, and tactile aids for the visually and hearing impaired. Additional projects involve visual-depth perception, chewing and swallowing, oto-acoustic emissions, and personal care products such as oral rinses and skin lotions. Research * Auditory * Somatosensory * Vision

Statistics Online Computational Resource
type: Resource
type: NamedIndividual
has db xref: nif-0000-32655
abbrev: SOCR
IAO_0000115: A hierarchy of portable online interactive aids for motivating, modernizing probability and statistics applications. The tools and resources include a repository of interactive applets, computational and graphing tools, instructional and course materials. The core SOCR educational and computational components include the following suite of web-based Java applets: * Distributions (interactive graphs and calculators) * Experiments (virtual computer-generated games and processes) * Analyses (collection of common web-accessible tools for statistical data analysis) * Games (interfaces and simulations to real-life processes) * Modeler (tools for distribution, polynomial and spectral model-fitting and simulation) * Graphs, Plots and Charts (comprehensive web-based tools for exploratory data analysis), * Additional Tools (other statistical tools and resources) * SOCR Java-based Statistical Computing Libraries * SOCR Wiki (collaborative Wiki resource) * Educational Materials and Hands-on Activities (varieties of SOCR educational materials), * SOCR Statistical Consulting In addition, SOCR provides a suite of tools for volume-based statistical mapping (http://wiki.stat.ucla.edu/socr/index.php/SOCR_EduMaterials_AnalysesCommandLine) via command-line execution and via the LONI Pipeline workflows (http://www.nitrc.org/projects/pipeline). Course instructors and teachers will find the SOCR class notes and interactive tools useful for student motivation, concept demonstrations and for enhancing their technology based pedagogical approaches to any study of variation and uncertainty. Students and trainees may find the SOCR class notes, analyses, computational and graphing tools extremely useful in their learning/practicing pursuits. Model developers, software programmers and other engineering, biomedical and applied researchers may find the light-weight plug-in oriented SOCR computational libraries and infrastructure useful in their algorithm designs and research efforts. The three typ…

FMA
type: Resource
type: NamedIndividual
has db xref: nif-0000-00066
synonym: Foundational Model of Anatomy
synonym: Foundational Model of Anatomy Ontology
IAO_0000115: A domain ontology that represents a coherent body of explicit declarative knowledge about human anatomy. It is concerned with the representation of classes or types and relationships necessary for the symbolic representation of the phenotypic structure of the human body in a form that is understandable to humans and is also navigable, parseable and interpretable by machine-based systems. Its ontological framework can be applied and extended to all other species. The description of how the OWL version was generated is in Pushing the Envelope: Challenges in a Frame-Based Representation of Human Anatomy by N. F. Noy, J. L. Mejino, C. Rosse, M. A. Musen: http://bmir.stanford.edu/publications/view.php/pushing_the_envelope_challenges_in_a_frame_based_representation_of_human_anatomy The Foundational Model of Anatomy ontology has four interrelated components: # Anatomy taxonomy (At), # Anatomical Structural Abstraction (ASA), # Anatomical Transformation Abstraction (ATA), # Metaknowledge (Mk), The ontology contains approximately 75,000 classes and over 120,000 terms; over 2.1 million relationship instances from over 168 relationship types link the FMA's classes into a coherent symbolic model.

BestKeeper
type: Resource
type: NamedIndividual
has db xref: OMICS_02318
IAO_0000115: Excel-based tool using pair-wise correlations for determination of stable housekeeping genes, differentially regulated target genes and sample integrity. It determines the best suited standards, out of ten candidates, and combines them into an index. The index can be compared with further ten target genes to decide, whether they are differentially expressed under an applied treatment. All data processing is based on crossing points.

EXBIO Praha
type: Organization
type: NamedIndividual
has db xref: grid.447807.8
has db xref: nlx_152363
synonym: EXBIO
synonym: EXBIO Antibodies
synonym: EXBIO Praha a.s.
IAO_0000115: An Antibody supplier

NanoStringNorm
type: Resource
type: NamedIndividual
has db xref: biotools:nanostringnorm
has db xref: OMICS_02308
synonym: NanoStringNorm: Normalize NanoString miRNA and mRNA data
IAO_0000115: Software package for normalizing, diagnostics and visualization of NanoString nCounter data. Key features include an extensible environment for method comparison and new algorithm development, integrated gene and sample diagnostics, and facilitated downstream statistical analysis.

signalml.org
type: Resource
type: NamedIndividual
has db xref: nif-0000-32899
abbrev: SignalML
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.An XML-based language designed for metadescription of formats, used for digital storage of biomedical time series. Using SignalML, information on the structure of binary data files can be simply and efficiently coded. Once written, this information can be used by any software, which - owing to this metadescription - can read data files in the original format. This eliminates the need for conversions and duplication of data. signalml.org provides the following resources for interchange of relevant information and ideas: * SignalML wiki * Newsgroup / mailing list The main current software project is Svarog - a SignalML-compliant signal viewer, annotator, analyzer and (future) recorder. Svarog is written in Java and is currently best fitted for display of EEG and MEG signals. Also open platform for implementing advanced signal processing methods in user-friendly environment, at the moment interfacs for Java code, standalone executables and Matlab code via Matlab Builder for Java.

Sage Bionetworks
type: Organization
type: NamedIndividual
has db xref: grid.430406.5
has db xref: ISNI: 0000 0004 6023 5303
has db xref: nif-0000-32903
has db xref: nlx_42820
has db xref: Wikidata: Q891621
IAO_0000115: Non-profit biomedical research organization developing predictors of disease and accelerating health research through creation of open systems, incentives, and standards. Formed to coordinate and link academic and commercial biomedical researchers through Commons that represents new paradigm for genomics intellectual property, researcher cooperation, and contributor evolved resources.

Minimal Anatomical Terminology
type: Resource
type: NamedIndividual
has db xref: nlx_157480
abbrev: MAT
IAO_0000115: An ontology of minimal set of terms for anatomy.

NEMO Ontology
type: Resource
type: NamedIndividual
has db xref: nif-0000-32927
synonym: Neural ElectroMagnetic Ontology
IAO_0000115: Ontology that describes classes of event-related brain potentials (ERP) and their properties, including spatial, temporal, and functional (cognitive / behavioral) attributes, and data-level attributes (acquisition and analysis parameters). Its aim is to support data sharing, logic-based queries and mapping/integration of patterns across data from different labs, experiment paradigms, and modalities (EEG/MEG).

NormFinder
type: Resource
type: NamedIndividual
has db xref: OMICS_02317
synonym: NormFinder software - Determine the optimal normalization gene
IAO_0000115: Software for identifying the optimal normalization gene among a set of candidates. It ranks the set of candidate normalization genes according to their expression stability in a given sample set and given experimental design. It can analyze expression data obtained through any quantitative method e.g. real time RT-PCR and microarray based expression analysis. NormFinder.xla adds the NormFinder functionality directly to Excel. A version for R is also available.

NormqPCR
type: Resource
type: NamedIndividual
has db xref: biotools:normqpcr
has db xref: OMICS_02315
synonym: NormqPCR - Functions for normalisation of RT-qPCR data
IAO_0000115: Software package providing functions for the selection of optimal reference genes and the normalization of real-time quantitative PCR data.

PolymiRTS
type: Resource
type: NamedIndividual
has db xref: biotools:polymirts
has db xref: nif-0000-03324
has db xref: OMICS_00391
synonym: PolymiRTS Database
synonym: Polymorphism in microRNA Target Site
synonym: Polymorphism in microRNAs and their TargetSites
IAO_0000115: Database of naturally occurring DNA variations in microRNA (miRNA) seed regions and miRNA target sites. MicroRNAs pair to the transcripts of protein-coding genes and cause translational repression or mRNA destabilization. SNPs and INDELs in miRNAs and their target sites may affect miRNA-mRNA interaction, and hence affect miRNA-mediated gene repression. The PolymiRTS database was created by scanning 3'UTRs of mRNAs in human and mouse for SNPs and INDELs in miRNA target sites. Then, the potential downstream effects of these polymorphisms on gene expression and higher-order phenotypes are identified. Specifically, genes containing PolymiRTSs, cis-acting expression QTLs, and physiological QTLs in mouse and the results of genome-wide association studies (GWAS) of human traits and diseases are linked in the database. The PolymiRTS database also includes polymorphisms in target sites that have been supported by a variety of experimental methods and polymorphisms in miRNA seed regions.

NCI Flicker Web Server.
type: Resource
type: NamedIndividual
has db xref: nif-0000-32939
synonym: Flicker
synonym: NCI Flicker Web Server
IAO_0000115: The Flicker image viewer is a Java applet which reads two images from the Internet and then displays them in the your Web browser. It allows you to enhance them in various ways and to compare them visually in a third window called the flicker window. The Open-source Flicker downloadable application is now available. The program uses the "flicker method" used in GELLAB with and with Xconf. The flicker method is the alternate display in the same visual space of two images being compared which are aligned by aligning similar morphologic features. Images may first be enhanced by spatial warping, pseudo 3-Dimensional projections, image sharpening, contrast enhancement and other transforms. The transformed images may then be presented using flickering. Flicker is a method for comparing images from different Internet sources on your Web browser. Scientists around the world often work on similar image data. More of this data is being published on the Internet each year. In the case of 2D protein electrophoretic gel images, maps identifying proteins in these gels are becoming increasingly available. Visually comparing 2D sample gels against these 2D gel database maps may suggest putative protein spot identification in many cases. Flicker was originally developed for comparing 2D protein gels across the Internet.

Johns Hopkins University Pharmacology
type: Organization
type: NamedIndividual
has db xref: nif-0000-01975
synonym: JHU SOM Dept. of Pharmacology and Molecular Sciences
synonym: John Hopkins Medicine Department of Pharmacology and Molecular Sciences
synonym: John Hopkins Medicine Pharmacology and Molecular Sciences
synonym: Johns Hopkins University; School of Medicine; Department of Pharmacology and Molecular Sciences
synonym: Johns Hopkins University; School of Medicine; Pharmacology and Molecular Sciences
IAO_0000115: The Department of Pharmacology and Molecular Sciences is proud of its history. Founded in 1893 by John J. Abel, the "Father of Pharmacology" in the United States, the Johns Hopkins Pharmacology Department's advances over the years have included the first crystals of insulin, the first measurement of a drug level in a human, discovery of both the insulin and opiate receptors, and discovery of a cancer preventive principle in broccoli. Many of these and other key contributions have been made by students pursuing advanced degrees in our Department. We are also proud of our track record in student training. Many of our graduates have gone on to become academic and industrial leaders in biomedical research throughout the country and world. Not resting on our laurels, we are continuing to maintain our strong commitment to creative scholarship and education. Additionally, there is an Anti-Cancer Drug Development Training Program for predoctoral and postdoctoral students as well ad other Postdoctoral research opportunities. Each of our faculty is engaged in cutting-edge research spanning many areas including: chemical biology, immunology, virology, cancer, and neuroscience. We believe the opportunities for discovering new drug targets and developing novel therapeutics have never been brighter and will continue to be lustrous for the century ahead. The Johns Hopkins University and School of Medicine provide an excellent scientific environment, with a friendly and supportive atmosphere, filled with energetic students, faculty, fellows, and staff.

Mouse Biomedical Informatics Research Network
type: Resource
type: NamedIndividual
has db xref: nif-0000-00200
synonym: Mouse BIRN
abbrev: mBIRN
abbrev: MouseBIRN
IAO_0000115: Animal model data primarily focused on mice including high resolution MRI, light and electron microscopic data from normal and genetically modified mice. It also has atlases, and the Mouse BIRN Atlasing Toolkit (MBAT) which provides a 3D visual interface to spatially registered distributed brain data acquired across scales. The goal of the Mouse BIRN is to help scientists utilize model organism databases for analyzing experimental data. Mouse BIRN has ended. The next phase of this project is the Mouse Connectome Project (https://www.nitrc.org/projects/mcp/). The Mouse BIRN testbeds initially focused on mouse models of neurodegenerative diseases. Mouse BIRN testbed partners provide multi-modal, multi-scale reference image data of the mouse brain as well as genetic and genomic information linking genotype and brain phenotype. Researchers across six groups are pooling and analyzing multi-scale structural and functional data and integrating it with genomic and gene expression data acquired from the mouse brain. These correlated multi-scale analyses of data are providing a comprehensive basis upon which to interpret signals from the whole brain relative to the tissue and cellular alterations characteristic of the modeled disorder. BIRN's infrastructure is providing the collaborative tools to enable researchers with unique expertise and knowledge of the mouse an opportunity to work together on research relevant to pre-clinical mouse models of neurological disease. The Mouse BIRN also maintains a collaborative Web Wiki, which contains announcements, an FAQ, and much more.

Volume image object AnNOtation System
type: Resource
type: NamedIndividual
has db xref: nif-0000-32984
synonym: VANO - Volume image object AnNOtation System
synonym: Volume-object annotation system (VANO)
abbrev: VANO
IAO_0000115: VANO is a Volume image object AnNOtation System for 3D multicolor image stacks, developed by Hanchuan Peng, Fuhui Long, and Gene Myers. VANO provides a well-coordinated way to annotate hundreds or thousands of 3D image objects. It combines 3D views of images and spread sheet neatly, and is just easy to manage 3D segmented image objects. It also lets you incorporate your segmentation priors, and lets you edit your segmentation results! This system has been used in building the first digital nuclei atlases of C. elegans at the post-embryonic stage (joint work with Stuart Kim lab, Stanford Univ), the single-neuron level fruit fly neuronal atlas of late embryos (with Chris Doe lab, Univ of Oregon, HHMI), and the compartment-level of digital map(s) of adult fruit fly brains (several labs at Janelia Farm, HHMI). VANO is cross-platform software. Currently the downloadable versions are for Windows (XP and Vista) and Mac (Intel-chip based, Leopard or Tiger OS). If you need VANO for different systems (such as 64bit or 32bit, Redhat Linux, Ubuntu, etc), you can either compile the software, or send an email to pengh (at) janelia.hhmi.org. VANO is Open-Source. You can download both the source code files and pre-complied versions at the Software Downloads page.

NIH MRI Study of Normal Brain Development
type: Resource
type: NamedIndividual
has db xref: nif-0000-00201
synonym: NIH Pediatric MRI Data Repository
synonym: Pediatric MRI Data Repository
abbrev: Pediatric MRI Study
IAO_0000115: Data sets of clinical / behavioral and image data are available for download by qualified researchers from a seven year, multi-site, longitudinal study using magnetic resonance technologies to study brain maturation in healthy, typically-developing infants, children, and adolescents and to correlate brain development with cognitive and behavioral development. The information obtained in this study is expected to provide essential data for understanding the course of normal brain development as a basis for understanding atypical brain development associated with a variety of developmental, neurological, and neuropsychiatric disorders affecting children and adults. This study enrolled over 500 children, ranging from infancy to young adulthood. The goal was to study each participant at least three times over the course of the project at one of six Pediatric Centers across the United States. Brain MR and clinical/behavioral data have been compiled and analyzed at a Data Coordinating Center and Clinical Coordinating Center. Additionally, MR spectroscopy and DTI data are being analyzed. The study was organized around two objectives corresponding to two age ranges at the time of enrollment, each with its own protocols. * Objective 1 enrolled children ages 4 years, 6 months through 18 years (total N = 433). This sample was recruited across the six Pediatric Study Centers using community based sampling to reflect the demographics of the United States in terms of income, race, and ethnicity. The subjects were studied with both imaging and clinical/behavioral measures at two year intervals for three time points. * Objective 2 enrolled newborns, infants, toddlers, and preschoolers from birth through 4 years, 5 months, who were studied three or more times at two Pediatric Study Centers at intervals ranging from three months for the youngest subjects to one year as the children approach the Objective 1 age range. Both imaging and clinical/behavioral measures were collected at eac…

PPDB: Plant Promoter Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-03329
has db xref: OMICS_01874
synonym: Plant Promoter Database
abbrev: PPDB
IAO_0000115: A plant promoter database that provides information on transcription start sites (TSSs), core promoter structure and regulatory element groups (REGs) as putative and comprehensive transcriptional regulatory elements. Microarray data-based predictions have been appended as REG annotations which inform their putative physiological roles.

ddCt
type: Resource
type: NamedIndividual
has db xref: OMICS_02312
synonym: Delta-Delta-Ct
IAO_0000115: Software package providing an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. It requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The package implements a pipeline to collect, analyze and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions.

Louisiana State University Health Sciences Center, Department of Pharmacology, Toxicology and Neuroscience
type: Organization
type: NamedIndividual
has db xref: nif-0000-01984
synonym: Louisiana State University Health Sciences Center Department of Pharmacology Toxicology Neuroscience
synonym: LSUHSC Shreveport; Department of Pharmacology Toxicology & Neuroscience
synonym: LSUHSC Shreveport; Department of Pharmacology Toxicology and Neuroscience
synonym: LSUHSCS Department of Pharmacology Toxicology & Neuroscience
synonym: LSUHSCS Department of Pharmacology Toxicology and Neuroscience
abbrev: LSUHSCS Pharmacology Toxicology and Neuroscience
abbrev: LSUHSCS Pharmacology Toxicology Neuroscience
IAO_0000115: A major emphasis of the Department of Pharmacology, Toxicology and Neuroscience is in the areas of neuropharmacology, neuroscience, and toxicology, with research in drug and alcohol addiction research, stress, neurotransmitter receptor function, oxidative mechanisms of toxicity, molecular regulation of toxicity and apoptosis, gene therapy, carcinogenesis and cancer chemoprevention. The Department offers graduate programs of study in neuroscience and toxicology and maintains an NIH training grant for its program of study in drug and alcohol addiction research. An MD/PhD Program and a Summer Undergraduate Pharmacology Research program are also offered.

BrainTrap: Fly Brain Protein Trap Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-32989
synonym: Brain Trap
synonym: Fly Brain Protein Trap Database
abbrev: BrainTrap
IAO_0000115: This database contains information on protein expression in the Drosophila melanogaster brain. It consists of a collection of 3D confocal datasets taken from EYFP expressing protein trap Drosophila lines from the Cambridge Protein Trap project. Currently there are 884 brain scans from 535 protein trap lines in the database. Drosophila protein trap strains were generated by the St Johnston Lab and the Russell Lab at the University of Cambridge, UK. The piggyBac insertion method was used to insert constructs containing splice acceptor and donor sites, StrepII and FLAG affinity purification tags, and an EYFP exon (Venus). Brain images were acquired by Seymour Knowles-Barley, in the Armstrong Lab at the University of Edinburgh. Whole brain mounts were imaged by confocal microscopy, with a background immunohistochemical label added to aid the identification of brain structures. Additional immunohistochemical labeling of the EYFP protein using an anti-GFP antibody was also used in most cases. The trapped protein signal (EYFP / anti-GFP), background signal (NC82 label), and the merged signal can be viewed on the website by using the corresponding channel buttons. In all images the trapped protein / EYFP signal appears green and the background / NC82 channel appears magenta. Original .lsm image files are also available for download.

Loyola University Chicago, Neuroscience
type: Organization
type: NamedIndividual
has db xref: nif-0000-01986
synonym: Loyola University Chicago Stritch School of Medicine; Neuroscience Graduate Program
synonym: LUC Stritch SOM Neuroscience Graduate Program
abbrev: Loyola Neuroscience Graduate Program
IAO_0000115: The Neuroscience Graduate Program at Loyola trains students to become the neuroscientists who will carry on exciting research. Since our program is interdepartmental and interdisciplinary, our students have an exceptionally broad choice of advisors and research topics on which to work. The neuroscience program offers a Ph.D., M.D./Ph.D., and Masters degree. Our students begin working towards their doctorate in neuroscience by first obtaining a broad base of knowledge in the whole field of neuroscience--brain anatomy, physiology, biochemistry, and pharmacology. After selecting a research advisor at the end of the first year, students usually take several electives in the advisor's home department to develop specialization and strength in one particular area. Each student is exposed to various situations where he or she learns how to express their ideas effectively, whether at a graduate seminar or as a teaching assistant in the medical neuroscience course. Throughout their training, students have the opportunity to interact and work closely with faculty and to receive individualized attention that continues until degree completion.

Loyola University Department of Molecular Pharmacology and Experimental Therapeutics
type: Organization
type: NamedIndividual
has db xref: nif-0000-01988
synonym: Loyola Stritch SOM Dept. of Pharmacology and Experimental Therapeutics
synonym: Loyola University Chicago Stritch School of Medicine Department of Molecular Pharmacology and Experimental Therapeutics
synonym: Loyola University Chicago Stritch SOM Department of Pharmacology and Experimental Therapeutics
synonym: Loyola University Chicago Stritch SOM Dept. of Pharmacology and Experimental Therapeutics
synonym: Loyola University Medical Center Department of Molecular Pharmacology and Experimental Therapeutics
synonym: Loyola University Medical Center Department of Pharmacology
synonym: LUC SSOM Department of Molecular Pharmacology and Experimental Therapeutics
synonym: LUC SSOM Department of Pharmacology
abbrev: LUC Department of Pharmacology
abbrev: LUMC Department of Pharmacology
IAO_0000115: Department committed to excellence in teaching and research offering degrees leading to Ph.D., M.S., M.D./Ph.D. and M.S./M.B.A. The commitment to teaching is exemplified by the innovative courses and programs that the department has developed, as well as a departmental emphasis on fostering student-faculty interactions. The department offers Summer Undergraduate Research Opportunities and Postdoctoral positions. Research in Pharmacology encompasses the understanding, prevention and treatment of human disease, and therefore is at the forefront in creating innovative therapeutic interventions to improve the human condition. Research interests of the Departmental faculty include Neuroscience, Cardiovascular, Hematology and Oncology.

GEOSS
type: Resource
type: NamedIndividual
has db xref: OMICS_00764
synonym: Gene Expression Open Source System
synonym: GeneX Va
synonym: GEOSS - Gene Expression Open Source System
synonym: GEOSS Gene Expression Open Source System
IAO_0000115: A complete software system used to store and analyze gene expression data.

Alberta Geological Survey
type: Resource
type: NamedIndividual
has db xref: nlx_157758
abbrev: AGS
IAO_0000115: Portal of geological information, including geology maps, reports, and GIS datasets, to help with the exploration, development and conservation of Alberta's resources.

PReMod
type: Resource
type: NamedIndividual
has db xref: nif-0000-03334
has db xref: OMICS_01873
synonym: Predicted Regulatory Modules
IAO_0000115: Database that describes more than 100,000 computational predicted transcriptional regulatory modules within the human genome. These modules represent the regulatory potential for 229 transcription factors families and are the first genome-wide / transcription factor-wide collection of predicted regulatory modules for the human genome. The algorithm used involves two steps: (i) Identification and scoring of putative transcription factor binding sites using 481 TRANSFAC 7.2 position weight matrices (PWMs) for vertebrate transcription factors. To this end, each non-coding position of the human genome was evaluated for its similarity to each PWM using a log-likelihood ratio score with a local GC-parameterized third-order Markov background model. Corresponding orthologous positions in mouse and rat genomes were evaluated similarly and a weighted average of the human, mouse, and rat log-likelihood scores at aligned positions (based on a Multiz (Blanchette et al. 2004) genome-wide alignment of these three species) was used to define the matrix score for each genomic position and each PWM. (ii) Detection of clustered putative binding sites. To assign a module score to a given region, the five transcription factors with the highest total scoring hits are identified, and a p-value is assigned to the total score observed of the top 1, 2, 3, 4, or 5 factors. The p-value computation takes into consideration the number of factors involved (1 to 5), their total binding site scores, and the length and GC content of the region under evaluation. Users can retrieve all information for a given region, a given PWM, a given gene and so on. Several options are given for textual output or visualization of the data.

Marquette University, Neuroscience
type: Organization
type: NamedIndividual
has db xref: nif-0000-01990
synonym: Marquette University College of Health Sciences Biomedical Sciences Neuroscience Graduate Program
synonym: Marquette University College of Health Sciences Neuroscience Graduate Program
synonym: Marquette University Neuroscience Graduate Program
abbrev: Marquette Neuroscience
abbrev: Marquette Neuroscience Graduate Program
IAO_0000115: Neuroscience specialization in Graduate Program in Biological Sciences at Marquette University brings together researchers from Departments of Biological and Biomedical Sciences at Marquette to offer quality graduate education in the field of neuroscience with the goal of training students for careers as neuroscience researchers and educators. The specialization is for students who wish to pursue a Ph.D. degree. The collaborative and multi-disciplinary neuroscience research environment at Marquette is supported by the Integrative Neuroscience Research Center (INRC), a consortium of researchers committed to advancing neuroscience research and education at Marquette. The Neuroscience Graduate Program offers the opportunity to conduct research in a collaborative, intellectually rigorous environment, with access to the most modern research tools.

Ontology Development and Information Extraction
type: Resource
type: NamedIndividual
has db xref: nif-0000-33009
synonym: ODIE - Ontology Enrichment & Information Extraction
abbrev: ODIE
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023. A software toolkit to code document sets with ontologies or to enrich existing ontologies with new concepts from the document set. It contains algorithms for Named Entity Recognition, Co-reference resolution, concept discovery, discourse reasoning and attribute value extraction. The project aimed to develop a toolkit that will provide the following functionality: * Build text processing pipelines that use ontologies to annotate documents. * Enrich ontologies with new concepts that are automatically discovered in documents. * Populate an information model automatically from information extracted from documents. ODIE is open source software released under the LGPL v3.0 License. ODIE is written in Java and uses the Eclipse RCP Framework for the UI. The source code is organized into Eclipse projects.

EasyqpcR
type: Resource
type: NamedIndividual
has db xref: OMICS_02313
IAO_0000115: Software package for low-throughput real-time quantitative PCR data analysis. The package allows you to import easily qPCR data files. Thereafter, you can calculate amplification efficiencies, relative quantities and their standard errors, normalization factors based on the best reference genes choosen (using the SLqPCR package), and then the normalized relative quantities, the NRQs scaled to your control and their standard errors.

NanoStriDE
type: Resource
type: NamedIndividual
has db xref: OMICS_02307
synonym: NanoStriDE - NanoString Differential Expression
synonym: NanoString Differential Expression
IAO_0000115: Web application that accepts the raw count data produced by the NanoString nCounter analysis system, normalizes it according to guidelines provided by NanoString Technologies, performs differential expression analysis on the normalized data, and provides a heatmap of the results from the differential expression analysis.

GeneChip Operating Software
type: Resource
type: NamedIndividual
has db xref: nif-0000-33019
synonym: DNA Array Core Facility GeneChip Operating Software
synonym: DNA Array Core Facility GeneChip Operating Software (GCOS)
synonym: GeneChip Operating Software (GCOS)
abbrev: GCOS
IAO_0000115: Affymetrix has recently released a new software for the acquisition, management, and analysis of gene expression data. The new GeneChip Operating Software (GCOS) platform enables researchers to perform gene expression, SNP mapping and resequencing analysis with integrated data management and scalable client server configurations. * Compatible with additional Affymetrix analysis software such as Data Mining Tool (DMT) and GeneChip DNA Analysis Software (GDAS) * Supports Gene Expression, Resequencing and Genotyping Applications * Baseline Comparison Analysis Input: Affymetrix .DAT file Output: Affymetrix files (.CEL, .CHP, .RPT, .EXP, .TXT) Availability: The Core Facility has a copy of GCOS, as well as an older version of the Affymetrix software, Microarray Suite (MAS), available for use upon request.

caTRIP
type: Resource
type: NamedIndividual
has db xref: nif-0000-33400
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE documented June 4, 2013. Allows users to query across a number of caBIG data services, join on common data elements (CDEs), and view results in a user-friendly interface. With an initial focus on enabling outcomes analysis, caTRIP allows clinicians to query across data from existing patients with similar characteristics to find treatments that were administered with success. In doing so, caTRIP can help inform treatment and improve patient care, as well as enable the searching of available tumor tissue, enable locating patients for clinical trials, and enable investigating the association between multiple predictors and their corresponding outcomes such as survival caTRIP relies on the vast array of open source caBIG applications, including: * Tumor Registry, a clinical system that is used to collect endpoint data * cancer Text Information Extraction System (caTIES), a locator of tissue resources that works via the extraction of clinical information from free text surgical pathology reports. while using controlled terminologies to populate caBIG-compliant data structures * caTissue CORE, a tissue bank repository tool for biospecimen inventory, tracking, and basic annotation * Cancer Annotation Engine (CAE), a system for storing and searching pathology annotations * caIntegrator, a tool for storing, querying, and analyzing translational data, including SNP data Requires Java installation and network connectivity.

Honig Lab
type: Resource
type: NamedIndividual
has db xref: nif-0000-33026
synonym: Honig Laboratory
IAO_0000115: Laboratory portal, including software, web-based tools, databases and data sets, related to their research that focuses on the development and application of biophysical and bioinformatics methods aimed at understanding the structural and energetic origins of protein-protein, protein-nucleic acid, and protein-membrane interactions. Their work includes fundamental theoretical research, the development of software tools, and applications to problems of biological importance. In this regard they maintain an active collaborative computational and experimental research program on the molecular basis of cell-cell adhesion. Other problems of current interest include protein structure prediction, the organization of protein sequence/structure space, the prediction of protein function based on protein structure, the structural origins of specificity in protein-DNA interactions, RNA function and, more generally, the electrostatic properties of biological macromolecules.

Proteomics Identifications (PRIDE)
type: Resource
type: NamedIndividual
has db xref: biotools:pride
has db xref: nif-0000-03336
has db xref: r3d100011515
synonym: PRIDE
synonym: PRIDE Archive
synonym: PRIDE Archive - proteomics data repository
synonym: Proteomics Identifications
synonym: PRoteomics IDEntifications database
synonym: PRoteomics IDEntifications database (PRIDE)
IAO_0000115: Centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. Originally it was developed to provide a common data exchange format and repository to support proteomics literature publications. This remit has grown with PRIDE, with the hope that PRIDE will provide a reference set of tissue-based identifications for use by the community. The future development of PRIDE has become closely linked to HUPO PSI. PRIDE encourages and welcomes direct user submissions of protein and peptide identification data to be published in peer-reviewed publications. Users may Browse public datasets, use PRIDE BioMart for custom queries, or download the data directly from the FTP site. PRIDE has been developed through a collaboration of the EMBL-EBI, Ghent University in Belgium, and the University of Manchester.

PRINTS
type: Resource
type: NamedIndividual
has db xref: nif-0000-03338
IAO_0000115: Compendium of protein fingerprints. Diagnostic fingerprint database.

GBSA
type: Resource
type: NamedIndividual
has db xref: OMICS_00600
synonym: GBSA - Genome-Wide Bisulfite Sequencing Analyser Software
synonym: Genome-Wide Bisulfite Sequencing Analyser Software
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. Software for analyzing whole-genome bisulfite sequencing data.

Pristionchus.org
type: Resource
type: NamedIndividual
has db xref: nif-0000-03339
synonym: www.pristionchus.org
IAO_0000115: This data resource is a genetic, molecular, and genomic toolkit that establishes one particular species, Pristionchus pacificus, as a major satellite system for evolutionary developmental biology. Users may download Pristionchus Sequences and use the Pristionchus pacificus genome browser where they may find gene or gene prediction data. Users can also use the BLAST feature, which allows users to search the assembly for position information of bacs, reads and contigs using the mapping tool. The center of the site's research is the evolutionary analysis of vulva formation. The general aim of the Department is to develop the nematode vulva as a suitable case study into the evolutionary alterations of developmental processes. By studying and comparing two distantly related species of the same phylum, such as P. pacificus and C. elegans, macroevolutionary alterations of developmental processes and mechanisms can be identified. The final goal of the Department is to achieve a comprehensive description of macro- and microevolutionary changes of developmental mechanisms at the molecular level in a phylogenetic and ecological context.

ASAP: the Alternative Splicing Annotation Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-33105
synonym: Alternative Splicing
synonym: Alternative Splicing Annotation Project
synonym: Alternative Splicing Annotation Project database
abbrev: ASAP
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on 8/12/13. Database to access and mine alternative splicing information coming from genomics and proteomics based on genome-wide analyses of alternative splicing in human (30 793 alternative splice relationships found) from detailed alignment of expressed sequences onto the genomic sequence. ASAP provides precise gene exon-intron structure, alternative splicing, tissue specificity of alternative splice forms, and protein isoform sequences resulting from alternative splicing. They developed an automated method for discovering human tissue-specific regulation of alternative splicing through a genome-wide analysis of expressed sequence tags (ESTs), which involves classifying human EST libraries according to tissue categories and Bayesian statistical analysis. They use the UniGene clusters of human Expressed Sequence Tags (ESTs) to identify splices. The UniGene EST's are clustered so that a single cluster roughly corresponds to a gene (or at least a part of a gene). A single EST represents a portion of a processed (already spliced) mRNA. A given cluster contains many ESTs, each representing an outcome of a series of splicing events. The ESTs in UniGene contain the different mRNA isoforms transcribed from an alternatively spliced gene. They are not predicting alternative splicing, but locating it based on EST analysis. The discovered splices are further analyzed to determine alternative splicing events. They have identified 6201 alternative splice relationships in human genes, through a genome-wide analysis of expressed sequence tags (ESTs). Starting with 2.1 million human mRNA and EST sequences, they mapped expressed sequences onto the draft human genome sequence and only accepted splices that obeyed the standard splice site consensus. After constructing a tissue list of 46 human tissues with 2 million human ESTs, they generated a database of novel human alternative splices that is four times larger than our previous re…

Childrens Hospital of Philadelphia - Research Institute; Pennsylvania; USA
type: Organization
type: NamedIndividual
has db xref: Crossref Funder ID 100006458
has db xref: GRID grid.239552.a
has db xref: ISNI 0000000106808770
has db xref: nlx_151872
has db xref: Wikidata Q4569202
synonym: Children''s Hospital of Philadelphia - Research Institute
synonym: Children''s Hospital of Philadelphia - Research Institute; Pennsylvania; USA
synonym: Children's Hospital of Philadelphia (CHOP) Research Institute
synonym: Childrens Hospital of Philadelphia - Research Institute
abbrev: CHOP
IAO_0000115: Scientific organization dedicated to advancing pediatric medicine through translational research. Founded in 1922, it is currently one of the largest pediatric research programs in the United States.

probeBase
type: Resource
type: NamedIndividual
has db xref: nif-0000-03340
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. A database of probes and microbes that can be searched for target organisms, probe names, probe sequences, probe accession numbers, and references. The search target site function can assist in the development of new rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization (FISH), while the match tool can be used to rapidly retrieve all published probes targeting your query sequences (e.g. from a rRNA gene clone library) without prior phylogenetic analysis. probeBase is hyperlinked with PubMed, RDP-II, and Greengenes to provide additional bibliographic information and up-to-date data on probe specificity. Ribosomal RNA (rRNA) targeted oligonucleotide probes are widely used for fluorescence in situ, dot blot, and microarray hybridization in culture-independent studies of microbial communities and for the identification of uncultured prokaryotes in clincal and environmental samples. probeBase is a comprehensive database containing published rRNA-targeted oligonucleotide probe sequences, DNA microarray layouts and associated information.

LaSSO
type: Resource
type: NamedIndividual
has db xref: OMICS_04622
synonym: Lariat Sequence Site Origin
IAO_0000115: An R script that creates a FASTA database containing all possible lariat signatures from a given set of introns.

NAPPA
type: Resource
type: NamedIndividual
has db xref: OMICS_02310
synonym: NAPPA: Performs the processing and normalisation of Nanostring miRNA and mRNA data
IAO_0000115: Software that enables the processing and normalization of the standard mRNA data output from the Nanostring nCounter software.

nSolver Analysis Software
type: Resource
type: NamedIndividual
has db xref: OMICS_02309
IAO_0000115: Data analysis software program that offers nCounter users the ability to QC, normalize, and analyze data without having to purchase additional software packages.

Euro-Diagnostica
type: Organization
type: NamedIndividual
has db xref: nlx_152360
IAO_0000115: Antibody supplier.

MAGENTA
type: Resource
type: NamedIndividual
has db xref: OMICS_00236
synonym: Meta-Analysis Gene-set Enrichment of variaNT Associations
IAO_0000115: A computational tool that tests for enrichment of genetic associations in predefined biological processes or sets of functionally related genes, using genome-wide genetic data as input.

Ontology for Genetic Interval
type: Resource
type: NamedIndividual
has db xref: nlx_157517
abbrev: OGI
IAO_0000115: An ontology that formalized the genomic element by defining an upper class genetic interval using BFO as its framework. The definition of genetic interval is the spatial continuous physical entity which contains ordered genomic sets (DNA, RNA, Allele, Marker,etc.) between and including two points (Nucleic_Acid_Base_Residue) on a chromosome or RNA molecule which must have a liner primary sequence structure.

MiMI Plugin for Cytoscape
type: Resource
type: NamedIndividual
has db xref: nif-0000-33090
synonym: Cytoscape Plugin for MiMI
synonym: MiMI Plugin - Cytoscape Plugin for MiMI
abbrev: MiMI Plugin
IAO_0000115: The Cytoscape MiMI Plugin is an open source interactive visualization tool that you can use for analyzing protein interactions and their biological effects. The Cytoscape MiMI Plugin couples Cytoscape, a widely used software tool for analyzing bimolecular networks, with the MiMI database, a database that uses an intelligent deep-merging approach to integrate data from multiple well-known protein interaction databases. The MiMI database has data on 119,880 molecules, 330,153 interactions, and 579 complexes. By querying the MiMI database through Cytoscape you can access the integrated molecular data assembled in MiMI and retrieve interactive graphics that display protein interactions and details on related attributes and biological concepts. You can interact with the visualization by expanding networks to the next nearest neighbors and zooming and panning to relationships of interest. You also can perceptually encode nodes and links to show additional attributes through color, size and the visual cues. You can edit networks, link out to other resources and tools, and access information associated with interactions that has been mined and summarized from the research literature information through a biology natural language processing database (BioNLP) and a multi-document summarization system, MEAD. Additionally, you can choose sub-networks of interest and use SAGA, a graph matching tool, to match these sub-networks to biological pathways.

Mindtouch DekiWiki
type: Commercial Organization
type: NamedIndividual
has db xref: nif-0000-33097
synonym: Deki Wiki
synonym: DekiWiki
synonym: MindTouch (frmly deki wiki)
synonym: MindTouch Core
synonym: MindTouch Deki Wiki
abbrev: MindTouch
IAO_0000115: A web based social authoring and publishing environment that adheres to open standards and RESTful design principals. It provides wiki-like ease of use with a sophisticated web services framework for rapid application development, creating flexible workflows and rapid integration. MindTouch creates a vibrant real-time information fabric by federating content from across enterprise silos, such as CRM, ERP, file servers, email, databases, web services and more.

China Agricultural University; Beijing; China
type: NamedIndividual
has db xref: nlx_149089
synonym: China Agricultural University
abbrev: CAU

Ontology for Parasite LifeCycle
type: Resource
type: NamedIndividual
has db xref: nlx_157521
abbrev: OPL
IAO_0000115: A reference ontology that models the life cycle stage details of various parasites, including Trypanosoma sp., Leishmania major, and Plasmodium sp., etc. In addition to life cycle stages, the ontology also models necessary contextual details, such as host information, vector information, and anatomical location. OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium.

Ontology of Adverse Events
type: Resource
type: NamedIndividual
has db xref: nlx_157522
abbrev: OAE
IAO_0000115: Biomedical ontology in the domain of adverse events that aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. AEO is a community-based ontology. Its development follows the OBO Foundry principles.

MetABEL
type: Resource
type: NamedIndividual
has db xref: OMICS_00237
IAO_0000115: Software for meta-analysis of genome-wide SNP association results.

NeuroImaging Tools and Resources Collaboratory (NITRC)
type: Resource
type: NamedIndividual
has db xref: nif-0000-00202
has db xref: r3d100010784
has db xref: r3d100011515
synonym: Neuroimaging Informatics Tools and Resources Clearinghouse
synonym: Neuroimaging Informatics Tools Resources Clearinghouse
synonym: NeuroImaging Tools and Resources Collaboratory
synonym: NITRC - Neuroimaging Informatics Tools and Resources Clearinghouse
synonym: NITRC - Neuroimaging Informatics Tools Resources Clearinghouse
abbrev: NITRC
IAO_0000115: Software repository for comparing structural (MRI) and functional neuroimaging (fMRI, PET, EEG, MEG) software tools and resources. NITRC collects and points to standardized information about structural or functional neuroimaging tool or resource.

ProNIT
type: Resource
type: NamedIndividual
has db xref: nif-0000-03347
has db xref: OMICS_00541
IAO_0000115: Database that provides experimentally determined thermodynamic interaction data between proteins and nucleic acids. It contains the properties of the interacting protein and nucleic acid, bibliographic information and several thermodynamic parameters such as the binding constants, changes in free energy, enthalpy and heat capacity.

Nature Online Video Streaming Archive
type: Resource
type: NamedIndividual
has db xref: nlx_144531
synonym: naturevideo
abbrev: Nature Video
IAO_0000115: For selected articles and letters Nature presents streaming videos featuring interviews with scientists behind the research and analysis from Nature editors. To view the videos you will need the free Flash browser plugin. You can also visit the Nature Video YouTube channel which enables you to easily embed and share our videos through websites, mobile devices, blogs and email.

ProbeMatchDB 2.0
type: Resource
type: NamedIndividual
has db xref: nif-0000-33156
abbrev: ProbeMatchDB
IAO_0000115: Matches a list of microarray probes across different microrarray platforms (GeneChip, EST from different vendors, Operon Oligos) and species (human, mouse and rat), based on NCBI UniGene and HomoloGene. The capability to match protein sequence IDs has just been added to facilitate proteomic studies. The ProbeMatchDB is mainly used for the design of verification experiments or comparing the microarray results from different platforms. It can be used for finding equivalent EST clones in the Research Genetics sequence verified clone set based on results from Affymetirx GeneChips. It will also help to identify probes representing orthologous genes across human, mouse and rat on different microarray platforms.

Substructure Index-based Approximate Graph Alignment
type: Resource
type: NamedIndividual
has db xref: nif-0000-33157
synonym: SAGA (Substructure Index-based Approximate Graph Alignment)
synonym: SAGA - Substructure Index-based Approximate Graph Alignment
synonym: SAGA: A Fast and Flexible Graph Matching Tool
abbrev: SAGA
IAO_0000115: SAGA (Substructure Index-based Approximate Graph Alignment) is a tool for querying a biological graph database to retrieve matches between subgraphs of molecular interactions and biological networks. SAGA implements an efficient approximate subgraph matching algorithm that can be used for a variety of biological graph matching problems such as the pathway matching SAGA uses to compare pathways in KEGG and Reactome. You can also use SAGA to find matches in literature databases that have been parsed into semantic graphs. In this use of SAGA, portions of PubMed have been parsed into graphs that have nodes representing gene names. A link is drawn between two genes if they are discussed in the same sentence (indicating there is potential association between the two genes). SAGA lets you match graphs between different databases even though the content is distinct and the databases organize pathways in different ways. This cross-database matching is achieved by SAGA's flexible approximate subgraph matching model that computes graph similarity, and allows for node gaps, node mismatches, and graph structural differences. Comparing pathways from different databases can be a useful precursor to pathway data integration. SAGA is very efficient for querying relatively small graphs, but becomes prohibitory expensive for querying large graphs. Large graph data sets are common in many emerging database applications, and most notably in large-scale scientific applications. To fully exploit the wealth of information encoded in graphs, effective and efficient graph matching tools are critical. Due to the noisy and incomplete nature of real graph datasets, approximate, rather than exact, graph matching is required. Furthermore, many modern applications need to query large graphs, each of which has hundreds to thousands of nodes and edges. TALE is an approximate subgraph matching tool for matching graph queries with a large number of nodes and edges. TALE employs a novel indexing techni…

genomation
type: Resource
type: NamedIndividual
has db xref: biotools:genomation
has db xref: OMICS_02306
IAO_0000115: Software R package for simplfiying common tasks in genomic feature analysis. Toolkit to summarize, annotate and visualize genomic intervals. Provides functions for reading BED and GFF files as GRanges objects, summarizing genomic features over predefined windows so users can make average enrichment of features over defined regions or produce heatmaps. Can annotate given regions with other genomic features such as exons,introns and promoters.

Gene Reference into Function
type: Resource
type: NamedIndividual
has db xref: nlx_157765
synonym: GeneRIF: Gene Reference into Function
abbrev: GeneRIF
IAO_0000115: A database and annotation tool that provides a simple mechanism to allow scientists to add to the functional annotation of genes described in Gene. To be processed, a valid Gene ID must exist for the specific gene, or the Gene staff must have assigned an overall Gene ID to the species. The latter case is implemented via records in Gene with the symbol NEWENTRY.

Massachusetts Institute of Technology; Department of Brain and Cognitive Sciences
type: Organization
type: NamedIndividual
has db xref: nif-0000-01995
synonym: Massachusetts Institute of Technology; Department of Brain Cognitive Sciences
synonym: MIT Brain and Cognitive Sciences
synonym: MIT Department of Brain and Cognitive Sciences
synonym: MIT Dept. of Brain and Cognitive Sciences
abbrev: MIT BCS
IAO_0000115: MIT's Department of Brain and Cognitive Sciences stands at the nexus of neuroscience, biology and psychology. We combine these disciplines to study specific aspects of the brain and mind including: vision, movement systems, learning and memory, neural and cognitive development, language and reasoning. Together, MIT's Department of Brain and Cognitive Sciences offers extraordinary learning opportunities for undergraduate, graduate and postdoctoral students. Because the human brain is immensely complex in many different ways at once, we pursue every level of inquiry - from molecules to cells to circuits to the mystery of the mind itself. As we study its diseases and disorders, its development and daily feats, like vision, speech, movement and memory, we also integrate methods and insights from every area of brain research. This unusual diversity of expertise fosters an intensely creative atmosphere that sparks startling collaborations. Already known for remarkable contributions to the field, our faculty members continually stretch the limits of knowledge, and bring the same passion to educating our exceptional students. A key part of the BCS mission is to offer its graduate and undergraduate students an educational experience of the highest quality. Our graduate students benefit from the impressive range of our program, and from the ability to participate in research projects with faculty members who are leaders in their fields. The department's undergraduate program, which includes both neuroscience and cognitive science, is one of the fastest-growing majors at MIT.

National Mesothelioma Virtual Bank
type: Resource
type: NamedIndividual
has db xref: nif-0000-33179
synonym: Mesothelioma Virtual Bank
synonym: MVB
abbrev: NMVB
IAO_0000115: A virtual biospecimen registry designed to support and facilitate basic science, clinical, and translational research that will advance understanding of mesothelioma pathophysiology with the goal of expediting the discovery of preventive measures, novel therapeutic interventions, and ultimately, cures for mesothelioma. The NMVB resource is designed to provide mesothelioma tissue samples with high-quality and well-characterized multimodal annotated data to researchers. The NMVB team strongly believes that progress in translational and clinical research - in cancer as well as other disease areas - depends on the ability of researchers to access high-quality tissue that is associated with meaningful annotation. MVB database version 3.0 has been released that provides researchers real-time access to demographic, epidemiologic, pathologic, genotype, and follow-up data associated with biospecimens at no cost. Researchers interested in utilizing NMVB samples for their research may submit an application. All researchers (academic or commercial, United States or foreign) may apply for NMVB tissue specimens. NMVB currently has 966 annotated cases and 1198 biospecimens including: * Paraffin Embedded Tissue * Fresh Frozen Tissue * Blood and DNA Samples The NMVB also has developed mesothelioma tissue microarrays (TMAs) with associated multimodal data annotation. Additional TMAs will be available shortly.

Ontology of Medically Related Social Entities
type: Resource
type: NamedIndividual
has db xref: nlx_157534
abbrev: OMRSE
IAO_0000115: An ontology covering the domain of social entities that are related to health care, such as demographic information (social entities for recording gender (but not sex) and marital status, for example) and the roles of various individuals and organizations (patient, hospital, etc.)

Chinese University of Hong Kong; Hong Kong; China
type: Organization
type: NamedIndividual
has db xref: GRID: grid.10784.3a; ISNI: 0000 0004 1937 0482; Crossref Funder ID: 501100004853; Wikidata: Q15570;
has db xref: nlx_60377
synonym: CUHK
IAO_0000115: Public research university in Sha Tin, New Territories, Hong Kong.

Proteome Commons Tranche repository
type: Resource
type: NamedIndividual
has db xref: nif-0000-33195
synonym: Tranche Project
abbrev: Tranche
IAO_0000115: A distributed file storage system that you can upload files to and download files from. All files uploaded to the repository are replicated several times to protect against their accidental loss. Files uploaded to the repository can be of any size, can be of any file type, and can be encrypted with a passphrase of your choosing. The Proteome Commons Tranche repository is the first instance of a Tranche repository. Tranche, was created so that anybody can take it and make their own Tranche repository. This is the first implementation of the Tranche software, and is useful as a test bed for the software. This repository relies on educational institutions to provide the hardware and facilities for Tranche servers. While we maintain a set of servers, the continued growth of this public resource will rely on the generosity of the institutions that use the repository most.

Ontology of Vaccine Adverse Events
type: Resource
type: NamedIndividual
has db xref: nlx_157538
abbrev: OVAE
IAO_0000115: A biomedical ontology in the area of vaccine adverse events aimed to represent and analyze various vaccine-specific adverse events. OVAE is an extension of the Ontology of Adverse Events (OAE) and the Vaccine Ontology (VO).

metagen
type: Resource
type: NamedIndividual
has db xref: biotools:metagen
has db xref: OMICS_00238
IAO_0000115: Software program providing a method for meta-analysis of case-control genetic association studies using random-effects logistic regression.

caTIES - Cancer Text Information Extraction System
type: Resource
type: NamedIndividual
has db xref: nif-0000-33212
synonym: Cancer Text Information Extraction System
synonym: Cancer Text Information Extraction System (caTIES)
abbrev: caTIES
IAO_0000115: The Cancer Text Information Extraction System (caTIES) provides tools for de-identification and automated coding of free-text structured pathology reports. It also has a client that can be used to search these coded reports. The client also supports Tissue Banking and Honest Broker operations. caTIES focuses on two important challenges of bioinformatics * Information extraction (IE) from free text * Access to tissue. Regarding the first challenge, information from free-text pathology documents represents a vital and often underutilized source of data for cancer researchers. Typically, extracting useful data from these documents is a slow and laborious manual process requiring significant domain expertise. Application of automated methods for IE provides a method for radically increasing the speed and scope with which this data can be accessed. Regarding the second challenge, there is a pressing need in the cancer research community to gain access to tissue specific to certain experimental criteria. Presently, there are vast quantities of frozen tissue and paraffin embedded tissue throughout the country, due to lack of annotation or lack of access to annotation these tissues are often unavailable to individual researchers. caTIES has three goals designed to solve these problems: * Extract coded information from free text Surgical Pathology Reports (SPRs), using controlled terminologies to populate caBIG-compliant data structures. * Provide researchers with the ability to query, browse and create orders for annotated tissue data and physical material across a network of federated sources. With caTIES the SPR acts as a locator to tissue resources. * Pioneer research for distributed text information extraction within the context of caBIG. caTIES focuses on IE from SPRs because they represent a high-dividend target for automated analysis. There are millions of SPRs in each major hospital system, and SPRs contain important information for researchers. SPRs act as tissue l…

REDCap
type: Resource
type: NamedIndividual
has db xref: nif-0000-33254
synonym: RED Cap
synonym: Research Electronic Data Capture
synonym: The REDCap Consortium
IAO_0000115: Web application that allows users to build and manage online surveys and databases. Using REDCap's stream-lined process for rapidly developing projects, you may create and design projects using 1) the online method from your web browser using the Online Designer; and/or 2) the offline method by constructing a "data dictionary" template file in Microsoft Excel, which can be later uploaded into REDCap. Both surveys and databases (or a mixture of the two) can be built using these methods. REDCap provides audit trails for tracking data manipulation and user activity, as well as automated export procedures for seamless data downloads to Excel, PDF, and common statistical packages (SPSS, SAS, Stata, R). Also included are a built-in project calendar, a scheduling module, ad hoc reporting tools, and advanced features, such as branching logic, file uploading, and calculated fields. REDCap has a quick and easy software installation process, so that you can get REDCap running and fully functional in a matter of minutes. Several language translations have already been compiled for REDCap (e.g. Chinese, French, German, Portuguese), and it is anticipated that other languages will be available in full versions of REDCap soon. The REDCap Shared Library is a repository for REDCap data collection instruments and forms that can be downloaded and used by researchers at REDCap partner institutions.

BMIQ
type: Resource
type: NamedIndividual
has db xref: OMICS_02304
synonym: Beta MIxture Quantile dilation
synonym: bmiq - Beta Mixture Quantile Model
IAO_0000115: Software using a beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data.

miniTUBA
type: Resource
type: NamedIndividual
has db xref: nif-0000-33272
synonym: Medical Inference by Network Integration of Temporal Data using Bayesian Analysis tool
synonym: Medical Inference by Network Integration of Temporal Data using Bayesian Analysis tool (miniTUBA)
synonym: miniTUBA - Medical Inference by Network Integration of Temporal Data using Bayesian Analysis tool
synonym: The Medical Inference by Network Integration of Temporal Data using Bayesian Analysis tool
IAO_0000115: miniTUBA is a web-based modeling system that allows clinical and biomedical researchers to perform complex medical/clinical inference and prediction using dynamic Bayesian network analysis with temporal datasets. The software allows users to choose different analysis parameters (e.g. Markov lags and prior topology), and continuously update their data and refine their results. miniTUBA can make temporal predictions to suggest interventions based on an automated learning process pipeline using all data provided. Preliminary tests using synthetic data and laboratory research data indicate that miniTUBA accurately identifies regulatory network structures from temporal data. miniTUBA represents in a network view possible influences that occur between time varying variables in your dataset. For these networks of influence, miniTUBA predicts time courses of disease progression or response to therapies. minTUBA offers a probabilistic framework that is suitable for medical inference in datasets that are noisy. It conducts simulations and learning processes for predictive outcomes. The DBN analysis conducted by miniTUBA describes from variables that you specify how multiple measures at different time points in various variables influence each other. The DBN analysis then finds the probability of the model that best fits the data. A DBN analysis runs every combination of all the data; it examines a large space of possible relationships between variables, including linear, non-linear, and multi-state relationships; and it creates chains of causation, suggesting a sequence of events required to produce a particular outcome. Such chains of causation networks - are difficult to extract using other machine learning techniques. DBN then scores the resulting networks and ranks them in terms of how much structured information they contain compared to all possible models of the data. Models that fit well have higher scores. Output of a miniTUBA analysis provides the ten top-scoring net…

FadE
type: Resource
type: NamedIndividual
has db xref: OMICS_00599
synonym: fade - Estimation of position specific methylation parameters in color or nucleotide space with NR optimization
IAO_0000115: A software package designed to determine the methylation parameter at each cytosine or cytosine-guanine position in the human genome. FadE uses color reads produced by the SOLiD sequencer or nucleotide reads produced by the Illumina or 454 sequencing platforms.

Rat Strain Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157544
has db xref: nlx_157569
IAO_0000115: Ontology that defines hierarchical display of different rat strains as derived from parental strains. Ontology Browser allows to retrieve all genes, QTLs, strains and homologs annotated to particular term. Covers all types of biological pathways including altered and disease pathways, and to capture relationships between them within hierarchical structure. Five nodes of ontology include classic metabolic, regulatory, signaling, drug and disease pathways. Ontology allows for standardized annotation of rat. Serves as vehicle to connect between genes and ontology reports, between reports and interactive pathway diagrams, between pathways that directly connect to one another within diagram or between pathways that in some fashion are globally related in pathway suites and suite networks.

metaphor
type: Resource
type: NamedIndividual
has db xref: OMICS_00240
synonym: The metafor package
synonym: The metafor package: A meta-analysis package for R
IAO_0000115: A free and open-source add-on for conducting meta-analyses with the statistical software environment R.

Einstein-Montefiore ICTR Research Informatics Core
type: Resource
type: NamedIndividual
has db xref: nif-0000-33284
synonym: Einstein-Montefiore Institute for Clinical & Translational Research - Research Informatics Core
synonym: Einstein-Montefiore Institute for Clinical and Translational Research - Research Informatics Core
synonym: Research Informatics Core - Einstein-Montefiore Institute for Clinical and Translational Research (ICTR)
abbrev: Einstein-Montefiore ICTR RIC
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Primary informatics resource for joint research efforts of the Albert Einstein College of Medicine and Montefiore Medical Center to facilitate the study and understanding of biological processes, clinical disorders, pathologic abnormalities, and the relationships among them, using a wide variety of informatics techniques, applications, and user training. Their services include: * Collaboration on research design to enable effective data management throughout all phases of a project * Provision of management capability for large volumes of data generated by microarrays and related technologies * Provision and supports a software toolchest for data capture, retrieval, and analysis * Design and implementation of custom interfaces to incorporate existing or separately designed databases into the central data management architecture * Support for data management for the Biorepository, to enhance specimen storage, identification, and linkage with clinical data * Ensuring conformity of data elements and structures to national standards via participation in standards organizations, facilitating intramural and extramural collaboration * Providing individualized support to end-users with bioinformatics training needs * Serving as a bioinformatics liaison to other research institutes and organizations * Providing data management support for clinical research * Providing a common, secure repository for clinical, experimental, and biosample storage data

T-profiler
type: Resource
type: NamedIndividual
has db xref: biotools:t-profiler
has db xref: nif-0000-33354
synonym: T-profiler: Scoring the Activity of Pre-defined Groups of Genes Using Gene Expression Data
IAO_0000115: One of the key challenges in the analysis of gene expression data is how to relate the expression level of individual genes to the underlying transcriptional programs and cellular state. The T-profiler tool hosted on this website uses the t-test to score changes in the average activity of pre-defined groups of genes. The gene groups are defined based on Gene Ontology categorization, ChIP-chip experiments, upstream matches to a consensus transcription factor binding motif, and location on the same chromosome, respectively. If desired, an iterative procedure can be used to select a single, optimal representative from sets of overlapping gene groups. A jack-knife procedure is used to make calculations more robust against outliers. T-profiler makes it possible to interpret microarray data in a way that is both intuitive and statistically rigorous, without the need to combine experiments or choose parameters. Currently, gene expression data from Saccharomyces cerevisiae and Candida albicans are supported. Users can submit their microarray data for analysis by clicking on one of the two organism-specific tabs above. Platform: Online tool

Stanford Translational Research Integrated Database Environment and Clinical Data Warehouse
type: Resource
type: NamedIndividual
has db xref: nif-0000-33359
synonym: STRIDE and the Clinical Data Warehouse
synonym: STRIDE Clinical Data Warehouse
abbrev: STRIDE
abbrev: STRIDE and the CDW
IAO_0000115: Research and development project at Stanford University to create a standards-based informatics platform supporting clinical and translational research. STRIDE consists of three integrated components: a clinical data warehouse, based on the HL7 Reference Information Model (RIM), containing clinical information on over 1.6 million pediatric and adult patients cared for at Stanford University Medical Center since 1995; an application development framework for building research data management applications on the STRIDE platform and a biospecimen data management system. STRIDE's semantic model uses standardized terminologies, such as SNOMED, RxNorm, ICD and CPT, to represent important biomedical concepts and their relationships. STRIDE receives clinical data for research use via HL7 feeds from both SUMC hospitals: Lucile Packard Children's Hospital and Stanford Hospital and Clinics. This clinical data is used to support a wide variety of translational research services including: * Anonymized Patient Research Cohort Discovery * Electronic Chart Review for Research * IRB-Approved Clinical Data Extraction * Biospecimen Data Management * Multimedia Research * Data Management and Research Registries STRIDE is a highly secure environment utilizing encryption, fine-grained access control, robust auditing and detailed data segregation. Additionally, STRIDE has a robust access control framework with well-defined access granting authorities and access control groups. Consequently STRIDE meets or exceeds the requirements of the HIPAA Privacy and Security regulations. Privacy protection is further enhanced by requiring IRB approval for all research projects using STRIDE clinical data. From a technology and standards perspective, STRIDE is hosted on the Oracle 11g database platform. STRIDE application software provides access to the web services of a three-tier infrastructures using SSL encryption with strong authentication. These programs are cross-platform, self-updating thick-c…

GCG/SeqWeb
type: Resource
type: NamedIndividual
has db xref: nif-0000-33361
synonym: GCG
synonym: Genetics Computer Group
synonym: Sequence Analysis Software Package
synonym: SeqWeb GCG
abbrev: GCG SeqWeb
abbrev: GCG-SeqWeb
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVCE, documented January 28, 2019. Core Facility provides the software and support for computer assisted protein and DNA sequence analysis and database access. The Genetics Computer Group GCG-Wisconsin package is currently available on PBRC's UNIX platform that is accessible via modem or direct connection. The package can be accessed via three interfaces: the command-line interface (UNIX C-shell), the web-based interface (SeqWeb) and the X-Windows based graphics interface (SeqLab). Applications in the package include sequence editing, alignment, comparison, primer design, restriction analysis, mapping, data presentation, database browsing, etc. In addition to local databases, access to remote databases (BLAST) is integrated into the package. The local databases are updated quarterly. Databases available include GenBank, EMBL, PIR-Protein, SWISS-PROT and Restriction Enzymes (REBASE).

SWAN
type: Resource
type: NamedIndividual
has db xref: OMICS_02303
synonym: Subset-quantile Within Array Normalization
IAO_0000115: Software that improves the results from the Illumina infinium HumanMethylation450 BeadChips by reducing technical variation within and between arrays. SWAN is available in the minfi Bioconductor package.

Everest Biotech
type: Organization
type: NamedIndividual
has db xref: nlx_152362
IAO_0000115: An Antibody supplier

PROSITE
type: Resource
type: NamedIndividual
has db xref: nif-0000-03351
has db xref: OMICS_01699
synonym: PROSITE - Database of protein domains families and functional sites
IAO_0000115: Database of protein families and domains that is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. ScanProsite finds matches of your protein sequences to PROSITE signatures. PROSITE currently contains patterns and profiles specific for more than a thousand protein families or domains. Each of these signatures comes with documentation providing background information on the structure and function of these proteins. The database is available via FTP.

Medical College of Georgia Department of Physiology
type: Organization
type: NamedIndividual
has db xref: nif-0000-02002
synonym: GHSU MCG Department of Physiology
synonym: GHSU MCG Dept. of Physiology
synonym: MCG Department of Physiology
synonym: MCG Dept. of Physiology
IAO_0000115: Department that trains independent, creative, productive scholars in the physiological sciences. The department offers programs leading to the Ph.D. degree. A combined M.D./Ph.D. or D.M.D./Ph.D. degree program is available for students who obtain prior or concurrent admission to the Schools of Medicine or Dentistry respectively. The primary research interests of the department are Cardiovascular Physiology, Endocrinology, and Neuroscience. Physiology faculty currently hold more than $7,000,000 in extramural funding, ranking 21st out of Medical School Physiology Departments nationally. Members of the Department teach in the Medical and Graduate Schools including Medical Physiology and Intergated Systems Biology, Neuroscience and advanced courses in cardiovascular and endocrine physiology.

Protein Clusters
type: Resource
type: NamedIndividual
has db xref: nif-0000-03354
has db xref: r3d100010861
synonym: Entrez Protein Clusters
synonym: NCBI Protein Clusters
synonym: Protein Clusters Database
abbrev: ProtClustDB
IAO_0000115: Database of related protein sequences (clusters) consisting of proteins derived from the annotations of whole genomes, organelles and plasmids. It currently limited to Archaea, Bacteria, Plants, Fungi, Protozoans, and Viruses. It contains annotation information, publications, domains, structures, and external links and analysis tools including multiple alignments, phylogenetic trees, and genomic neighborhoods (ProtMap). Data is available for download via Protein Clusters FTP

Plant Environmental Conditions
type: Resource
type: NamedIndividual
has db xref: nlx_157554
abbrev: EO
abbrev: PECO
IAO_0000115: A structured controlled vocabulary for the representation of plant environmental conditions.

Plant Trait Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157556
abbrev: PTO
abbrev: TO
IAO_0000115: A controlled vocabulary to describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant, or a plant part.

Population and Community Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157557
abbrev: PCO
IAO_0000115: An ontology that models material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. The PCO is compliant with the Basic Formal Ontology (BFO) and is designed to be compatible with other OBO Foundry ontologies, such as the Gene Ontology (GO), which covers biological processes, and the Phenotypic Quality Ontology (PATO).

Solstice
type: Resource
type: NamedIndividual
has db xref: nif-0000-33380
IAO_0000115: A Web application development framework for Perl. Based on the MVC programming paradigm, it provides a sensible layout for Web applications that helps you write applications faster and with fewer mistakes. Solstice serves as the foundation for a suite of enterprise communication and collaboration tools used at the University of Washington. Many of these tools, such as the WebQ survey and quiz creation application, the UMail anonymous email form, and the CrowdControl module for managing groups of users, are available for download now. More are on the way. They will offer you rich starting points, examples, and solutions for your own applications. Solstice is designed to support large, complex applications that have a serious need for structured navigation. Its state-machine based navigation system ensures that users stay on the paths they need to follow within your Web application. With any mod_perl enabled Apache server, Solstice offers easy installation and proven scalability. Specifically, Solstice provides your application with: * a state-machine based navigation system, * integrated validation, * highly reusable and embeddable page elements, * session management, * user and group models for flexible, built-in authorization, * a development mode for realtime diagnostics, and * a focus on scalability. When you work with Solstice, you can also use Majere, a Web-based development tool that automates the creation of applications and manages their configuration. Majere frees you to focus on the more interesting parts of application development and is available along with Solstice on our Download page. Solstice provides support for RESTful development.

Parseq
type: Resource
type: NamedIndividual
has db xref: biotools:parseq
has db xref: OMICS_02302
IAO_0000115: Statistical software for transcription landscape reconstruction at a basepair resolution from RNA Seq read counts. It is based on a state-space model which describes, in terms of abrupt shifts and more progressive drifts, the transcription level dynamics along the genome. Alongside variations of transcription level, it incorporates a component of short-range variation to pull apart local artifacts causing correlated dispersion. Reconstruction of the transcription level relies on a conditional sequential Monte Carlo approach that is combined with parameter estimation in a Markov chain Monte Carlo algorithm known as particle Gibbs. The method allows to estimate the local transcription level, to call transcribed regions, and to identify the transcript borders.

Software Distribution Sets
type: Resource
type: NamedIndividual
has db xref: nif-0000-33396
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 24, 2013. These distribution sets contain software modules and/or data sets extracted from the Visualization and Analysis Software Tools (VAST) library developed at the Minneapolis VA Medical Center, the University of Minnesota and/or the International Consortium for Neuroimaging (INC) (partially funded by the Human Brain Project )

University of Toledo Health Sciences Campus; Neurosciences
type: Organization
type: NamedIndividual
has db xref: nif-0000-02008
synonym: University of Toledo Health Sciences Campus; Department of Neurosciences
synonym: UT Health Sciences Campus; Dept. of Neurosciences
synonym: UT Health Sciences Campus; Neurosciences
IAO_0000115: The Department of Neurosciences is highly committed to advancing the state of knowledge of nervous system structure and function through a tripartite mission of innovative research, state-of-the-art teaching methods, and dedicated service to the broader academic and surrounding communities. The teaching mission of our Department effectively communicates the current state of knowledge in neuroscience to the medical, graduate, and post-graduate students of the University using innovative methods. We are nationally known for using the most current technologies to teach human anatomy, embryology, and neurobiology to medical and graduate students. We teach critical thinking and problem solving skills and also provide opportunities for the students to excel in the laboratory and develop as life-long learners. Faculty participate in our Neurosciences and Neurological Disorders (NND) training track which awards both Ph.D. and M.S. degrees. We also train students towards the M.D./Ph.D and M.D./ M.S.B.S. joint degrees. Our research mission incorporates molecular, cellular, and systems neuroscience and cuts across the boundaries of traditional departments and disciplines. Our funded research in neurodevelopment, neurodegeneration, regeneration and repair, sensory function, and drug abuse comprise just a few of our interests. We employ cutting edge technologies and focus on the solution of fundamentally important problems pertinent to nervous system diseases and processes that can be translated feasibly to clinical issues. We work towards a synergistic interaction between the clinical and basic sciences that prompts unexpected discoveries of causes and novel treatments for the diseased nervous system. We also coordinate the Human Body Donation Program at the University of Toledo College of Medicine.

Montana State University, Department of Cell Biology and Neuroscience
type: Organization
type: NamedIndividual
has db xref: nif-0000-02019
synonym: Montana State University Department of Cell Biology and Neuroscience
synonym: Montana State University Department of Cell Biology Neuroscience
synonym: MSU Dept. of Cell Biology and Neuroscience
abbrev: CBN
IAO_0000115: The academic programs and scientific research interests in our department cover a wide range of topics, with special emphasis on Cell Biology, Neurobiology, Developmental Biology, Physiology, Anatomy, Biophysics, and Neuroinformatics. Together, faculty and students in our department study biological processes that span the continuum from single cells to the entire human body. The Department of Cell Biology and Neuroscience offer both an Undergraduate and Graduate Program, which includes Ph.D. or M.S. degrees in Neuroscience or Biological Science. Two different undergraduate degree options are available within the Cell Biology and Neuroscience major: Biomedical Sciences and Cell Biology & Neuroscience. The Department of Cell Biology and Neuroscience offers exciting opportunities to work with nationally and internationally recognized faculty on a wide range of research topics, including cognitive neuroscience, neurophysiology, neuroinformatics, developmental biology, cell biology, biophysics and computational neuroscience.

Mouse Genome Informatics Transgenes
type: Resource
type: NamedIndividual
has db xref: nif-0000-34000
abbrev: MGI Transgene
IAO_0000115: Data set of collected and annotated expression and activity data for recombinase-containing transgenes and knock-in alleles. As the authoritative source of official names for mouse genes, alleles, and strains, MGI makes this list of transgenes available as a service and includes all known transgenes and synonyms. NIF provides a database interface so that researchers may have a better idea whether the trangene or transgenic animal that they are searching for is available. Nomenclature follows the rules and guidelines established by the International Committee on Standardized Genetic Nomenclature for Mice.

qPrimerDepot
type: Resource
type: NamedIndividual
has db xref: nif-0000-03381
has db xref: OMICS_02324
synonym: qPrimerDepot - A quantitative real time PCR primer database
IAO_0000115: A database that provides quantitative real time (qRT) PCR primers for 99.96% human RefSeq sequences. For 99% of intron-bearing genes, the PCR product will cross an exon-exon border which overlaps one of the largest introns. Primers are assumed to have a uniform annealing temperature of 60C, allowing them to be used in large-scale assays.

RNA Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157566
abbrev: RNAO
IAO_0000115: An ontology to capture all aspects of RNA - from primary sequence to alignments, secondary and tertiary structure from base pairing and base stacking to sophisticated motifs.

Bpipe
type: Resource
type: NamedIndividual
has db xref: biotools:bpipe
has db xref: OMICS_02301
synonym: bpipe - A tool for running and managing bioinformatics pipelines
IAO_0000115: Software tool for running and managing bioinformatics pipelines. It specializes in enabling users to turn existing pipelines based on shell scripts or command line tools into highly flexible, adaptable and maintainable workflows with a minimum of effort. Bpipe ensures that pipelines execute in a controlled and repeatable fashion and keeps audit trails and logs to ensure that experimental results are reproducible. Requiring only Java as a dependency, it is fully self-contained and cross-platform, making it very easy to adopt and deploy into existing environments.

Nestly
type: Resource
type: NamedIndividual
has db xref: OMICS_02300
IAO_0000115: A Python package to facilitate running tools with nested combinations of parameters and inputs. It provides three components: a module to build nested directory structures corresponding to choices of parameters; the nestrun script to run a given command using each set of parameter choices; the nestagg script to aggregate results of the individual runs into a CSV file, as well as support for more complex aggregation. Also included is a module for easily specifying nested dependencies for the SCons build tool, enabling incremental builds.

Biological Biochemical Image Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-00205
synonym: BBID-Biological Biochemical Image Database
abbrev: BBID
IAO_0000115: Database of images of putative biological pathways, macromolecular structures, gene families, and cellular relationships. It is of use to those who are working with large sets of genes or proteins using cDNA arrays, functional genomics, or proteomics. The rationale for this collection is that: # Except in a few cases, information on most biological pathways in higher eukaryotes is non-existent, incomplete, or conflicting. # Similar biological pathways differ by tissue context, developmental stages, stimulatory events, or for other complex reasons. This database allows comparisons of different variations of pathways that can be tested empirically. # The goal of this database is to use images created directly by biomedical scientists who are specialists in a particular biological system. It is specifically designed to NOT use average, idealized or redrawn pathways. It does NOT use pathways defined by computer algorithm or information search approaches. # Information on biological pathways in higher eukaryotes generally resides in the images and text of review papers. Much of this information is not easily accessible by current medical reference search engines. # All images are attributable to the original authors. All pathways or other biological systems described are graphic representations of natural systems. Each pathway is to be considered a work in progress. Each carries some degree of error or incompleteness. The end user has the ultimate responsibility to determine the scientific correctness and validity in their particular biological system. Image/pathway submissions are welcome.

Snakemake
type: Resource
type: NamedIndividual
has db xref: biotools:snakemake
has db xref: OMICS_02299
synonym: snakemake - A Python based language and execution environment for make-like workflows
IAO_0000115: A Python based language and execution environment for make-like workflows. The system supports the use of automatically inferred multiple named wildcards (or variables) in input and output filenames.

SNAPE-pooled
type: Resource
type: NamedIndividual
has db xref: OMICS_05820
synonym: snape-pooled: Computes the minor allele frequency spectrum in pooled DNA (sequenced) samples
IAO_0000115: Software that computes the probability distribution for the frequency of the minor allele in a certain population, at a certain position in the genome.

Meharry Medical College Pharmacology
type: Organization
type: NamedIndividual
has db xref: nif-0000-02012
synonym: Meharry Graduate Program in Pharmacology
synonym: Meharry Medical College School of Graduate Studies and Research; Graduate Program in Pharmacology
synonym: Meharry Medical College School of Graduate Studies and Research; Pharmacology
synonym: Meharry Pharmacology
synonym: Meharry SOGSR Graduate Program in Pharmacology
synonym: Meharry SOGSR Pharmacology
synonym: MMC Pharmacology
synonym: MMC SOGSR Pharmacology
IAO_0000115: Graduate Program in Pharmacology at Meharry Medical College embraces the broad definition of pharmacology as the study of how chemical agents affect living processes; the chemicals involved include agents such as endogenous hormones, neurotransmitters, and/or growth factors; toxic substances in our environment; and pharmaceutically developed drugs. The breadth of our scientific environment is manifested by faculty who study the fate of drugs once ingested and the variability of drug response in varying patient populations (a discipline known as pharmacokinetics), as well as faculty who study the mechanisms by which drugs and endogenous agents work (a discipline known as pharmacodynamics). A unique strength of our research and training environment is the inter-disciplinary nature of the program, which encompasses faculty from the four divisions of the Department of Biomedical Science and Departments of Internal Medicine and Neurology.

NGSANE
type: Resource
type: NamedIndividual
has db xref: OMICS_02298
synonym: Next Generation Sequencing ANalysis for Enterprises
IAO_0000115: Software providing a Linux-based High Performance Computing (HPC) enabled framework for high-throughput data analysis that minimizes overhead for set up and processing of new projects yet maintains full flexibility of custom scripting when processing raw sequence data.

Mercer University College of Pharmacy and Health Sciences; Department of Pharmaceutical Sciences
type: Organization
type: NamedIndividual
has db xref: nif-0000-02014
synonym: Mercer COPHS Dept. of Pharmaceutical Sciences
synonym: Mercer University COPHS Department of Pharmaceutical Sciences
IAO_0000115: The mission of the Department of Pharmaceutical Sciences is to make scholarly contributions to the discipline of pharmaceutical sciences and related fields. Education within the department offers a high quality learning environment that includes Ph.D. and Pharm.D./Ph.D. degree programs. Although not required for entry into pharmacy practice, a one-year residency is offered and affords the Pharm.D. graduate an opportunity to develop expertise in clinical pharmacy practice and specialty areas. The graduate program leading to the Ph.D. degree in pharmaceutical sciences is designed for students seeking teaching and research careers in academic institutions, the pharmaceutical industry and other health-related agencies. An interdisciplinary approach prepares graduates to perform independent research, to encourage scholarly development and to acquire teaching skills. Areas of specialization include pharmacology, pharmaceutics, toxicology, and medicinal chemistry. The Doctor of Pharmacy (Pharm.D.)/Doctor of Philosophy (Ph.D.) Degree Program enables highly qualified students to obtain both degrees in a shortened period of time. This Pharm.D./Ph.D. Degree program is designed primarily for students who are strongly motivated toward an academic/ research career in the pharmaceutical sciences. The Program is flexible enough to accommodate individuals of varied educational backgrounds.

National Institute of General Medical Sciences Image Gallery
type: Resource
type: NamedIndividual
has db xref: nif-0000-33708
abbrev: NIGMS Image Gallery
IAO_0000115: Database of scientific photos, illustrations, and videos made available by the National Institute of General Medical Sciences.

jmzTab
type: Resource
type: NamedIndividual
has db xref: biotools:jmztab
has db xref: OMICS_04542
IAO_0000115: A Java interface to the mzTab data exchange format for reporting a summary of proteomics results.

JISTIC
type: Resource
type: NamedIndividual
has db xref: OMICS_02297
IAO_0000115: Software tool for analyzing datasets of genome-wide copy number variation to identify driver aberrations in cancer.

Michigan State University, Department of Pharmacology and Toxicology
type: Organization
type: NamedIndividual
has db xref: nif-0000-02016
synonym: Michigan State University Department of Pharmacology and Toxicology
synonym: Michigan State University Department of Pharmacology Toxicology
synonym: MSU Dept. of Pharmacology and Toxicology
abbrev: Michigan State Pharmacology and Toxicology
IAO_0000115: At the Department of Pharmacology & Toxicology at Michigan State University, we combine integrative research, active learning and intellectual enrichment to prepare the student for advancement and leadership in their chosen field. The Department provides courses for undergraduate students, graduate students, medical students of the allopathic, osteopathic and veterinary colleges, and nursing students. In addition, specialized courses of study are offered in areas of professional development and life-long learning. From molecular and cellular levels to organ systems and whole animal models, our graduate and undergraduate programs encompass multiple areas of study, empowering students to challenge the boundaries of knowledge and chart their own unique path in the biomedical sciences. The disciplines of pharmacology and toxicology play a momentous role in human health today, and their applications in the professional world are vast. The department offers: * Pharmacology & Toxicology Graduate Doctoral Program * Online MS Programs ** Online Professional Science Masters in Integrative Pharmacology ** Online Masters in Pharmacology * Undergraduate Courses in Pharmacology & Toxicology * Dual Major Graduate Program in Toxicology (joint Pharmacology & Toxicology/Environmental Toxicology graduate program) * NIGMS Integrative and Organ Systems Pharmacology Short Course * Summer Undergraduate Research Fellowships

Morehouse School of Medicine Neuroscience Institute
type: Organization
type: NamedIndividual
has db xref: nif-0000-02021
synonym: MSM NI
abbrev: MSMNI
IAO_0000115: The mission of the Morehouse School of Medicine Neuroscience Institute (MSMNI) is to create a supportive and challenging environment for the investigation and teaching of the functional organization of the nervous system, and to seek ways to reduce suffering brought about by neurological disorders. Members of the MSM NI are involved in teaching graduate students, medical students, and health care professionals about researching and treating medical conditions that are caused by or are rooted in the central nervous system. Additionally, MSM NI offers an 8-week Summer Research Program to qualified undergraduate, post-baccalaureate and first-year medical school students. Funding and administrative support were secured from the National Institutes of Health Office on Research for Minority Health and the National Institute for Neurological Disorders and Stroke (NINDS), respectively. The Neuroscience Institute is composed of selected faculty members from the Department of Neurobiology and the Department of Pharmacology at Morehouse School of Medicine who are conducting grant supported research. MSMNI research areas cover a broad range of cellular and molecular neuroscience and include the molecular biology and physiology of circadian rhythm, mechanisms of sleep and sleep disorders, mechanisms of stroke and stroke prevention, photoreceptor and retinal physiology, glutamate receptor physiology and mechanisms of hyperexcitability in epilepsy. Investigators use a variety of experimental preparations including whole animals, the intact portions of the central nervous system, and simplified preparations, such as tissue slices and single cells, to study cellular activities and cell-cell communication under more controlled conditions.

Reactome
type: Resource
type: NamedIndividual
has db xref: biotools:reactome
has db xref: nif-0000-03390
has db xref: r3d100010285
synonym: Reactome Functional Interaction Network
IAO_0000115: Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets.

Subcellular Anatomy Ontology
type: Resource
type: NamedIndividual
has db xref: nif-0000-00206
abbrev: NIF Subcellular
abbrev: SAO
IAO_0000115: Ontology that describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules. It is built according to ontology development best practices (re-use of existing ontologies; formal definitions of terms; use of foundational ontologies). It describes the parts of neurons and glia and how these parts come together to define supracellular structures such as synapses and neuropil. Molecular specializations of each compartment and cell type are identified. The SAO was designed with the goal of providing a means to annotate cellular and subcellular data obtained from light and electron microscopy, including assigning macromolecules to their appropriate subcellular domains. The SAO thus provides a bridge between ontologies that describe molecular species and those concerned with more gross anatomical scales. Because it is intended to integrate into ontological efforts at these other scales, particular care was taken to construct the ontology in a way that supports such integration.

L-Measure
type: Resource
type: NamedIndividual
has db xref: biotools:l-measure
has db xref: nif-0000-00003
abbrev: LM
IAO_0000115: A freely available software tool available for the Windows and Linux platform, as well as the Online version Applet, for the analysis, comparison and search of digital reconstructions of neuronal morphologies. For the quantitative characterization of neuronal morphology, LM computes a large number of neuroanatomical parameters from 3D digital reconstruction files starting from and combining a set of core metrics. After more than six years of development and use in the neuroscience community, LM enables the execution of commonly adopted analyses as well as of more advanced functions, including: (i) extraction of basic morphological parameters, (ii) computation of frequency distributions, (iii) measurements from user-specified subregions of the neuronal arbors, (iv) statistical comparison between two groups of cells and (v) filtered selections and searches from collections of neurons based on any Boolean combination of the available morphometric measures. These functionalities are easily accessed and deployed through a user-friendly graphical interface and typically execute within few minutes on a set of 20 neurons. The tool is available for either online use on any Java-enabled browser and platform or may be downloaded for local execution under Windows and Linux.

Savant
type: Resource
type: NamedIndividual
has db xref: OMICS_00923
IAO_0000115: Next-generation genome browser software designed for the latest generation of genome data.

MetaSKAT
type: Resource
type: NamedIndividual
has db xref: OMICS_00241
IAO_0000115: A R package for multiple marker meta-analysis.

MGH-USC Human Connectome Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-35789
synonym: Harvard/MGH-UCLA Consortium: Human Connectome Project
synonym: Harvard/MGH-UCLA Human Connectome Project
synonym: HCP Harvard/MGH-UCLA
synonym: MGH/UCLA Consortium: Human Connectome Project
abbrev: MGH/UCLA HCP
IAO_0000115: A multi-center project comprising two distinct consortia (Mass. Gen. Hosp. and USC; and Wash. U. and the U. of Minn.) seeking to map white matter fiber pathways in the human brain using leading edge neuroimaging methods, genomics, architectonics, mathematical approaches, informatics, and interactive visualization. The mapping of the complete structural and functional neural connections in vivo within and across individuals provides unparalleled compilation of neural data, an interface to graphically navigate this data and the opportunity to achieve conclusions about the living human brain. The HCP is being developed to employ advanced neuroimaging methods, and to construct an extensive informatics infrastructure to link these data and connectivity models to detailed phenomic and genomic data, building upon existing multidisciplinary and collaborative efforts currently underway. Working with other HCP partners based at Washington University in St. Louis they will provide rich data, essential imaging protocols, and sophisticated connectivity analysis tools for the neuroscience community. This project is working to achieve the following: 1) develop sophisticated tools to process high-angular diffusion (HARDI) and diffusion spectrum imaging (DSI) from normal individuals to provide the foundation for the detailed mapping of the human connectome; 2) optimize advanced high-field imaging technologies and neurocognitive tests to map the human connectome; 3) collect connectomic, behavioral, and genotype data using optimized methods in a representative sample of normal subjects; 4) design and deploy a robust, web-based informatics infrastructure, 5) develop and disseminate data acquisition and analysis, educational, and training outreach materials.

Human Variome Project
type: Resource
type: NamedIndividual
has db xref: nif-0000-36300
has db xref: OMICS_00282
synonym: The Human Variome Project
abbrev: HVP
IAO_0000115: Project facilitating the establishment and maintenance of standards systems and infrastructure for the worldwide collection and sharing of all genetic variations effecting human disease. The Human Variome Project produces two categories of recommendations: HVP Standards and HVP Guidelines. HVP Standards are those systems, procedures and technologies that the Human Variome Project Consortium has determined should be used by the community. These carry more weight than the less prescriptive HVP Guidelines, which cover those systems, procedures and technologies that the Human Variome Project Consortium has determined would be beneficial for the community to adopt. HVP Standards and Guidelines are central to supporting the work of the Human Variome Project Consortium and cover a wide range of fields and disciplines, from ethics to nomenclature, data transfer protocols to collection protocols from clinics. They can be thought of as both technical manuals and scientific documents, and while the impact of HVP Standards and Guidelines differ, they are both generated in a similar fashion. A document has been generated both as a guide for those collecting and distributing data and for those developing policy. Items should include those generated by HGVS/HVP collaborators as well as those generated by groups of individual Societies and Standards bodies in all relevant fields worldwide.

Software Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157591
abbrev: SWO
IAO_0000115: An ontology for describing software tools, their types, tasks, versions, provenance and data associated (the input and output data types and the uses the software can be put to).

Fusion ICA Toolbox
type: Resource
type: NamedIndividual
has db xref: nif-0000-36743
synonym: Fusion ICA Toolbox (FIT)
abbrev: FIT
IAO_0000115: A MATLAB toolbox which implements the joint Independent Component Analysis (ICA), parallel ICA and CCA with joint ICA methods. It is used to to extract the shared information across modalities like fMRI, EEG, sMRI and SNP data. * Environment: Win32 (MS Windows), Gnome, KDE * Operating System: MacOS, Windows, Linux * Programming Language: MATLAB * Supported Data Format: ANALYZE, NIfTI-1

PoPoolation
type: Resource
type: NamedIndividual
has db xref: biotools:popoolation
has db xref: OMICS_04414
IAO_0000115: A collection of tools to facilitate population genetic studies of next generation sequencing data from pooled individuals. It builds upon open source tools (bwa, samtools) and uses standard file formats (gtf, sam, pileup) to ensure a wide compatibility. PoPoolation allows to calculate Tajima's Pi, Watterson's Theta and Tajima's D for reference sequences using a sliding window approach. Alternatively these population genetic estimators may be calculated for a set of genes (provided as gtf). One of the main challenges in population genomics is to identify regions of intererest on a genome wide scale. PoPoolation will greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools.

RefSeq
type: Resource
type: NamedIndividual
has db xref: biotools:refseq
has db xref: nif-0000-03397
has db xref: OMICS_01659
has db xref: r3d100011306
has db xref: SCR_016579
synonym: NCBI
synonym: Reference Sequence
synonym: Reference Sequence Database
synonym: Reference Sequences
IAO_0000115: Collection of curated, non-redundant genomic DNA, transcript RNA, and protein sequences produced by NCBI. Provides a reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. Accessed through the Nucleotide and Protein databases.

Suggested Ontology for Pharmacogenomics
type: Resource
type: NamedIndividual
has db xref: nlx_157597
abbrev: SO-Pharm
abbrev: SOPHARM
IAO_0000115: A domain ontology implemented in OWL-DL, which proposes a formal description of pharmacogenomic knowledge. It articulates different ontologies that represent complementary sub-domains of pharmacogenomics, i.e. related to genotype, phenotype, drugs, and clinical trials. SO-Pharm enables the representation of pharmacogenomic relationships between a drug, a genomic variation and a phenotype trait. In addition, it enables the representation of a patient and more largely a panel included in trials, and populations. SO-Pharm enables the representation of measured items on patients such as results from the observation of a phenotype trait or of genomic variations. SO-Pharm supports knowledge about pharmacogenomic hypothesis, case study, and investigations in pharmacogenomics. SO-Pharm is designed to facilitate data integration and knowledge discovery in pharmacogenomics. In addition it provides a consistent articulation of ontologies of pharmacogenomic sub-domains.

MultiPhen
type: Resource
type: NamedIndividual
has db xref: biotools:multiphen
has db xref: OMICS_04397
synonym: MultiPhen: a package for the genetic association testing of multiple phenotypes
IAO_0000115: Software package that performs genetic association tests between SNPs (one-at-a-time) and multiple phenotypes (separately or in joint model).

RegulonDB
type: Resource
type: NamedIndividual
has db xref: biotools:regulondb
has db xref: nif-0000-03399
has db xref: OMICS_01868
IAO_0000115: Database on transcriptional regulation in Escherichia coli K-12 containing knowledge manually curated from original scientific publications, complemented with high throughput datasets and comprehensive computational predictions. Graphic and text-integrated environment with friendly navigation where regulatory information is always at hand. They provide integrated views to understand as well as organized knowledge in computable form. Users may submit data to make it publicly available.

CNS NeuroWIki
type: Resource
type: NamedIndividual
has db xref: nif-0000-37089
synonym: Congress of Neurological Surgeons NeuroWiki
synonym: University of Neurosurgery NeuroWiki
abbrev: NeuroWiki
IAO_0000115: Wiki dedicated to neurosurgical topics, maintained by the Congress of Neurological Surgeons. Members can log in to contribute by adding or editing an article. A wiki is a collaborative technology for organizing information. Visitors can add, remove, and edit content. Like all other wikis, the CNS University's NeuroWiki allows linking among any number of pages. This ease of interaction and operation will engender collaborative authoring.

Brain Atlas of the Mozambique Tilapia Oreochromis mossambicus
type: Resource
type: NamedIndividual
has db xref: nlx_157637
synonym: Mozambique Tilapia Brain Atlas
abbrev: Tilapia Brain Atlas
IAO_0000115: Digital three-dimensional MRI atlas of the Mozambique tilapia brain, supported by Nissl staining. Images were viewed and analyzed in all orientations (transverse, sagittal, and horizontal) and manually labelled to reveal structures in the olfactory bulb, telencephalon, diencephalon, optic tectum, and cerebellum. The MRI atlas data (16-bit int) and delineation data (8-bit int) are provided in Raw data (file_name.raw), Amira format (file_name.am) and in Analyze format (file_name.img and file_name.hdr).

Beijing: Short TR Study
type: Resource
type: NamedIndividual
has db xref: nlx_157642
synonym: Beijing Normal University State Key Laboratory of Cognitive Neuroscience and Learning Short TR Sample
synonym: BNU Short TR Sample
abbrev: Beijing Short TR
IAO_0000115: Dataset of resting state fMRI scans obtained using two different TR's in healthy college-aged volunteers. Specifically, for each participant, data is being obtained with a short TR (0.4 seconds) and a long TR (2.0 seconds). In addition this dataset contains a 64-direction DTI scan for every participant. The following data are released for every participant: * 8-minute resting-state fMRI scan (TR = 2 seconds, # repetitions = 240) * 8-minute resting-state fMRI scans (TR = 0.4 seconds, # repetitions = 1200) * MPRAGE anatomical scan, defaced to protect patient confidentiality * 64-direction diffusion tensor imaging scan (2mm isotropic) * Demographic information

Gene Cloud: Exploring Connections in the Mouse Genome
type: Resource
type: NamedIndividual
has db xref: nif-0000-37178
abbrev: Gene Cloud
IAO_0000115: Gene Cloud is a novel tool presenting gene-gene associations based on the scientific literature. It was developed by the Knockout Mouse Repository (www.komp.org) to help our customers find products related to other products they chose. We have built a detailed graph model of gene-gene associations based on how many times two genes are cited in the same article. If two genes are cited in many papers together, they are considered strongly connected. Each instance of Gene Cloud is centered around a specific gene. A list of the top most related genes is plotted as a branching structure from the center. A secondary branch can occur if a gene in the graph is more related a non-central gene than it is to the center gene. The font size of a branched gene indicates the relative strength of connection--always to the center gene. The distribution of genes in space is randomized each time Gene Cloud is run so a different picture will result for the same central gene. Color is used to indicate the availability of Knockout Mouse products at the KOMP Repository. If a gene is colored green in the graph there are products (mutant ES cells, sperm, embryos, or mice) ready to be ordered. Blue colored genes do not yet have products available, but you can follow the links back to the KOMP Repository and register interest to be alerted when products do become available. Gene Cloud is driven by a database of gene-gene associations that currently contains 82,000 genes and other biotypes, 113,000 annotated publications, and 467 million connections. The latest gene symbols, names and gene-publication annotation information is updated daily from the Mouse Genome Informatics database. The graphing is accomplished through the use of a modified version of jsViz.

eCAT electronic lab notebook
type: Resource
type: NamedIndividual
has db xref: nif-0000-37179
abbrev: eCAT
IAO_0000115: An online electronic lab notebook designed for lab scientists at research organizations that allows the creation and import research data, controlled sharing between lab members, and lets lab members communicate via messages and tasks. It also allows lab members to work from home or when travelling, in a secure, integrated collaborative environment.

RESID
type: Resource
type: NamedIndividual
has db xref: biotools:resid
has db xref: nif-0000-03400
has db xref: r3d100000023
synonym: RESID Database
synonym: RESID Database at PIR
synonym: RESID Database at the EBI
synonym: RESID Database of Protein Modifications
IAO_0000115: A comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. It provides: systematic and alternate names, atomic formulas and masses, enzyme activities generating the modifications, keywords, literature citations, Gene Ontology cross-references, Protein Information Resource (PIR) and SWISS-PROT protein sequence database feature table annotations, structure diagrams and molecular models. Each RESID Database entry presents a chemically unique modification and shows how that modification is currently annotated in the protein sequence databases, Swiss-Prot and the Protein Information Resource (PIR). The RESID Database provides a table of corresponding equivalent feature annotations that is used in the UniProt project, an international effort to combine the resources of the Swiss-Prot, TrEMBL and PIR. As an annotation tool, the RESID Database is used in standardizing and enhancing modification descriptions in the feature tables of Swiss-Prot entries.

Human Experimental/FunctionAL MaPper: Providing Functional Maps of the Human Genome
type: Resource
type: NamedIndividual
has db xref: nif-0000-37186
synonym: Human Experimental / FunctionAL MaPper
synonym: Human Experimental/FunctionAL MaPper
abbrev: HEFalMp
IAO_0000115: HEFalMp (Human Experimental/FunctionAL MaPper) is a tool developed by Curtis Huttenhower in Olga Troyanskaya's lab at Princeton University. It was created to allow interactive exploration of functional maps. Functional mapping analyzes portions of these networks related to user-specified groups of genes and biological processes and displays the results as probabilities (for individual genes), functional association p-values (for groups of genes), or graphically (as an interaction network). HEFalMp contains information from roughly 15,000 microarray conditions, over 15,000 publications on genetic and physical protein interactions, and several types of DNA and protein sequence analyses and allows the exploration of over 200 H. sapiens process-specific functional relationship networks, including a global, process-independent network capturing the most general functional relationships. Looking to download functional maps? Keep an eye on the bottom of each page of results: every functional map of any kind is generated with a Download link at the bottom right. Most functional maps are provided as tab-delimited text to simplify downstream processing; graphical interaction networks are provided as Support Vector Graphics files, which can be viewed using the Adobe Viewer, any recent version of Firefox, or the excellent open source Inkscape tool.

Colorado Assessment Tests - Tower of London
type: Resource
type: NamedIndividual
has db xref: nif-0000-00208
synonym: Tower of London
abbrev: CAT Tower of London
IAO_0000115: CATs Tower of London test is a free, computer-based software test originally developed by Shallice (1982) to investigate problem solving in subjects with damage to the frontal lobes. The CATs Tower of London Test comes with one preprogrammed test along with extensive normative data for that test. You can also create a test using your design. Briefly, subjects are required to move colored beads from a window on the left (working area) until they achieve the arrangement in the window on the right (goal position). Subjects are instructed to try to achieve the goal arrangement in as few moves as possible. The software contains a Tower of London test. The test contains trials with 3 beads and 3 pegs, 4 beads and 4 pegs, and 5 beads and 5 pegs. You can use the Setup screen to create a test using your design. A test can contain 3, 4, and 5 bead problems with varying number of moves required for the optimal solution. In Shallice's initial investigation using the Tower of London, patients with damage to the left anterior frontal lobe demonstrated impaired planning (i.e., greater number of moves required for solution). Patients with damage to the right anterior, and left or right posterior areas of the frontal lobes were not impaired. Thus, results from this initial study provided support for the view that the left anterior frontal lobe area is involved in the planning required for solving the Tower of London test. Recent studies using neuroimaging techniques support this notion. Studies using regional cerebral blood flow (rCBF) imaging indicate an involvement of the left frontal lobes in the planning required for successfully completing the Tower of London puzzle. Studies of patients with damage to the frontal lobes indicate less cortical specificity, but are consistent with the view that the frontal lobes are involved in the planning required for solving this puzzle.

Oregon Health and Science University Neuroscience Graduate Program
type: Resource
type: NamedIndividual
has db xref: nif-0000-02037
synonym: OHSU NGP
IAO_0000115: The Neuroscience Graduate Program (NGP) at OHSU provides outstanding, multidisciplinary training in neuroscience in one of the best-recognized neuroscience programs in the United States. Our graduates are distributed at top research institutions throughout the world, and the success of our faculty ensures that graduates have ready access to their next step ����?? be it postdoctoral fellowships in academia or industry, or other science-related careers. The program is particularly strong in cellular neuroscience, neuronal signaling, gene regulation, biophysics of channels and transporters, sensory systems, and neuroendocrinology with increasing strength in developmental neuroscience and disease-oriented neuroscience research. Faculty members are located within research institutes at OHSU including the Vollum Institute, the Oregon National Primate Research Center (ONPRC), Oregon Hearing Research Center, Jungers Center and the Center for Research on Occupational and Environmental Toxicology (CROET); as well as the basic and clinical departments in the OHSU School of Medicine. As time spent in the lab is the most important component of graduate science training, our program is designed such that core coursework is completed in the first year. During that first year, students also are immersed in research through lab rotations in several labs, eventually choosing one that gives a mutual fit. Because of the relatively small number of students compared to the number of neuroscience laboratories at OHSU, students have many options for a thesis lab. Our well funded faculty provide state-of-the-art exposure to the concepts and technology of modern neuroscience. OHSU also offers certificate and degree programs, e.g. technology transfer and translational science, for advanced students in the NGP who want to broaden their career options.

MF-GE
type: Resource
type: NamedIndividual
has db xref: OMICS_02295
synonym: Multiple Filters enhanced Genetic Ensemble System
synonym: Multiple Filters enhanced Genetic Ensemble System (MF-GE)
IAO_0000115: A hybrid software system for feature selection and sample classification of high-dimensional datasets. It is designed for microarray but can be applied to any other high-dimensional datasets. It uses multiple filters to produce a normalized score for each feature. The score is an indication of the usefulness of each feature. It is then translated into a frequency map with more useful features receive a higher frequency in the map.

Cell Image Library (CIL)
type: Resource
type: NamedIndividual
has db xref: biotools:cellimagelibrary
has db xref: nif-0000-37639
has db xref: r3d100011601
synonym: Cell Image Library. CIL
abbrev: CIL
IAO_0000115: Freely accessible, public repository of vetted and annotated microscopic images, videos, and animations of cells from a variety of organisms, showcasing cell architecture, intracellular functionalities, and both normal and abnormal processes. Explore by Cell Process, Cell Component, Cell Type or Organism. The Cell includes images acquired from historical and modern collections, publications, and by recruitment.

Structural Biology Grid
type: Resource
type: NamedIndividual
has db xref: nif-0000-37641
has db xref: r3d100010234
synonym: SBGrid Consortium
synonym: SBGrid Science Portal
synonym: SBGrid Software Consortium
abbrev: SBGrid
IAO_0000115: Computing resources structural biologists need to discover the shapes of the molecules of life, it provides access to web-enabled structural biology applications, data sharing facilities, biological data sets, and other resources valuable to the computational structural biology community. Consortium includes X-ray crystallography, NMR and electron microscopy laboratories worldwide.SBGrid Service Center is located at Harvard Medical School.SBGrid's NIH-compliant Service Center supports SBGrid operations and provides members with access to Software Maintenance, Computing Access, and Training. Consortium benefits include: * remote management of your customized collection of structural biology applications on Linux and Mac workstations; * access to commercial applications exclusively licensed to members of the Consortium, such as NMRPipe, Schrodinger Suite (limited tokens) and the Incentive version of Pymol; remote management of supporting scientific applications (e.g., bioinformatics, computational chemistry and utilities); * access to SBGrid seminars and events; and * advice about hardware configurations, operating system installations and high performance computing. Membership is restricted to academic/non-profit research laboratories that use X-ray crystallography, 2D crystallography, NMR, EM, tomography and other experimental structural biology technologies in their research. Most new members are fully integrated with SBGrid within 2 weeks of the initial application.

PheWAS R Package
type: Resource
type: NamedIndividual
has db xref: biotools:phewas
has db xref: OMICS_00242
synonym: Phenome-Wide Association Study
IAO_0000115: Software package contains methods for performing Phenome-Wide Association Study.

Colorado Assessment Tests - Visual Span
type: Resource
type: NamedIndividual
has db xref: nif-0000-00209
synonym: Visual Span
abbrev: CAT Visual Span
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Visual span tests have been frequently used to assess non-verbal short-term memory. The free computer-based CATs Visual Span provides you with a flexible package for designing tests of visual spatial memory. You can create your own unique tests or variations on previously reported versions of the visual span test. For example in the Corsis Block-Tapping Test the examiner places nine blocks on a board and taps them in a designated sequence. The participant is required to repeat the sequence. Over trials the length of the sequence is increased (see Milner, 1971). The Knox Cube Imitation Test uses four blocks and essentially follows the same logic. The Wechsler Memory Scale - Revised includes a two part visual memory span test. In this test the examiner points at boxes on an eight box card in a prearranged sequence and the subject is required to repeat back the sequence. The initial trial starts with a sequence of two blocks and increases over trials. The two parts of this test are a forward visual span test and a reverse visual span test. Tests similar to these and more can be setup with the CATs Visual Span.

brainfacts.org
type: Resource
type: NamedIndividual
has db xref: nlx_144565
synonym: brain facts
synonym: brainfacts
synonym: BrainFacts.org
IAO_0000115: A web portal that aggregates information and educational materials about the brain and brain diseases. Resources such as videos, key brain concepts, and hands-on activities may be used and shared with the public.

Pennsylvania State University College of Medicine Neuroscience
type: Organization
type: NamedIndividual
has db xref: nif-0000-02041
synonym: PennState Hershey Neuroscience Institute
synonym: Pennsylvania State University Hershey Neuroscience Institute
synonym: PSU Hershey Neuroscience Institute
IAO_0000115: Advances in our understanding of the brain are leading to new insights into how we think and to new opportunities to treat the devastating set of neurological diseases that affect all segments of our population. Penn State Hershey Neuroscience Institute integrates basic, translational and clinical neuroscience research; education of graduate students, medical students, postdoctoral fellows and residents; clinical care of patients with neurobehavioral diseases and disorders; and outreach to the local community, state, regional, national and international neuroscience organizations. With the neurosciences clearly established as a continuing priority in the overall strategic vision of Penn State Hershey, the leadership of the neuroscience community is seeking to establish the short and long term vision for excellence and continued growth in neuroscience. Those academic centers that can achieve the best collaboration and alignment among the various neuroscience disciplines will be best positioned to advance this field. We believe that the formation of Penn State Hershey Neuroscience Institute positions us to take a leading role in developing neuroscience knowledge and treatment.

Colorado Assessment Tests - Reaction Time
type: Resource
type: NamedIndividual
has db xref: nif-0000-00211
synonym: Reaction Time
abbrev: CAT Reaction Time
IAO_0000115: Reaction Time is free neuropsychological evaluation software designed to assess subject's speed of processing on three relatively simple tasks. Tasks include a simple reaction time test, a choice test, and a conditional choice test. Participants are shown a series of visual stimuli on a computer screen and asked to respond by pulling an appropriate trigger on a standard game pad. Both reaction time and the trigger pulled are recorded for subsequent analysis. Tasks to be used in the test, the average inter-stimulus interval and the number of stimuli presented for each task can be set by the investigator. The analysis includes means and standard deviations for response latencies for a single session, as well as the capability of evaluating a participant's performance on a particular session against their performance on a series of sessions. This test requires the use of a game pad that supports at least four buttons and provides a right and left trigger button. We have tested several different brands of inexpensive game pads and have found them acceptable; however we have standardized on Microsoft's SideWinder and have used it in collecting the normative data for this test.

Colorado Assessment Tests: n-Back
type: Resource
type: NamedIndividual
has db xref: nif-0000-00212
synonym: n-Back
abbrev: CAT n-Back
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. The modifiable n-Back test is free software presumed to measure executive control of the updating of information in working memory. The task requires the participant to monitor some dimension (e.g. content, position, numerosity) of a temporally present sequence of items, responding when the currently presented item matches on the relevant dimension an item that was just recently presented. The match can be with an item present either 1 back, 2 back, 3 back or n back. Considerable flexibility is provided to the experimenter in specifying various parameters of the experiment (e.g. presentation rate, n back, content, position, color). The n-Back test is presumed to measure executive control of the updating of information in working memory. (Shimamura, 2000) Watter, Geffen and Geffen (2001) based on their work with the P300 event-related-potential have suggested that the n-Back is a dual task in that latencies of the P300 did not change with increasing task difficulty, that is memory load while amplitude did reflecting in their view a reallocation of attention and processing capacity away from the matching subtask. The n-Back task is one in which the participant is presented a series of stimuli at a constant rate. The task of the participant is to determine if the currently presented stimulus is similar (along some dimension) to one they have recently (usually one, two or three positions back) seen in the stream. Match criteria can be dimensions like material, position on the screen, color or some combination. CATs n-Back allows for substantial control over the position in which the material is presented (nine different positions), the nature of the material (any character or dingbat string, and any color. The experimenter can set the speed at which the sequence is presented including both the stimulus on time and the inter-stimulus interval. Participant responses can be made either using the keyboard o…

Vertebrate Taxonomy Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157625
abbrev: VTO
IAO_0000115: An ontology that includes both extinct and extant vertebrates, aiming to provide one comprehensive hierarchy. The hierarchy backbone for extant taxa is based on the NCBI taxonomy. Since the NCBI taxonomy only includes species associated with archived genetic data, to complement this, they also incorporate taxonomic information across the vertebrates from the Paleobiology Database (PaleoDB). The Teleost Taxonomy Ontology (TTO) and AmphibiaWeb (AWeb) are incorporated to provide a more authoritative hierarchy and a richer set of names for specific taxonomic groups.

MINC Brain Imaging Toolbox
type: Resource
type: NamedIndividual
has db xref: nlx_10430
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023.Comprised of a large array of sophisticated programs, this comprehensive software package with tools based around the MINC file format. Utilities are provided for conversion, viewing, editing, registering, segmentation, and a wide array of analysis. Many programs are in Perl. MINC software tools for neurological imaging are free. Input format: Analyze, DICOM, Minc

Colorado Assessment Tests - Symptom Validity
type: Resource
type: NamedIndividual
has db xref: nif-0000-00213
synonym: Symptom Validity
abbrev: CAT Symptom Validity
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. Memory impairment is one of the most common complaints after head injury, and accordingly, individuals may attempt to feign memory impairment or exaggerate symptoms of memory impairment. This free neuropsychological evaluation software contains some of the most common tests used to detect malingering of memory impairment. This software package contains a number of tests of declarative memory that assess recall of information that has a personal and temporal context. The typical example of declarative tests used for detecting malingering are the auditory verbal learning test and forced choice test. These tests are included in Symptom Validity along with other tests of declarative memory (e.g., prose recall, questionnaire tests). Unfortunately, classification of individuals is not completely accurate even with the use of multiple declarative memory tests. Thus, other tests that can complement previously used declarative memory measures by enhancing classification accuracy may be of great value to the neuropsychologist assessing the possibility of malingering. Your software contains two tests of nondeclarative memory that have been previously shown to be useful in the detection of malingered memory deficits (Davis et al., 1997a, 1997b). These tests take advantage of the general laypersons misunderstanding of the test performance of a truly memory impaired individual. That is, amnesic patients have been shown to perform normally on these nondeclarative memory tests and this is counterintuitive to the memory performance expectations of the general layperson. The nondeclarative tests included in Symptom Validity are two repetition priming tests of word stem completion and two tests of pattern categorization learning. Note: At this time this program will run only on Windows 98. We are currently working on a version that will run under the newer operating systems.

Michigan Molecular Interactions
type: Resource
type: NamedIndividual
has db xref: nif-0000-00214
abbrev: MiMI
IAO_0000115: MiMi Web gives you an easy to use interface to a rich NCIBI data repository for conducting your systems biology analyses. This repository includes the MiMI database, PubMed resources updated nightly, and text mined from biomedical research literature. The MiMI database comprehensively includes protein interaction information that has been integrated and merged from diverse protein interaction databases and other biological sources. With MiMI, you get one point of entry for querying, exploring, and analyzing all these data. MiMI provides access to the knowledge and data merged and integrated from numerous protein interactions databases and augments this information from many other biological sources. MiMI merges data from these sources with deep integration into its single database with one point of entry for querying, exploring, and analyzing all these data. MiMI allows you to query all data, whether corroborative or contradictory, and specify which sources to utilize. MiMI displays results of your queries in easy-to-browse interfaces and provides you with workspaces to explore and analyze the results. Among these workspaces is an interactive network of protein-protein interactions displayed in Cytoscape and accessed through MiMI via a MiMI Cytoscape plug-in. MiMI gives you access to more information than you can get from any one protein interaction source such as: * Vetted data on genes, attributes, interactions, literature citations, compounds, and annotated text extracts through natural language processing (NLP) * Linkouts to integrated NCIBI tools to: analyze overrepresented MeSH terms for genes of interest, read additional NLP-mined text passages, and explore interactive graphics of networks of interactions * Linkouts to PubMed and NCIBI's MiSearch interface to PubMed for better relevance rankings * Querying by keywords, genes, lists or interactions * Provenance tracking * Quick views of missing information across databases. Data Sources include: BIND, BioGRID,…

OppNet - Basic Behavioral and Social Science Opportunity Network
type: Resource
type: NamedIndividual
has db xref: nif-0000-38232
synonym: OppNet: Basic Behavioral and Social Science Opportunity Network
abbrev: OppNet
IAO_0000115: OppNet is a trans-NIH initiative to expand the agency's funding of basic behavioral and social sciences research (b-BSSR). Basic-BSSR studies mechanisms and processes that influence behavior at the individual, group, community and population level. Research results lead to new approaches for reducing risky behaviors and improving the adoption of healthy practices. The mission of OppNet is to pursue opportunities for strengthening basic behavioral and social science research (b-BSSR) at the NIH while innovating beyond existing investments. * OppNet advances basic behavioral and social science research through activities and initiatives that build a body of knowledge about the nature of behavior and social systems. * OppNet prioritizes activities and initiatives that focus on basic mechanisms of behavior and social processes; that are relevant to the missions and public health challenges of multiple NIH Institutes, Centers and Offices (ICOs); and that build upon existing NIH investments without replicating them. All NIH Institutes and Centers (ICs) share the mission of supporting b-BSSR. OppNet will also develop a plan for focused multi-year programs across ICs to advance priority topics within b-BSSR.

Open Science Data Cloud
type: Resource
type: NamedIndividual
has db xref: nlx_157679
abbrev: OSDC
IAO_0000115: Service that provides petabyte-scale cloud resources to analyze, manage, and share scientific data. It is designed to serve medium to large sized research projects by managing and operating a secure cloud computing infrastructure that can be shared across a project. This Science as a Service approach to research saves scientists and their funders valuable time and money. All of the software developed is open source and hosted on GitHub. The OSDC also has 1PB of public data in a wide variety of disciplines. The data sets can downloaded over the internet or high performance networks such as Internet2, as well as computed over directly on the OSDC.

iDASH
type: Resource
type: NamedIndividual
has db xref: biotools:iDASH
has db xref: nif-0000-38239
has db xref: https://api.datacite.org/dois
synonym: iDASH Repository
synonym: Integrating Data for Analysis Anonymization and SHaring
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. National Center for Biomedical Computing (NCBC) that develops new algorithms, opensource tools, computational infrastructure, and services for biomedical and behavioral researchers nationwide to promote the secure sharing and consuming of biomedical and behavioral resources (software, data, and computing systems) with iDASH collaborators. The center addresses fundamental challenges to research progress by providing a secure, privacypreserving environment in which researchers can analyze genomic, transcriptomic, clinical, behavioral, and social data relevant to health. Three driving biological projects in iDASH (Molecular Phenotyping of Kawasaki Disease, Post-Marketing Surveillance of Hematologic Medications, and Individualized Intervention to Enhance Physical Activity) span the molecular-individualpopulation spectrum, and they will motivate, inform, and support tool development. iDASH will collaborate with other NCBCs and will disseminate tools via annual workshops, presentations at major conferences, and scientific publications.

Human Physiology
type: Resource
type: NamedIndividual
has db xref: nlx_10645
IAO_0000115: Human Physiology is a featured book on Wikibooks because it contains substantial content, it is well-formatted, and the Wikibooks community has decided to feature it on the main page or in other places. Please continue to improve it and thanks for the great work so far! A printable and PDF version are available. You can edit its advertisement template. Contents: 1. Homeostasis 2. Cell Physiology 3. Integumentary System 4. The Nervous System 5. Senses 6. The Muscular System 7. Blood Physiology 8. The Cardiovascular System 9. The Immune System 10. The Urinary System 11. The Respiratory System 12. The Gastrointestinal System 13. Nutrition 14. The Endocrine System 15. The Male Reproductive System 16. The Female Reproductive System 17. Pregnancy and Birth 18. Genetics and Inheritance 19. Development: Birth through Death 20. Appendix 1: Answers to Review Questions 21. Authors 22. Further Reading

EBSeq
type: Resource
type: NamedIndividual
has db xref: biotools:ebseq
has db xref: OMICS_01307
IAO_0000115: Software R package for RNA-Seq Differential Expression Analysis.

MRC Laboratory of Molecular Biology
type: Organization
type: NamedIndividual
has db xref: grid.42475.30
has db xref: ISNI: 0000 0004 0605 769X
has db xref: nif-0000-38323
has db xref: Wikidata: Q185800
abbrev: LMB
IAO_0000115: The MRC Laboratory of Molecular Biology (LMB) has long been, and remains, a world-class research laboratory. Our primary goal is to understand biological processes at the molecular level, through the application of methods drawn from physics, chemistry and genetics. This quest extends from structural studies of individual macromolecules, through their interactions and beyond to the functioning of subcellular systems, cells and multicellular systems in whole organisms, with the ultimate aim of using this knowledge to tackle specific problems in human health and disease. The LMB is one of the birthplaces of modern molecular biology. Many techniques were pioneered at the laboratory, most notably methods for determining the three-dimensional structure of proteins and DNA sequencing. Whole genome sequencing was initiated at the LMB. Another landmark discovery was the invention of monoclonal antibodies. Over the years, the work of LMB scientists has attracted 9 Nobel Prizes, shared between 13 LMB scientists, as well as numerous other prizes and scientific awards.

alt-metrics: a manifesto
type: Resource
type: NamedIndividual
has db xref: nif-0000-39065
synonym: altmetrics
abbrev: alt-metrics
IAO_0000115: altmetrics is the creation and study of new metrics based on the Social Web for analyzing, and informing scholarship. No one can read everything. We rely on filters to make sense of the scholarly literature, but the narrow, traditional filters are being swamped. However, the growth of new, online scholarly tools allows us to make new filters; these alt-metrics reflect the broad, rapid impact of scholarship in this burgeoning ecosystem. We call for more tools and research based on alt-metrics. * Tools: Browse a directory of noteworthy altmetrics apps. * Media: Watch videos of altmetrics presentations.

PharmGKB Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157636
abbrev: pharmgkb-owl
IAO_0000115: An OWL representation of the data in PharmGKB, Comparative Toxicogenomics Database (CTD) and DrugBank and linked to related ontologies: ChEBI ontology, the Human Disease Ontology (DO), the Anatomical Therapeutic Chemical Classification System (ATC) and the Medical Subject Headings Thesaurus (MESH). The combined knowledge base can be exploited using the ELK reasoner.

Physico-Chemical Process
type: Resource
type: NamedIndividual
has db xref: nlx_157639
synonym: Physico-Chemical Process (REX)
abbrev: REX
IAO_0000115: An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. It includes both microscopic processes (involving molecular entities or subatomic particles) and macroscopic processes. Some biochemical processes from Gene Ontology (GO Biological process) can be described as instances of REX.

BAMS Cells
type: Resource
type: NamedIndividual
has db xref: nif-0000-90175
synonym: Brain Architecture Management System Cells
abbrev: BAMS Cell
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023.BAMS is an online resource for information about neural circuitry. The BAMS Cell view focuses on the major brain regions and which cells are contained therein.

MSMS
type: Resource
type: NamedIndividual
has db xref: OMICS_04381
IAO_0000115: A coalescent simulation software program for a structured population including recombination, demographic structure and selection at a single diploid locus.

Eton Bioscience
type: Organization
type: NamedIndividual
has db xref: nlx_152359
synonym: Eton Bioscience Inc.
IAO_0000115: An Antibody supplier

FSSP - Families of Structurally Similar Proteins
type: Resource
type: NamedIndividual
has db xref: nlx_10193
synonym: families of structurally similar proteins
abbrev: FSSP
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented September 6, 2016. FSSP (families of structurally similar proteins) is a database of structural alignments of proteins in the Protein Data Bank. The database currently contains an extended structural family for each of…

RNA Modification Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-03414
abbrev: RNAmods
IAO_0000115: The RNA modification database provides a comprehensive listing of posttranscriptionally modified nucleosides from RNA. Information provided for each nucleoside includes: the type of RNA in which it occurs and phylogenetic distribution; common chemical name and symbol; Chemical Abstracts registry number and index name; chemical structure; initial literature citations for structural characterization or occurrence, and for chemical synthesis. Both the structural diversity and extent of posttranscriptional modification in RNA is remarkable, with 107 different nucleosides presently known in all types of RNA. The discovery of new modified nucleosides as well as increasing knowledge of the array of functional roles of modification, based largely on extensive studies of tRNA, mandates a need for a comprehensive database of RNA nucleosides. The RNA Modification Database is maintained as an extension of the initial version published in mid-1994. The database consists of all RNA-derived ribonucleosides of known structure, including those from established sequence positions, as well as those detected or characterized from hydrolysates of RNA. The information provided permits access to the modified nucleoside literature through provision of both computer-searchable Chemical Abstracts registry numbers and key literature citations. This database also provides an historical record of the initial reports of occurrence, characterization and chemical synthesis of modified nucleosides from RNA. It is our judgement that the total number of RNA nucleosides listed, and the chemical structures reported, are very accurate. However, the distributions listed are in some cases a matter of concern, due primarily to the possibility of inhomogeneity of the RNA isolate and the use of methods of nucleoside identification that are not sufficiently rigorous. Reinvestigation of some of the unusual or single-report source distributions is warranted, and will likely lead to future refinements in the lis…

SpecimenCentral.com
type: Resource
type: NamedIndividual
has db xref: nlx_10317
synonym: Specimen Central
synonym: SpecimenCentral
IAO_0000115: World's open biospecimen research database where biobanks and biomedical researchers meet to exchange human biospecimen needs and supply: whole blood, serum, plasma, solid tissue samples and more. The connection is accelerated so researchers save valuable time and money and tissue banks utilize inventory. The pace of specimen procurement remains unacceptably slow to the biomedical research community. Specimen Central is the foremost global resource to aid biomedical researchers in expediting their search for high quality human biospecimens, tissues, samples and specimens. They facilitate your search for blood, whole blood, buccal swab, DNA, RNA, protein, cell lines, plasma, serum, RBC, white cells, buffy coat, fluid, marrow, urine, stem cells, and solid tissue such as tumor, tumor and biopsy materials spanning all manner of common and rare pathologies and indications including Alzheimer's, basal cell carcinoma, bladder cancer, bone cancer, brain cancer, breast cancer, cerebrospinal fluid, amniotic fluid, colorectal cancer, colon cancer, hodgkins and non-hodgkins lymphoma, kidney/renal cancer, leukemia, liver cancer, lung cancer, melanoma, multiple sclerosis, myeloma neuroblastoma, neurodegenerative diseases, ovarian cancer, pancreatic cancer, prostate cancer, urinary cancer. This includes adult and pediatric indications. Specimen Central users specify a number of variables in their Specimen Requests, including preparation, preservation and handling requirements such as cryo-preserved, FFPE (Formalin-fixed paraffin-embedded), formalin, frozen, refrigerated, OCT, snap frozen, paraffin block, fresh, prospective, autopsy or cadaveric, etc. Many users require clinically annotated date associated with their specimens, as well as documentation of IRB or ethics committee approval and informed consents. For Researchers Most specimen databases require researchers to waste time and effort entering lengthy registrations and search queries that yield poor results, if anything. S…

Neuro Bureau - Berlin Mind and Brain Sample
type: Resource
type: NamedIndividual
has db xref: nlx_157646
synonym: Neuro Bureau - Berlin: Mind & Brain Sample
synonym: Neuro Bureau/Berlin Mind and Brain Institute Sample
abbrev: Neuro Bureau/Berlin Mind and Brain Sample
IAO_0000115: Dataset consisting of a community sample of individuals ranging in age from 18 to 60 years old with at least two 7.5-minute resting state fMRI scans. During the resting state scan participants were instructed to relax while keeping their eyes open. In part of the sample eye status was randomized between scans. The particular eye status for each scan is indicated in the phenotypic information. No visual stimulus was presented. A subset of participants completed the ICS and PANAS affective behavior scales. The following data are released for every participant: * Scanner Type: Siemens, 3T Trio Tim * 7.5-minute resting state fMRI scan (R-fMRI) * MPRAGE anatomical scan, defaced to protect patient confidentiality * Demographic information, inluding ICS and PANAS scores (included in the release file).

Quiron-Valencia Sample
type: Resource
type: NamedIndividual
has db xref: nlx_157647
abbrev: CQV Sample
IAO_0000115: Resting state datasets, including an anatomical as well as a resting state fMRI scan, collected from a community sample in Valencia, Spain. The first release includes data for 45 participants. Participants were instructed to keep their eyes open during the resting state scan, no visual stimulus was presented. The following data are released for every participant: * Scanner Type: Philips Achieva 3T-TX * One high-resolution T1-weighted mprage, defaced to protect patient confidentiality * At least one 6-minute resting state fMRI scan (R-fMRI), eyes open, no visual stimulus presented * Demographic Information

Christopher Newport University; Virginia; USA
type: Organization
type: NamedIndividual
has db xref: nlx_143956
synonym: Christopher Newport University
abbrev: CNU
IAO_0000115: Public university in Newport News, Virginia. Academic programs at CNU encompass more than 80 areas of study, from biology to business administration and political science to performing arts.

Open Rotterdam Glaucoma Imaging Data Sets
type: Resource
type: NamedIndividual
has db xref: nlx_157652
abbrev: ORGIDS
IAO_0000115: Data sets resulting from glaucoma research including visual fields, various imaging modalities and other data from both glaucomatous and normal subjects. The Longitudinal Glaucomatous Visual Fields data set contains IOP (Intraocular pressure) measurements and 24-2 Full Threshold visual fields obtained with a Humphrey Field Analyzer (Zeiss). Data of both eyes of 139 patients over a mean period of over 9 years is included, with on average more than 17 fields per eye. Local threshold and total deviation values are included.

eyeMoviePedia
type: Resource
type: NamedIndividual
has db xref: nlx_157655
has db xref: r3d100012558
IAO_0000115: Archive and access films from the field of Ophthalmology for free on highly secure servers for permanent access and citeability. A citeable identification number (specific addressing using DOI), allows for citation of individual films in journal publications. Films may be commented by the author either in speech, or in text. Key wording provided by the authors at the time of submission, make each film recognizable to internet search machines.

Sage Bionetworks Podcasts
type: Resource
type: NamedIndividual
has db xref: nlx_10797
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented September 6, 2016. Sage Bionetworks video podcasts feature the plenary talks from the April 2011 Commons Congress in San Francisco. The Keynote and project update video posts are in reverse chronological order; the ful…

MapMan
type: Resource
type: NamedIndividual
has db xref: nlx_157682
synonym: MapMan Application Software
IAO_0000115: Software tool that displays large genomics datasets (e.g. gene expression data from Arabidopsis Affymetrix arrays) onto diagrams of metabolic pathways or other biological processes.

Arizona Cancer Center Tumor Bank
type: Resource
type: NamedIndividual
has db xref: nlx_10808
abbrev: AZCC Tumor Bank
IAO_0000115: TACMASS collects, preserves, and banks biospecimens obtained from Arizona Cancer Center surgical patients who are seen by University Medical Center surgeons and oncologists. Biospecimens collected at the time of surgery include fresh surgical tissue, blood and urine. Serum, plasma and genomic DNA are harvested from the whole blood. AZCC Members and collaborators may request the use of banked biospecimens through TACMASS. The patient's surgeon or oncologist is responsible for consenting the patient for submission of surgical specimens to the AZCC BioRepository (IRB #06-0609-04, Setsuko Chambers, PI). The surgeon and the Department of Pathology attending physicians and residents are responsible for identifying appropriate tissue for banking that will not compromise pathological diagnosis. Tumor and/or normal adjacent tissue, identified by gross examination, that will not be needed for pathological diagnosis are preserved by fixing in formalin, snap freezing, and/or fixing in RNALater. Histological diagnosis is rendered on each piece of formalin-fixed and snap frozen tissue by Hematoxylin and Eosin staining (H&E). Everyone involved in submitting specimens to the Tumor Bank must maintain a current CITI Certification.

GraphML
type: Resource
type: NamedIndividual
has db xref: nlx_157666
synonym: The GraphML File Format
IAO_0000115: A file format for graphs that consists of a language core to describe the structural properties of a graph and a flexible extension mechanism to add application-specific data. It is based on XML and is ideally suited as a common denominator for all kinds of services generating, archiving, or processing graphs. Its main features include support of * directed, undirected, and mixed graphs, * hypergraphs, * hierarchical graphs, * graphical representations, * references to external data, * application-specific attribute data, and * light-weight parsers.

Integrated Molecular Interaction Database
type: Resource
type: NamedIndividual
has db xref: nlx_157667
abbrev: IMID
IAO_0000115: Database for molecular interaction information integrated with various other bio-entity information, including pathways, diseases, gene ontology (GO) terms, species and molecular types. The information is obtained from several manually curated databases and automatic extraction from literature. There are protein-protein interaction, gene/protein regulation and protein-small molecule interaction information stored in the database. The interaction information is linked with relevant GO terms, pathway, disease and species names. Interactions are also linked to the PubMed IDs of the corresponding abstracts the interactions were obtained from. Manually curated molecular interaction information was obtained from BioGRID, IntAct, NCBI Gene, and STITCH database. Pathway related information was obtained from KEGG database, Pathway Interaction database and Reactome. Disease information was obtained from PharmGKB and KEGG database. Gene ontology terms and related information was obtained from Gene Ontology database and GOA database.

Chung-Ang University; Seoul; South Korea
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100002460
has db xref: grid.254224.7
has db xref: ISNI:0000 0001 0789 9563
has db xref: nlx_10442
has db xref: Wikidata:Q41790
synonym: CAU
IAO_0000115: Private comprehensive research university in South Korea. Starting as a church-run kindergarten in 1918, CAU transformed into a school for female kindergarten teachers in 1922 and was granted university status in 1953.

Equitech-Bio
type: Organization
type: NamedIndividual
has db xref: nlx_152358
IAO_0000115: Provides animal and human serums, plasmas, purified proteins, and antisera.

Program on Ontologies of Neural Structures
type: Resource
type: NamedIndividual
has db xref: nlx_157669
synonym: INCF Program on Ontologies of Neural Structures
abbrev: PONS
IAO_0000115: Program consisting of three Task Forces and one Working Group to promote data exchange and integration in the neurosciences by developing terminology standards and formal ontologies for neural structures. Closely linked to the Program on Digital Brain Atlasing, the Program aims to establish a structured lexicon for the translation and definition of terms describing neural structures at multiple levels of granularity. The three Task Forces and one Working Group involved in the PONS effort: * Structural lexicon * Neuron registry * Representation and deployment * KnowledgeSpace Working Group Structural lexicon, Neuron registry, Representation and deployment, and KnowledgeSpace Working Group.

AAL
type: Resource
type: NamedIndividual
has db xref: nlx_157677
synonym: Automated Anatomical Labeling
IAO_0000115: Software for automated anatomical labeling of activations in SPM (Statistical Parametric Mapping) using a macroscopic anatomical parcellation of the MNI MRI single-subject brain. The software was used for an automated anatomical parcellation of the spatially normalized single-subject high-resolution T1 volume provided by the Montreal Neurological Institute (MNI) (D. L. Collins et al., 1998, Trans. Med. Imag. 17, 463468, PubMed). Using this parcellation method, three procedures to perform the automated anatomical labeling of functional studies were proposed: (1) labeling of an extremum defined by a set of coordinates, (2) percentage of voxels belonging to each of the anatomical volumes of interest (AVOI) intersected by a sphere centered by a set of coordinates, and (3) percentage of voxels belonging to each of the AVOI intersected by an activated cluster. An interface with the Statistical Parametric Mapping package is provided as a freeware to researchers of the neuroimaging community.

NIH Data Sharing Repositories
type: Resource
type: NamedIndividual
has db xref: nlx_157683
IAO_0000115: A listing of NIH supported data sharing repositories that make data accessible for reuse. Most accept submissions of appropriate data from NIH-funded investigators (and others), but some restrict data submission to only those researchers involved in a specific research network. Also included are resources that aggregate information about biomedical data and information sharing systems. The table can be sorted according by name and by NIH Institute or Center and may be searched using keywords so that you can find repositories more relevant to your data. Links are provided to information about submitting data to and accessing data from the listed repositories. Additional information about the repositories and points-of-contact for further information or inquiries can be found on the websites of the individual repositories.

Biomine
type: Resource
type: NamedIndividual
has db xref: nlx_157687
IAO_0000115: Service that integrates cross-references from several biological databases into a graph model with multiple types of edges, such as protein interactions, gene-disease associations and gene ontology annotations. Edges are weighted based on their type, reliability, and informativeness. In particular, it formulates protein interaction prediction and disease gene prioritization tasks as instances of link prediction. The predictions are based on a proximity measure computed on the integrated graph.

International Classification for Patient Safety
type: Resource
type: NamedIndividual
has db xref: nlx_157446
abbrev: ICPS
IAO_0000115: Ontology network about Patient Safety Incident. This work has been carried out by the Ontological Engineering Group, using sources from the University of Saint Etienne and the Australian Patient Safety Foundation.

SEGS
type: Resource
type: NamedIndividual
has db xref: nlx_157688
synonym: Search for Enriched Gene Sets
IAO_0000115: A web tool for descriptive analysis of microarray data. The analysis is performed by looking for descriptions of gene sets that are statistically significantly over- or under-expressed between different scenarios within the context of a genome-scale experiments (DNA microarray). Descriptions are defined by using the terms from the Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and gene-gene interactions found in the ENTREZ database. Gene annotations by GO and KEGG terms can also be found in the ENTREZ database. The tool provides three procedures for testing the enrichment of the gene sets (over- or under-expressed): Fisher's exact test, GSEA and PAGE, and option for combining the results of the tests. Because of the multiple-hypothesis testing nature of the problem, all the p-values are computed using the permutation testing method.

Global Alliance for Genomics and Health
type: Resource
type: NamedIndividual
has db xref: nlx_157691
synonym: GA4GH
synonym: Global Alliance for Genomics & Health
abbrev: Global Alliance
IAO_0000115: An international coalition formed to enable the sharing of genomic and clinical data to help unlock potential advancements in medicine and science. Bringing together more than 145 leading institutions working in healthcare, research, disease advocacy, life science, and information technology, the Global Alliance is working together to create and promulgate harmonized approaches to enable the responsible, voluntary, and secure sharing of genomic and clinical data.

WikiSurgery - The Free Surgical Encyclopedia
type: Resource
type: NamedIndividual
has db xref: nlx_11092
synonym: Wikisurgery
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. A free surgical encyclopedia for surgeons and their patients. Contributions in the form of new articles and editing can be made by anyone at anytime anywhere in the world. With over 33,000 articles for surgeons and patients, including news, articles, operation scripts, biographies and images. The website is a "wiki" which allows for the collaborative editing and building of content. Contributions in the form of new articles and editing can be made by those who register on the site, confirm their email address and whose application is accepted by an administrator. Wikisurgery is more than just a depot of surgical knowledge, not just articles about facts but also articles about controversy, debates, with none of the usual editorial limits on space. Indeed we hope it will become a record of surgical thought, experience and progression. Key Topics: Operation Scripts, Basic Surgical Skills Training Program, Basic Laparoscopic Training Program, Operative Images, Patient Information; there is also a Featured Videos section.

GSE4922
type: Resource
type: NamedIndividual
has db xref: nlx_157796
IAO_0000115: Curated data set of a study that investigated the expression profiles of 347 primary invasive breast tumors on Affymetrix microarrays. Three separate breast cancer cohorts were analyzed: 1) Uppsala (n=249), 2) Stockholm (n=58), 3) Singapore (n=40). The Uppsala and Singapore data can be accessed in GSE4922. The Stockholm cohort data can be accessed at GEO Series GSE1456.

Cryogenic Laboratories, Inc
type: Resource
type: NamedIndividual
has db xref: nlx_11110
IAO_0000115: A US sperm bank that offers superior donor sperm and sperm banking services, including sperm storage and embryo storage. We provide the highest quality in the industry as one of the few sperm banks fully accredited by the American Association of Tissue Banks (AATB). Cryogenic Laboratories is fully compliant with FDA regulations. Extensive donor Information is downloaded FREE for ALL sperm donors. Searching for a donor is fun, easy and free of charge. Most other sperm banks require you to pay for each donor information product you view. So look and listen for free 24/7. Childhood photos, audio clips, medical and personal profiles are all free. Monthly specials are also there to make the process easier.

Partners HealthCare Biorepository
type: Resource
type: NamedIndividual
has db xref: nlx_11156
synonym: Partners HealthCare Center for Personalized Genetic Medicine Biorepository
synonym: PCPGM Biorepository
abbrev: Partners Biorepository
IAO_0000115: Two biorepositories, operated by the Partners HealthCare Center for Personalized Genetic Medicine, to serve the research community at Partners HealthCare. The BioSample Services Facility (BSF) provides sample storage and processing services. The Partners Biorepository for Medical Discovery (PBMD) is an enterprise-wide repository of high-quality, consented samples available to foster genetic research and advance understanding of genetic causes of common, complex diseases. Services provided by these cores include assistance with the collection and processing of samples for research use, extraction of DNA and isolation of serum and or plasma with monitored cryogenic storage to provide stability and availability of the materials. After processing, and in conjunction with the BioSample Services Facility, the samples stored within the Biorepository for Medical Discovery may be arrayed for further processing via multiple molecular techniques such as - sequencing, genotyping, and expression profiling.

Automatic Analysis
type: resource
type: NamedIndividual
has db xref: nlx_157695
synonym: AutomaticAnalysis
synonym: automaticanalysis
abbrev: aa
IAO_0000115: Integration framework for major open source packages in neuroimaging including SPM, FSL, FreeSurfer, EEGLAB, and Fieldtrip. Efficient neuroimaging workflows and parallel processing using Matlab and XML. Addresses challenges of processing multimodal datasets, like combining anatomy, functional MRI, diffusion, and EEG, to yield integrated views of brain. Allows to design, execute, and share pipelines utilizing multiple open source packages. Supports parallelized execution to address challenges of large cohort studies and provides quality control offering group statistics and reporting facilities to help identify outlier subjects and erroneous processing steps.

Donders Machine Learning Toolbox
type: Resource
type: NamedIndividual
has db xref: nlx_157696
abbrev: DMLT
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. A machine learning toolbox written in Matlab and C that provides a general interface to support the integration of new statistical machine learning methods by writing high level wrappers. It allows complex methods to be built from simple building blocks and makes the use of cross-validation and permutation testing as easy as writing one line of Matlab code. The code requires at least Matlab distribution 7.6.0.324 (R2008a).

PheWAS Catalog
type: Resource
type: NamedIndividual
has db xref: nlx_157697
synonym: Phenome-wide association studies Catalog
IAO_0000115: Catalog of phenome-wide association study (PheWAS) results for 3,144 single-nucleotide polymorphisms (SNPs) present in the NHGRI GWAS Catalog as of 4/17/2012 in 13,835 European-ancestry individuals from five sites of the Electronic Medical Records and Genomics (eMERGE) network. A total of 1,358 EMR-derived phenotypes were analyzed for each SNP. This PheWAS replicated 66% (51/77) of sufficiently powered prior GWAS associations, and 210/751 of all prior GWAS associations. They also identified 63 potentially pleiotropic associations with p < 4.6x10-6 (false discovery rate < 0.1); the strongest of these novel associations replicated in an independent cohort (n=7,406). The catalog contains all associations with p < 0.05 (uncorrected)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

NCI Thesaurus
type: Resource
type: NamedIndividual
has db xref: nlx_157698
synonym: ncithesaurus
abbrev: NCIt
IAO_0000115: A reference terminology and core biomedical ontology for NCI that covers approximately 100,000 key biomedical concepts with terms, codes, definitions, and more than 200,000 inter-concept relationships. It is the reference terminology for NCI, NCI Metathesaurus and NCI informatics infrastructure covering vocabulary for clinical care, translational and basic research, and public information and administrative activities. It includes broad coverage of the cancer domain, including cancer related diseases, findings and abnormalities; anatomy; agents, drugs and chemicals; genes and gene products and so on. In certain areas, like cancer diseases and combination chemotherapies, it provides the most granular and consistent terminology available. It combines terminology from numerous cancer research related domains, and provides a way to integrate or link these kinds of information together through semantic relationships. NCIt features: * Stable, unique codes for biomedical concepts; * Preferred terms, synonyms, definitions, research codes, external source codes, and other information; * Links to NCI Metathesaurus and other information sources; * Over 200,000 cross-links between concepts, providing formal logic-based definition of many concepts; * Extensive content integrated from NCI and other partners, much available as separate NCIt subsets * Updated frequently by a team of subject matter experts. NCIt is a widely recognized standard for biomedical coding and reference, used by a broad variety of public and private partners both nationally and internationally including the Clinical Data Interchange Standards Consortium Terminology (CDISC), the U.S. Food and Drug Administration (FDA), the Federal Medication Terminologies (FMT), and the National Council for Prescription Drug Programs (NCPDP).

Cure Alzheimers Fund
type: Resource
type: NamedIndividual
has db xref: nlx_11948
abbrev: CAF
IAO_0000115: Cure Alzheimer's Fund is a 501(c)(3) public charity. At Cure Alzheimer's Fund, our mission is to fund research with the highest probability of slowing, stopping or reversing Alzheimer's disease. This topical portal has a lot of information including news and blog. Cure Alzheimer's Fund is governed by a board of directors; administered by a small, full-time staff; and guided scientifically by a Research Consortium. A Scientific Advisory Board audits the research program to make sure it is consistent with the objectives of the foundation. Cure Alzheimer's Fund is a doing business as name for the Alzheimer's Disease Research Foundation, federal tax ID # 52-2396428.

NCI Metathesaurus
type: Resource
type: NamedIndividual
has db xref: nlx_157699
abbrev: NCIm
IAO_0000115: A wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. NCIm features: * Maps 4,000,000 terms from more than 75 sources into 2,000,000 biomedical concepts that represent their meaning. * Displays preferred terms, synonyms, definitions, and other information from each source. * Links to NCI Thesaurus and other related information sources. * Contains 22,000,000 cross-links between content elements. * Updated frequently by a team of biomedical terminology and subject matter experts. NCIm contains most public domain terminologies from the National Library of Medicine's UMLS Metathesaurus, as well as many other biomedical terminologies created by or of interest to NCI and its partners. Some propriety terminologies are included, with permission, and have restrictions on their use. The current version of the NCI Metathesaurus, based on the UMLS build 2013AA, covers up to National Cancer Institute Thesaurus, 13.12d. A viewer for the UMLS changes document can be downloaded.

BTMORPH
type: Resource
type: NamedIndividual
has db xref: nlx_157700
IAO_0000115: Small Python library containing a data structure and tools to represent and analyze neuronal morphologies stored in the de facto standard SWC format.

NetPath
type: Resource
type: NamedIndividual
has db xref: nlx_157701
has db xref: r3d100011009
IAO_0000115: A manually curated resource of signal transduction pathways in humans. All pathways are freely available for download in BioPAX level 3.0, PSI-MI version 2.5 and SBML version 2.1 formats. The slim pathway models representing only core reactions in each pathway are available at NetSlim. All the NetPath pathway models are also submitted to WikiPathways., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

PDZBase
type: Resource
type: NamedIndividual
has db xref: nlx_157703
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022.A manually curated protein-protein interaction database developed specifically for interactions involving PDZ domains. It currently contains 339 experimentally determined protein protein interactions.

SignaLink
type: Resource
type: NamedIndividual
has db xref: nlx_157704
IAO_0000115: An integrated resource to analyze signaling pathway cross-talks, transcription factors, miRNAs and regulatory enzymes. The multi-layered database structure is made up of signaling pathways, their pathway regulators (e.g., scaffold and endocytotic proteins) and modifier enzymes (e.g., phosphatases, ubiquitin ligases), as well as transcriptional and post-transcriptional regulators of all of these components. The website allows the interactive exploration of how each signaling protein is regulated. Features * experimental data not only from humans but from two invertebrate model organisms, C. elegans and D. melanogaster; * combines manual curation with large-scale datasets; * provides confidence scores for each interaction; * operates a customizable download page with multiple file formats (e.g., BioPAX, Cytoscape, SBML).

Chungbuk National University; Cheongju; South Korea
type: NamedIndividual
has db xref: nlx_152135
synonym: Chungbuk National University
abbrev: CBNU

Adverse Event Reporting Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_11209
abbrev: AERO
IAO_0000115: An ontology aimed at supporting clinicians at the time of data entry, increasing quality and accuracy of reported adverse events.

HealthGrid Wiki
type: Resource
type: NamedIndividual
has db xref: nlx_12797
synonym: HealthGrid
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. HealthGrid is a wiki dedicated to grids for health. It is maintained as a dynamic knowledge resource for the healthgrid community. The HealthGrid community (a world-wide initiative) gathers individuals from the public and private domain world-wide who are actively exploring the beneficial impact of healthgrid technology on healthcare provision and research.

RAREMETAL
type: Resource
type: NamedIndividual
has db xref: biotools:raremetal
has db xref: OMICS_00243
IAO_0000115: A software program that facilitates the meta-analysis of rare variants from genotype arrays or sequencing.

Experimental Factor Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_11363
abbrev: EFO
IAO_0000115: An application focused ontology modelling the experimental factors in ArrayExpress and Gene Expression Atlas. It has been developed to increase the richness of the annotations that are currently made in the ArrayExpress repository, to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The ontology describes cross-product classes from reference ontologies in area such as disease, cell line, cell type and anatomy. The methodology employed in the development of EFO involves construction of mappings to multiple existing domain specific ontologies, such as the Disease Ontology and Cell Type Ontology. This is achieved using a combination of automated and manual curation steps and the use of a phonetic matching algorithm. The ontology is evaluated with use cases from the ArrayExpress repository and ArrayExpress Atlas. You may also browse the EFO in the NCBO Bioportal. Term submissions are welcome.

Corpus Callosum Thickness Profile Analysis Pipeline
type: Resource
type: NamedIndividual
has db xref: nlx_157716
abbrev: ccsegthickness
IAO_0000115: An end-to-end pipeline for corpus callosum processing that provides automated midsagittal alignment, CC segmentation with a quality control tool, and thickness profile generation. Groupwise analysis is facilitated by permutation testing with FWER and FDR multiple comparison correction. Results display is facilitated by a display script that shows p-values on a 3D pipe representation of a CC. This pipeline is implemented in MATLAB and requires the Image Processing Toolbox. There are plans to implement it completely in Python.

BIND
type: Resource
type: NamedIndividual
has db xref: nlx_11393
synonym: Biomolecular Interaction Network Database
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. Designed to capture protein function, defined at molecular level as set of other molecules with which protein interacts or reacts along with molecular outcome. Archives biomolecular interaction, complex and pathway information. A web-based system is available to query, view and submit records. BIND continues to grow with the addition of individual submissions as well as interaction data from the PDB and a number of large-scale interaction and complex mapping experiments using yeast two hybrid, mass spectrometry, genetic interactions and phage display.

Synapse Web
type: Resource
type: NamedIndividual
has db xref: nif-0000-00026
synonym: SynapseWeb
IAO_0000115: A portal into the 3D ultrastructure of the brain providing: Anatomy of astrocytes, axons, dendrites, hippocampus, organelles, synapses; procedures of 3D reconstruction and tissue preparation; as well as an atlas of ultrastructural neurocytology (by Josef Spacek), online aligned images, and reconstructed dendrites. Synapse Web hosts an ultrastructural atlas containing more than 500 electron micrographs (added to regularly) that identify unique ultrastructural and cellular components throughout the brain. Additionally, Synapse Web has raw images, reconstructions, and quantitative data along with tutorial instructions and numerous tools for investigating the functional structure of objects that have been serial thin sectioned for electron microscopy.

RNAdb
type: Resource
type: NamedIndividual
has db xref: nif-0000-03417
synonym: RNAdb 2.0 - A database of mammalian noncoding RNAs
IAO_0000115: A comprehensive mammalian noncoding RNA database containing sequences and annotations for tens of thousands of noncoding RNAs. These include a wide range of microRNAs, small nucleolar RNAs and larger mRNA-like ncRNAs. All raw data from the original RNAdb 2.0 database can be downloaded in XML or FASTA format. This website serves to archive the final snapshot of the RNAdb 2.0 datasets for legacy purposes. It will remain active indefinitely.

Mass Spectrometry Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157465
abbrev: MS
IAO_0000115: A structured controlled vocabulary for the annotation of mass spectrometry experiments.

Torrey Pines Biolabs
type: Organization
type: NamedIndividual
has db xref: nlx_152481
synonym: Torrey Pines Biolabs Inc
synonym: Torrey Pines Biolabs Inc.
IAO_0000115: An Antibody supplier

RevMan
type: Resource
type: NamedIndividual
has db xref: OMICS_00244
synonym: Review Manager
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A software package that does meta-analysis and provides results in tabular format and graphically., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

KNOSSOS
type: Resource
type: NamedIndividual
has db xref: nlx_157725
IAO_0000115: Software tool for the visualization and annotation of 3D image data and was developed for the rapid reconstruction of neural morphology and connectivity. By dynamically loading only data from the surround of the current view point, seamless navigation is not limited to datasets that fit into the available RAM but works with much larger dataset stored in a special format on disk. Currently, KNOSSOS is limited to 8-bit data. In addition to viewing and navigating, KNOSSOS allows efficient manual neurite annotation (''skeletonization''). KNOSSOS is being used mostly for reconstructing cell morphologies from 3D electron microscopic data generated by Serial Block-Face Electron Microscopy (SBEM), with an occasional application to 2-photon and confocal optical microscopy data.

National Neurological AIDS Bank
type: Resource
type: NamedIndividual
has db xref: nlx_12023
synonym: National Neurology AIDS Bank (NNAB)
abbrev: NNAB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 23, 2012. The National Neurologic AIDS Bank (NNAB) is a site of the HIV/CNS Tissue Network. Based in Los Angeles, which has the largest and most diverse AIDS population in the western United States, the NNAB provides researchers with well-characterized neural tissue from HIV-1-infected and seronegative control donors. The NNAB collaborates with the other designated sites, funding agencies, and outside experts to develop local and national tissue networks. There are plans to create a Network Steering Committee, a panel of outside advisers, and a protocol to recruit and characterize human donors. The NNAB collects pre- and post-mortem clinical data and neural tissues using a standardized autopsy protocol, and the bank stores, codes, catalogs, and distributes this tissue. An electronic database and an Internet-based application process that researchers can use to access the Network's resources are being designed.

nornir-buildmanager
type: Resource
type: NamedIndividual
has db xref: nlx_157730
abbrev: Nornir-buildmanager
IAO_0000115: Software package that constructs 2D and 3D datasets from 2D image mosaics using the nornir tools. This produces a set of images and transforms on disk which can be accessed via Viking, HTTP, or written as a stack of images.

Nornir
type: Resource
type: NamedIndividual
has db xref: nlx_157731
IAO_0000115: A set of Python software packages that takes large sets of overlapping images in 2D and 3D and produces registered (aligned) 3D volumes at any size and scale. These tools were originally designed to construct 3D connectomics volumes from terabytes of image data for the Marc lab at the University of Utah Moran Eye Center.

Mount Sinai Allograft Technologies
type: Resource
type: NamedIndividual
has db xref: nlx_12054
synonym: Rubinoff Bone Bank
synonym: The Rubinoff Bone Bank
IAO_0000115: Mount Sinai Allograft Technologies, a department of Mount Sinai Hospital formerly known as the The Rubinoff Bone Bank, has been a leader in advanced tissue innovations since 1972. We are committed to providing the highest quality bone and tissue allograft products as well as continued innovation in the development of allograft implants for transplantation. We are dedicated to meeting all surgical needs and to exceed all client expectations. We work closely with the Trillium Gift of Life Network to promote their mission of increasing donor awareness and to ensure that the wishes of Ontario donor families' are carried out with the utmost care and respect. Our allograft implants are 100% Ontario produced, human allograft tissues. To produce the safest and highest quality Canadian produced allograft implants, Mount Sinai Allograft Technologies leverages the expertise of a variety of medical experts, state-of-the art laboratory testing, proven bio-processing techniques, validated irradiation methods and preferred packaging systems.

Datavyu
type: Resource
type: NamedIndividual
has db xref: nlx_157734
IAO_0000115: Free, Java-based video coding and data visualization tool for collecting behavioral data from video. It supports all video formats that Quicktime or VLC can play, including .asf, .wmv, .avi, .flv, .mov, .mpf, .ogg, .mpg, .nsc, .wav, and .dts. It exports data in a variety of forms depending on analysis needs.

ALLBUS - German General Social Survey
type: Resource
type: NamedIndividual
has db xref: nlx_157750
synonym: ALLBUS (Allgemeine Bev?lkerungsumfrage der Sozialwissenschaften) (German General Social Survey)
synonym: Allgemeine Bev?lkerungsumfrage der Sozialwissenschaften
synonym: German General Social Survey
abbrev: ALLBUS
IAO_0000115: Data set of up-to-date data on attitudes, behavior, and social structure in Germany. Every two years since 1980 a representative cross section of the population is surveyed using both constant and variable questions. The ALLBUS data become available to interested parties for research and teaching as soon as they are processed and documented.

Dartmouth Science Division Electronics Shop
type: Resource
type: NamedIndividual
has db xref: nlx_156242
IAO_0000115: Core facility that provides the following services: Printed circuit fabrication, Printed circuit board assembly, System design and fabrication. David Collins is NASA certified for electrical assembly.

DTU Center for Biological Sequence Analysis
type: Resource
type: NamedIndividual
has db xref: nlx_12329
abbrev: CBS
abbrev: DTU CBS
IAO_0000115: Center for Biological Sequence Analysis of the Technical University of Denmark conducts basic research in the field of bioinformatics and systems biology and directs its research primarily towards topics related to the elucidation of the functional aspects of complex biological mechanisms. A large number of computational methods have been produced, which are offered to others via WWW servers. Several data sets are also available. The center also has experimental efforts in gene expression analysis using DNA chips and data generation in relation to the physical and structural properties of DNA. The on-line prediction services at CBS are available as interactive input forms. Most of the servers are also available as stand-alone software packages with the same functionality. In addition, for some servers, programmatic access is provided in the form of SOAP-based Web Services. The center also educates engineering students in biotechnology and systems biology and offers a wide range of courses in bioinformatics, systems biology, human health, microbiology and nutrigenomics.

Phenotree
type: Resource
type: NamedIndividual
has db xref: nlx_157736
synonym: Forward Genomics - Phenotree search
synonym: Forward Genomics - Phenotree server
IAO_0000115: Web server to search for genes involved in given phenotypic difference between mammalian species. The mouse-referenced multiple alignment data files used to perform the forward genomics screen is also available. The webserver implements one strategy of a Forward Genomics approach aiming at matching phenotype to genotype. Forward genomics matches a given pattern of phenotypic differences between species to genomic differences using a genome-wide screen. In the implementation, the divergence of the coding region of genes in mammals is measured. Given an ancestral phenotypic trait that is lost in independent mammalian lineages, it is shown that searching for genes that are more diverged in all trait-loss species can discover genes that are involved in the given phenotype.

Enhancer Trap Line Browser
type: Resource
type: NamedIndividual
has db xref: nlx_157737
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Database and atlas of transgenic mouse lines that are generated by random insertion of enhancer trap probes. The trapped lines have highly restricted expression of tet transcription activator (some lines also have Cre DNA recombinase), which enables genetic manipulations in specific cell types.

TPA
type: Resource
type: NamedIndividual
has db xref: nlx_157738
has db xref: r3d100010506
synonym: NCBI Third Party Annotation
synonym: NCBI TPA
synonym: Third Party Annotation
IAO_0000115: Database designed to capture experimental or inferential results that support submitter-provided annotation for sequence data that the submitter did not directly determine but derived from GenBank primary data. Records are divided into two categories: * TPA:experimental: Annotation of sequence data is supported by peer-reviewed wet-lab experimental evidence. * TPA:inferential: Annotation of sequence data by inference (where the source molecule or its product(s) have not been the subject of direct experimentation) TPA records are retrieved through the Nucleotide Database and feature information on the sequence, how it was cataloged, and proper way to cite the sequence information.

BCM Department of Neuroscience Andreas Tolias Lab
type: Resource
type: NamedIndividual
has db xref: nlx_157739
synonym: Andreas Tolias Lab
abbrev: Tolias Lab
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Code and algorithms produced by the Andreas Tolias lab (Baylor College of Medicine, Department of Neuroscience) where the goal is to understand the rules by which networks of nerves cells in the neocortex orchestrate their activity to process information; to decipher the neural code.

hdf5matlab
type: Resource
type: NamedIndividual
has db xref: nlx_157741
IAO_0000115: Software library for manipulating neural data files generated in Andreas Tolias Lab.

TwoPhoton
type: Resource
type: NamedIndividual
has db xref: nlx_157742
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6,2023. Code used for analysis of TwoPhoton data.

GEPAT
type: Resource
type: NamedIndividual
has db xref: biotools:gepat
has db xref: OMICS_00765
synonym: Genome Expression Pathway Analysis Tool
IAO_0000115: A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context.

Integrated Ocean Observing System
type: Resource
type: NamedIndividual
has db xref: nlx_157745
synonym: U.S. Integrated Ocean Observing System
abbrev: IOOS
abbrev: U.S. IOOS
IAO_0000115: Organization to lead the integration of ocean, coastal, and Great Lakes observing capabilities, in collaboration with Federal and non-Federal partners, to maximize access to data and generation of information products, inform decision making, and promote economic, environmental, and social benefits to the nation and the world. This national-regional partnership is working to provide new tools and forecasts to improve safety, enhance the economy, and protect the environment. Integrated ocean information is available in near real time, as well as retrospectively. Easier and better access to this information is improving their ability to understand and predict coastal events - such as storms, wave heights, and sea level change. Such knowledge is needed for everything from retail to development planning. The Integrated Ocean Observing System (IOOS) program achieves its objectives by funding organizations through a competitive process.

EuroBioBank
type: Resource
type: NamedIndividual
has db xref: nlx_12526
synonym: EuroBioBank: European Network of DNA Cell and Tissue BioBanks for Rare Diseases
abbrev: EBB Network
IAO_0000115: The EuroBioBank network is the first operating network of biobanks in Europe providing human DNA, cell and tissue samples as a service to the scientific community conducting research on rare diseases. It is the only network dedicated to rare disease research in Europe. By creating a critical mass of collections and facilitating the exchange of biological material, the EuroBioBank network helps accelerate research on these diseases. * Over 440,000 samples are available across the network and can be requested via the online catalogue. Approximately 13,000 samples are collected each year and 7,000 samples distributed in Europe and beyond. The biological samples are obtained from patients affected by rare diseases, including rare neuromuscular disorders. * The EuroBioBank Network is currently composed of 18 members, of which 16 biobanks from 8 European countries (France, Germany, Hungary, Italy, Malta, Slovenia, Spain and the United-Kingdom) as well as Israel and Canada. Goals * Identify and localize biological material of interest to researchers * Build a critical mass of rare disease sample collections * Distribute high quality material and associated data to users * Promote best-practice guidelines for biobanking activities * Disseminate knowledge and know-how to the scientific community through training courses * Enhance collaboration with the medical and scientific community in the field of rare diseases EuroBioBank acts as a clearing house or virtual bank, with all samples listed in the central online catalogue remaining in the possession of the member biobanks, where they are located and can be requested. The network was established by patients and researchers to facilitate research on rare diseases by guaranteeing quick and easy access to samples via an online catalogue. The catalogue lists the samples available throughout the EuroBioBank network by type of biomaterial. A search engine enables a search by disease or by bank contact. Once a sample has been locate…

BioText Search Engine
type: Resource
type: NamedIndividual
has db xref: nlx_12705
synonym: BioText
IAO_0000115: Developed as part of the BioText project at the University of California, Berkeley, the BioText Search Engine is a freely available Web-based application that provides biologists with new ways to access the scientific literature. The system indexes all open access articles available at PubMed Central. New articles are indexed daily. The current collection consists of more than 300 journals, 40,000 articles, 100,000 figures, and 60,000 tables. The Full Text & Abstract view searches the full text of articles (in addition to title, author, and abstract information) and returns full-text excerpts that match users' queries. Three selection boxes at the top (ABSTRACTS, FULL-TEXT EXCERPTS and FIGURES allow users to choose what the view displays. The BioText Search Engine allows users to search in tables. When the table view is selected, BioText searches in article titles, table captions, and table contents. The Grid View allows users to search over captions. It returns figures and truncated captions in a grid arrangement.

NICHD Brain and Tissue Bank for Developmental Disorders
type: Resource
type: NamedIndividual
has db xref: nif-0000-00217
synonym: Eunice Kennedy Shriver NICHD BTB
synonym: NICHD Brain and Tissue Bank
synonym: NICHD Brain Tissue Bank for Developmental Disorders
synonym: NICHD BTB for Developmental Disorders
abbrev: NICHD BTB
IAO_0000115: The objective of this human tissue repository is to systematically collect, store, and distribute brain and other tissues for research dedicated to the improved understanding, care, and treatment of individuals with developmental disorders. Brain sections are primarily frozen in isopentane / dry ice. Tissues are stored in 10% formalin and frozen at -85 degrees C. Of special interest are individuals with Down syndrome and other chromosomal defects, mitochondrial encephalopathies, phenylketonuria and other aminoacidopathies, maternal PKU, Rett syndrome, leukodystrophies, lysosomal disorders, dyslexia, autism, and other neurodevelopmental disorders. The brain and tissue banks have extensive experience in arranging for the rapid retrieval of tissue upon the death of individuals who die while at home, in hospitals or hospice care. As a special service, the brain and tissue banks are able to assist researchers who are working with patients who intend to donate tissues at the time of their death. Immediately after retrieval of the tissue, the brain and tissue banks will forward needed tissue to the referring investigators and ensure proper storage and cataloging of any additional tissues as part of the brain and tissue banks. The recipient of tissue and the brain and tissue banks are required to sign a Tissue Transfer Agreement before any tissues are transferred.

Polyester
type: Resource
type: NamedIndividual
has db xref: OMICS_04272
IAO_0000115: An R package designed to simulate RNA sequencing experiments with differential transcript expression. Given a set of annotated transcripts, it will simulate the steps of an RNA-seq experiment (fragmentation, reverse-complementing, and sequencing) and produce files containing simulated RNA-seq reads. Simulated reads can be analyzed using a choice of downstream analysis tools. Polyester has a built-in wrapper function to simulate a case/control experiment with differential transcript expression and biological replicates. Users are able to set the levels of differential expression at transcripts of their choosing. This means they know which transcripts are differentially expressed in the simulated dataset, so accuracy of statistical methods for differential expression detection can be analyzed. Polyester offers several unique features: * Built-in functionality to simulate differential expression at the transcript level * Ability to explicitly set differential expression signal strength * Simulation of small datasets, since large RNA-seq datasets can require lots of time and computing resources to analyze * Generation of raw RNA-seq reads, as opposed to alignments or transcript-level abundance estimates * Transparency/open-source code

Knowledge Blog
type: Resource
type: NamedIndividual
has db xref: nlx_12901
synonym: Knowledge Blog - Scientific Publishing for the Web Generation
abbrev: Knowledgeblog
IAO_0000115: Blog investigating a light-weight way of publishing scientific, academic and technical knowledge on the web where you can read about current events. It is used in a number of different ways: hosting tutorials on ontologies and bioinformatics; as a conference website; and as a mechanism for documenting Knowledge Blog. They also provide software for extending WordPress, enabling referencing, adding metadata to posts, and supporting mathematics on the web. Together, these pieces of software have had many thousands of downloads, representing 100s of installations; it can be used to provide a formal personal publication framework for the researcher. Finally, they provide Greycite, a service which provides bibliographic metadata for any website, supporting their referencing plugin, and helping authors to link to the many web archiving services, enabling increased digital preservation. Blogs and blog technology has been designed to allow people to discuss, share and disseminate their opinion in a simple and light-weight way. Adding a little formality to this, and we have a journal.

Agency for Healthcare Research and Quality
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100000133
has db xref: grid.413404.6
has db xref: ISNI: 0000 0004 0507 6696
has db xref: nlx_157753
has db xref: Wikidata: Q4692008
synonym: Agency for Healthcare Research and Quality (AHRQ)
abbrev: AHRQ
IAO_0000115: Agency that produces evidence to make health care safer, higher quality, more accessible, equitable, and affordable. Funding opportunities, grants, and a large collection of longitudinal hospital care data in the United States including the Systematic Review Data Repository and data sources on healthcare cost, quality, and accessibility, emergency room visits, hospitalization, and medical insurance are available. It works within the U.S. Department of Health and Human Services and with other partners to make sure that the evidence is understood and used.

SET
type: Resource
type: NamedIndividual
has db xref: OMICS_02294
synonym: SET (Signature Evaluation Tool)
synonym: SET (Signature Evaluation Tool) - a Java tool to evaluate and visualize the sample discrimination abilities of gene expression signatures
synonym: SET - a Java tool to evaluate and visualize the sample discrimination abilities of gene expression signatures
synonym: Signature Evaluation Tool
synonym: Signature Evaluation Tool (SET)
IAO_0000115: A Java tool to evaluate and visualize the sample discrimination abilities of gene expression signatures. This tool provides a filtration function for signature identification and lies between clinical analyses and class prediction (or feature selection) tools.

National Brain Databank
type: Resource
type: NamedIndividual
has db xref: nif-0000-00071
synonym: National Brain Databank: Brain Tissue Gene Expression Repository
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016. A publicly accessible data repository to provide neuroscience investigators with secure access to cohort collections. The Databank collects and disseminates gene expression data from microarray experiments on brain tissue samples, along with diagnostic results from postmortem studies of neurological and psychiatric disorders. All of the data that is derived from studies of the HBTRC collection is being incorporated into the National Brain Databank. This data is available to the general public, although strict precautions are undertaken to maintain the confidentiality of the brain donors and their family members. The system is designed to incorporate MIAME and MAGE-ML based microarray data sharing standards. Data from various types of studies conducted on brain tissue in the HBTRC collection will be available from studies using different technologies, such as gene expression profiling, quantitative RT-PCR, situ hybridization, and immunocytochemistry and will have the potential for providing powerful insights into the subregional and cellular distribution of genes and/or proteins in different brain regions and eventually in specific subregions and cellular subtypes.

Roswell Park Data Bank and BioRepository
type: Resource
type: NamedIndividual
has db xref: nlx_13096
synonym: Roswell Park Cancer Institute Data Bank and BioRepository
synonym: Roswell Park Cancer Institute Data Bank BioRepository
synonym: Roswell Park Cancer Institute DataBank and BioRepository
synonym: Roswell Park Data Bank BioRepository
synonym: Roswell Park DataBank and BioRepository
synonym: RPCI Data Bank and BioRepository
synonym: RPCI Data Bank BioRepository
synonym: RPCI DataBank and BioRepository
synonym: RPCI DBBR
abbrev: DBBR
IAO_0000115: Collects and provides de-identified biospecimens and associated epidemiological and clinical data to meet the scientific needs of investigators. Newly diagnosed patients are asked to contribute data and specimens to the DBBR prior to treatment. Other patients with who have benign disease or advanced disease and have undergone treatment are also enrolled based on anticipated use of data and samples for research. Additionally, non-patients (family members and friends of patients and community members) with no personal history of cancer are asked to participate in the biorepository as controls. Specimens and data are procured with protected health information (PHI) and de-identified prior to distribution to investigators with hypothesis driven IRB reviewed studies. An extensive data collection and management system is in place to track informed consent, questionnaire collection and follow up, epidemiological questionnaire data, clinical data, biospecimens and their derivatives. Research Services * Availability of a bank of prospectively collected blood specimens (serum, plasma, buffy coat, red blood cells and DNA) from cancer patients, high risk individuals and healthy controls for research. * Collection, linking and distribution of epidemiologic and clinical data with biospecimens. * Study-specific biospecimen and data procurement to meet the needs of individual studies, including: ** Participant identification, eligibility screening and informed consent ** Serial biospecimen procurement prior to and throughout treatment ** Study specific collection of biospecimens other than blood (buccal cells, sputum, and urine) ** Procurement and distribution of fresh biospecimens ** Collection of extended clinical and risk factor data

GOCat
type: Resource
type: NamedIndividual
has db xref: nlx_157764
synonym: GOCat - the Gene Ontology Categorizer
synonym: GOCat the Gene Ontology Categorizer
IAO_0000115: Software tool that uses a machine learning (ML) approach to classify text, based on the Gene Ontology. It relies on a k-Nearest Neighbours algorithm, a simple algorithm which assigns to a new text the categories that are the most prevalent among the k most similar instances contained in the knowledge base. The ML classifier operates in two steps and combines two components. First, a related article search engine retrieves instances (i.e. abstracts) in the knowledge base that are the most similar to the input text (its nearest neighbours); second, a score computer infers the functional profile from the k most similar instances.

J-Express
type: Resource
type: NamedIndividual
has db xref: biotools:j-express
has db xref: OMICS_00767
synonym: J-Express: Gene expression analysis software
IAO_0000115: Gene expression analysis software using Java.

Alaska Satellite Facility
type: Resource
type: NamedIndividual
has db xref: nlx_157757
has db xref: r3d100013015
synonym: Alaska Satellite Facility - Synthetic Aperture Radar Distributed Active Archive Center
abbrev: ASF
abbrev: ASF SAR DAAC
IAO_0000115: Satellite facility that downlinks, processes, archives, and distributes remote-sensing data to scientific users around the world. Three major components: * Satellite Tracking Ground Station: Part of NASA?s Near Earth Network system of ground stations around the world. * Synthetic Aperture Radar Distributed Active Archive Center (SAR DAAC): ASF maintains the NASA archive of SAR data from a variety of satellites and aircraft, and provides these data and associated specialty support services to U.S. Government-approved researchers in support of NASA?s Earth Science Data and Information System project. * ASF Enterprise Center (ASFE): In support of UAF?s mission to be a student-centered research university, the ASF-E focuses on applications of remote-sensing data, specifically for UAF research. The ASF-E includes the GeoData Center (GDC), which provides data management and archive services for UAF principal investigators and maintains a variety of geophysical data collections in support of scientific research.

Current German Weather Stations
type: Resource
type: NamedIndividual
has db xref: nlx_157759
synonym: Aktuelle Wetterwerte deutscher Stationen
IAO_0000115: Data sets of current German weather stations updated hourly or every twelve hours. Data sets, in German, include: * Daily mean values ??of temperature, updated hourly. Daily archive since 29.1.2008 * Daily maximum and minimum temperature, updated every 12 hours. Daily archive since 21.7.2008 * Monthly mean values ??of temperature and deviation, updated daily . * Rainfall in the last 12 hours and monthly total, updated every 12 hours . * Monthly totals of precipitation and relative to langj. means in%, updated every 12 hours. Monthly Archive since Feb. 2008 * Air pressure and pressure tendency, updated hourly.

ABIDE
type: Resource
type: NamedIndividual
has db xref: nlx_157761
synonym: Autism Brain Imaging Data Exchange
IAO_0000115: Resting state functional magnetic resonance imaging (R-fMRI) datasets from 539 individuals with autism spectrum disorder (ASD) and 573 typical controls. This initiative involved 16 international sites, sharing 20 samples yielding 1112 datasets composed of both MRI data and an extensive array of phenotypic information common across nearly all sites. This effort is expected to facilitate discovery science and comparisons across samples. All datasets are anonymous, with no protected health information included.

Integrated Videos
type: Resource
type: NamedIndividual
has db xref: nlx_13182
synonym: Integrated Video
synonym: Integrated Video View
synonym: Integrated Videos View
synonym: NIF Integrated Video
synonym: NIF Integrated Video View
synonym: NIF Integrated Videos
synonym: NIF Integrated Videos View
synonym: NIF Video
synonym: NIF Videos
IAO_0000115: A virtual database indexing video and other multimedia content from: NIH VideoCasting and Podcasting, JoVE: Journal of Visualized Experiments, The Guardian: Science Videos, Biointeractive, goCognitive, UCSF Laboratory for Visual Neuroscience, and Clarity resources.

rOGED: Rat Ovarian Gene Expression Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-03422
abbrev: rOGED
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. rOGED is a searchable database containing ovarian gene sequences, data, and images of ovarian genes expressed in rats. The site also provides customized gene expression profiles in the rat oviduct and uterus or mouse ovary. The database was constructed from total RNA isolated from intact ovaries, granulosa cells, or residual ovarian tissues collected from immature PMSG/hCG-treated rats at 0 (no PMSG), 12, and 48 h post-PMSG, as well as 6 and 12 h post-hCG. The total RNA was used for DNA microarray analysis using Affymetrix Rat Expression Arrays 230A and B. The microarray data was compiled and utilized for display of individual gene expression profiles through specially developed software. The final rOGED provides immediate analysis of temporal gene expression profiles for over 28,000 genes in intact ovaries, granulosa cells, and residual ovarian tissue during follicular growth and the preovulatory period. The accuracy of the rOGED was validated against the gene profiles for over 100 known genes. The utility of the rOGED was demonstrated by identifying seven genes which have not been described in the rat periovulatory ovary. The rOGED can be used as an instant reference for ovarian gene expression profiles, as well as reliable resource for identifying important yet, to date, unknown ovarian genes. Category: Microarray Data and other Gene Expression Databases

NIH Toolbox Dimensional Change Card Sort Test
type: Resource
type: NamedIndividual
has db xref: nlx_157769
abbrev: DCCS
IAO_0000115: Assessment test that measures the cognitive flexibility of patients. Two target pictures are presented that vary along two dimensions (e.g., shape and color). Participants are asked to match a series of bivalent test pictures (e.g., yellow balls and blue trucks) to the target pictures, first according to one dimension (e.g., color) and then, after a number of trials, according to the other dimension (e.g., shape). Switch trials are also employed, in which the participant must change the dimension being matched. For example, after 4 straight trials matching on shape, the participant may be asked to match on color on the next trial and then go back to shape, thus requiring the cognitive flexibility to quickly choose the correct stimulus. Scoring is based on a combination of accuracy and reaction time, and the test takes approximately 4 minutes to administer. This test is recommended for ages 3-85.

NIH Toolbox Flanker Inhibitory Control and Attention Test
type: Resource
type: NamedIndividual
has db xref: nlx_157770
synonym: Flanker Inhibitory Control and Attention Test
abbrev: Flanker task
IAO_0000115: Assessment test that measures both a participant''s attention and inhibitory control. The test requires the participant to focus on a given stimulus while inhibiting attention to stimuli (fish for ages 3-7 or arrows for ages 8-85) flanking it. Sometimes the middle stimulus is pointing in the same direction as the flankers (congruent) and sometimes in the opposite direction (incongruent). Scoring is based on a combination of accuracy and reaction time, and the test takes approximately 3 minutes to administer. This test is recommended for ages 3-85.

NIH Toolbox Picture Sequence Memory Test
type: Resource
type: NamedIndividual
has db xref: nlx_157771
abbrev: Picture Sequence Memory Test
IAO_0000115: A measure for the assessment of episodic memory that involves recalling increasingly lengthy series of illustrated objects and activities that are presented in a particular order on the computer screen. The participants are asked to recall the sequence of pictures that is demonstrated over two learning trials; sequence length varies from 6-18 pictures, depending on age. Participants are given credit for each adjacent pair of pictures (i.e., if pictures in locations 7 and 8 and placed in that order and adjacent to each other anywhere such as slots 1 and 2 one point is awarded) they correctly place, up to the maximum value for the sequence, which is one less than the sequence length (if there are 18 pictures in the sequence, the maximum score is 17, because that is the number of adjacent pairs of pictures that exist). The test takes approximately 7 minutes to administer. This test is recommended for ages 3-85.

NIH Toolbox Auditory Verbal Learning Test (Rey)
type: Resource
type: NamedIndividual
has db xref: nlx_157772
synonym: NIH Toolbox Auditory Verbal Learning Test-Rey
IAO_0000115: Supplemental instrument that is a measure of immediate recall in which the participant is presented with a list of 15 unrelated words via audio recording and is asked to recall as many as he/she can. This process is repeated twice more, and the score is equal to the total number of words recalled across all three trials. This instrument is recommended for ages 8-85 as a supplement to the Picture Sequence Memory Test or as a potential alternative in cases where a participant's visual limitations would preclude administering the Picture Sequence Memory Test. The test takes approximately 3 minutes to administer. (The NIH Toolbox version of this test differs from some other available versions in that there are three rather than five learning trials and there is neither a delayed recall trial nor an interference trial.)

UEA sRNA toolkit
type: Resource
type: NamedIndividual
has db xref: OMICS_00369
IAO_0000115: Software tools for the analysis of high-throughput small RNA data.

NIH Toolbox 9-Hole Pegboard Dexterity Test
type: Resource
type: NamedIndividual
has db xref: nlx_157780
synonym: 9-Hole Pegboard Dexterity Test
IAO_0000115: Assessment test that measures manual dexterity recording the time required for the participant to accurately place and remove 9 plastic pegs into a plastic pegboard. The protocol includes 1 practice and 1 timed trial with each hand. Raw scores are recorded as time in seconds that it takes the participant to complete the task with each hand (a separate score for each). The test takes approximately 4 minutes to administer and is recommended for ages 3-85.

NIH Toolbox Oral Reading Recognition Test
type: Resource
type: NamedIndividual
has db xref: nlx_157774
synonym: Oral Reading Recognition Test
IAO_0000115: Assessment test that measures the ability of patients to identify words and letters. The participant is asked to read and pronounce letters and words as accurately as possible. The test administrator scores them as right or wrong. For the youngest children, the initial items require them to identify letters (as opposed to symbols) and to identify a specific letter in an array of 4 symbols. The test is given in a computerized adaptive format and requires approximately 3 minutes. This test is recommended for ages 7-85, but is available for use as young as age 3, if requested. Separate but parallel reading tests have been developed in English and in Spanish.

NIH Toolbox Pattern Comparison Processing Speed Test
type: Resource
type: NamedIndividual
has db xref: nlx_157775
synonym: Pattern Comparison Processing Speed Test
IAO_0000115: Assessment test that measures speed of processing by asking participants to discern whether two side-by-side pictures are the same or not. Participants' raw score is the number of items correct in a 90-second period. The items are designed to be simple to most purely measure processing speed. The test overall takes approximately 3 minutes to administer. This test is recommended for ages 7-85, but is available for use as young as age 3, if requested.

NIH Toolbox Oral Symbol Digit Test
type: Resource
type: NamedIndividual
has db xref: nlx_157776
synonym: Oral Symbol Digit Test
IAO_0000115: A supplemental instrument that is a measure of speed of processing. The participant is presented with a set of nine symbols on the computer screen, each associated with a number 1-9, and is then presented with a series of symbols without numbers and is asked to orally say each number that should go with that symbol, without skipping any. The score is equal to the number of symbols correctly identified orally within two minutes. Recommended for ages 8-85 as a supplement to the Pattern Comparison Processing Speed Test or as a potential alternative in cases where a participant's motoric limitations would preclude administering the Pattern Comparison Processing Speed Test. Takes approximately 3 minutes to administer.

Religion Aging and Health Survey
type: Resource
type: NamedIndividual
has db xref: nlx_157777
IAO_0000115: Data set that looked at religion, self-rated health, depression, and psychological well-being in a sample of older Blacks and older Whites (aged 65 and over) within the United States. Questions were asked regarding religious status, activities, and beliefs among those who currently practice the Christian faith, those who used to be Christian but are not now, and those who have never been associated with any religion during their lifetimes. Demographic variables include age, race, sex, education, and income. Wave II was collected in 2004 and reinterviewed 1,024 respondents. There were 75 respondents who refused to participate, 112 who could not be located, 70 that were too ill for participation, 11 who had moved to nursing homes and 208 were deceased. * Dates of Study: 2001- 2004 * Study Features: Longitudinal, Minority Oversample * Sample Size: 1,500

NIH Toolbox List Sorting Working Memory Test
type: Resource
type: NamedIndividual
has db xref: nlx_157778
synonym: List Sorting Working Memory Test
IAO_0000115: Assessment test to measure the memory of patients using their ability to sort objects. It requires immediate recall and sequencing of different visually and orally presented stimuli. Pictures of different foods and animals are displayed with accompanying audio recording and written text (e.g., elephant), and the participant is asked to say the items back in size order from smallest to largest, first within a single dimension (either animals or foods, called 1-List) and then on 2 dimensions (foods, then animals, called 2-List). The score is equal to the number of items recalled and sequenced correctly, and the test takes approximately 7 minutes to administer. This test is recommended for ages 7-85, but is available for use as young as age 3, if requested.

Osprey
type: Resource
type: NamedIndividual
has db xref: OMICS_00832
synonym: Osprey: Oligonucleotide Design Software
IAO_0000115: Oligonucleotide design software that calculates optimal oligonucleotides for a range of tasks: sequence assembly, differential expression, and microarrays (cDNA and spotted oligos)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

NIH Toolbox Standing Balance Test
type: Resource
type: NamedIndividual
has db xref: nlx_157779
synonym: Standing Balance Test
IAO_0000115: A measure to assess static standing balance that involves the participant assuming and maintaining up to 5 poses for 50 seconds each. The sequence of poses is: eyes open on a solid surface, eyes closed on solid surface, eyes open on foam surface, eyes closed on foam surface, eyes open in tandem stance. Detailed stopping rules are in place to ensure participant safety with these progressively demanding poses. Postural sway is recorded for each pose using an accelerometer that the participant wears at waist level. This test takes approximately 7 minutes to administer and is recommended for ages 3-85.

Common Upper Mammalian Brain Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157809
synonym: Common Upper Mammalian Brain Ontology (CUMBO)
synonym: INCF-CUMBO
abbrev: CUMBO
IAO_0000115: Ontology of formal definitions (i.e., machine processable) for the types of structures commonly described in neuroanatomy.

TopoGEN
type: Organization
type: NamedIndividual
has db xref: nlx_152480
synonym: TopoGEN Inc
synonym: TopoGEN Inc.
synonym: TopoGEN inc.
IAO_0000115: An Antibody supplier

NIH Toolbox 2-Minute Walk Endurance Test
type: Resource
type: NamedIndividual
has db xref: nlx_157781
synonym: 2-Minute Walk Endurance Test
IAO_0000115: Assessment test that measures sub-maximal cardiovascular endurance by recording the distance that the participant is able to walk on a 50-foot (out and back) course in 2 minutes. The participant's raw score is the distance in feet and inches walked in 2 minutes. The test is adapted from the American Thoracic Society's 6-Minute Walk Test Protocol. The test overall takes approximately 4 minutes to administer (with instructions and practice). This test is recommended for ages 3-85.

NIH Toolbox 4-Meter Walk Gait Speed Test
type: Resource
type: NamedIndividual
has db xref: nlx_157782
synonym: 4-Meter Walk Gait Speed Test
IAO_0000115: Assessment test to measure gait speed where participants are asked to walk a short distance (4 meters) at their usual pace. Participants complete one practice and then two timed trials. Raw scores are recorded as the time in seconds required to walk 4 meters on each of the two trials, with the better trial used for scoring. The 4-Meter Walk Gait Speed Test is adapted from the 4-meter walk test in the Short Physical Performance Battery. The test takes approximately 3 minutes to administer (including instructions and practice). This test is recommended for ages 7-85.

NIH Toolbox Grip Strength Test
type: Resource
type: NamedIndividual
has db xref: nlx_157783
synonym: Grip Strength Test
IAO_0000115: Assessment test that measures grip strength. Participants are seated in a chair with their feet touching the ground. With the elbow bent to 90 degrees and the arm against the trunk, wrist at neutral, participants squeeze the Jamar Plus Digital dynamometer as hard as they can for a count of three. The dynamometer provides a digital reading of force in pounds. A practice trial at less than full force and 1 test trial are completed with each hand. This protocol is adapted from the grip strength testing protocol of the American Society of Hand Therapy. The test takes approximately 3 minutes to administer and is recommended for ages 3-85.

NIH Toolbox Odor Identification Test
type: Resource
type: NamedIndividual
has db xref: nlx_157785
synonym: Odor Identification Test
IAO_0000115: Assessment test to assess a person's ability to identify various odors. Participants use scratch 'n' sniff cards and after scratching them one at a time, are asked to identify which of four pictures on the computer screen matches the odor they have just smelled. Participants ages 10-85 are administered nine odor cards, while those ages 3-9 are administered five odor cards. Child participants (ages 3 -9 years) are first asked to identify the eight pictures that are used as answer choices, to ensure they can complete the task. Having identified the pictures, they are asked if they have tasted or smelled the objects or foods depicted. This test takes approximately 4 to 5 minutes to administer and is recommended for ages 3-85.

NIH Toolbox Pain Interference Survey
type: Resource
type: NamedIndividual
has db xref: nlx_157786
synonym: Pain Interference Survey
IAO_0000115: A self-report scale that measures the degree to which pain interferes with other activities in life in adults. Pain interference items were developed as part of the NIH PROMIS. This measure is administered as a computer-adaptive test and takes approximately three minutes. It is recommended for ages 8-85.

NIH Toolbox Pain Intensity Survey
type: Resource
type: NamedIndividual
has db xref: nlx_157787
synonym: Pain Intensity Survey
IAO_0000115: A measure that consists of a single item measuring immediate (i.e., acute) pain in adults. As part of Toolbox, a single pain intensity item measures immediate (a.k.a. acute) pain for use in adults. It takes less than one minute to administer and is recommended for ages 18-85.

NIH Toolbox Regional Taste Intensity Test
type: Resource
type: NamedIndividual
has db xref: nlx_157788
synonym: Regional Taste Intensity Test
IAO_0000115: Assessment test that measures the perceived intensity of quinine (a bitter tastant) and salt administered in liquid solutions. The tastants are applied to the tip of the tongue as well as the whole mouth and rated on a generalized labeled magnitude scale (ranging from no sensation at all to strongest sensation of any kind). The test is recommended for administration to participants ages 12-85 and takes approximately six minutes to administer.

Resources for Enhancing Alzheimers Caregiver Health
type: Resource
type: NamedIndividual
has db xref: nlx_157789
synonym: Resources for Enhancing Alzheimer's Caregiver Health
synonym: Resources for Enhancing Alzheimer's Caregiver Health (REACH)
abbrev: REACH
IAO_0000115: Data set from six research sites that examined the feasibility and outcomes of the most promising home and community-based intervention approaches for enhancing family caregiving for Alzheimers Disease (AD) and related disorders (ADRD). A unique feature is the examination of AD burdens and interventions in three ethnic groups (Caucasians, Hispanics, and African Americans). Caregiver/care recipient dyads are entered into the study using standardized eligibility criteria. The dyads are randomized at each intervention site using site-specific procedures. Standardized assessment batteries are administered at baseline, 6, 12, and 18 months. The five general types of REACH interventions are: Individual Information and Support strategies that increase caregivers' understanding of dementia and their particular caregiving situation; Group Support and Family Systems efforts that provide caregivers with multiple forms of social support; Psychoeducational and Skill-Based Training approaches that teach caregivers coping and behavioral management strategies; Home-Based Environmental interventions that modify the home environment's effect on the care recipient and support the caregiver; and Enhanced Technology Systems such as home-centered computer/telephone networks that are designed to reduce caregiver distress and isolation. REACH II was funded in 2001 to test a single multi-component intervention among family caregivers of persons with ADRD, building upon the findings of REACH. Recruitment for REACH II was completed in January 2004 with 642 participants entering the study across 5 participating sites.

Autism-Spectrum Quotient
type: Resource
type: NamedIndividual
has db xref: nlx_157818
synonym: Autism Spectrum Quotient (AQ)
abbrev: AQ
IAO_0000115: A 50 question psychological assessment that measures the symptoms of autism in adults, children and adolescents.

NIH Toolbox Dynamic Visual Acuity Test
type: Resource
type: NamedIndividual
has db xref: nlx_157790
synonym: Dynamic Visual Acuity Test
abbrev: DVA Test
IAO_0000115: Assessment test that is a measure of gaze stability, which helps identify individuals who may have a deficit of the vestibular system (which regulates internal balance). The NIH Toolbox Visual Acuity Test must be administered followed by the DVA Test. Participants are seated 12.5 feet from a computer monitor at eye level. For the DVA Test, participants wear lightweight headgear that contains a rate sensor, and are asked to move the head back and forth, as if saying no. Once the head is measured to be moving at greater than 180 degrees per second, an optotype flashes on the monitor, and the participant is asked to identify it. Smaller optotypes are displayed as the participant correctly identifies letters, and larger ones are displayed if the participant cannot correctly identify the letter shown, until the computer has calculated the smallest size that the participant can see with the head moving. This is calculated separately for head rotation leftward and rightward from center (though the participant continues shaking the head both ways), and this performance is compared to the participant's visual acuity when the head was stationary (the NIH Toolbox Visual Acuity Test score, sometimes referred to as static visual acuity in the context of the DVA test). The difference between static and dynamic visual acuity represents the vestibular contribution to gaze stability. The DVA Test takes approximately six minutes to administer and is recommended for ages 3-85.

NIH Toolbox Visual Acuity Test
type: Resource
type: NamedIndividual
has db xref: nlx_157791
synonym: Visual Acuity Test
IAO_0000115: Assessment test that directly measures participants' visual acuity, or distance vision. The participant is seated 12.5 feet away from a computer monitor at eye level, and letters (called optotypes) are displayed one at a time on the screen for the participant to identify, using both eyes at the same time. As the participant successfully identifies optotypes of a given size, smaller ones appear on the screen, until the computer program ascertains the smallest-size optotype the participant can successfully see. Conversely, the program displays larger optotypes if the participant cannot see the letter size that is first displayed, until a size that he/she can accurately see is found. For participants ages 3-7, only the letters H, O, T, and V are used, and children may point to a laminated card showing the letters if they cannot verbalize or cannot recall the letter names. For participants ages 8 and above, the entire set of optotypes is used, following a common protocol used in professional vision testing. This test takes approximately three minutes to administer and is recommended for ages 3-85.

GSE1456
type: Resource
type: NamedIndividual
has db xref: nlx_157793
IAO_0000115: Curated series of expression data for 159 tumors from which RNA could be collected in sufficient amounts and quality for analysis from breast cancer patients. Tissue material was collected from all breast cancer patients receiving surgery at Karolinska Hospital from 1994-1996.

GSE4271
type: Resource
type: NamedIndividual
has db xref: nlx_157794
IAO_0000115: Curated data set from a study that investigated 77 primary high-grade astrocytomas and 23 matched recurrences so that changes in gene expression related to both survival and disease progression can be identified. Samples in the study include WHO grade III and IV astrocytomas with a wide range of survival times.

GSE4698
type: Resource
type: NamedIndividual
has db xref: nlx_157795
IAO_0000115: Curated data set where gene expression profiling was performed on 60 prospectively collected samples of children with first relapse of acute lymphoblastic leukemia enrolled on the relapse trial ALL-REZ BFM 2002 of the Berlin-Frankfurt-Muenster study group.

GSE20194
type: Resource
type: NamedIndividual
has db xref: nlx_157797
IAO_0000115: Curated data set of gene expression data from 230 stage I-III breast cancers that were generated from fine needle aspiration specimens of newly diagnosed breast cancers before any therapy. The biopsy specimens were collected sequentially during a prospective pharmacogenomic marker discovery study between 2000 and 2008. These specimens represent 70-90% pure neoplastic cells with minimal stromal contamination. In the study, patients received 6 months of preoperative (neoadjuvant) chemotherapy including paclitaxel, 5-fluorouracil, cyclophosphamide and doxorubicin followed by surgical resection of the cancer.

GSE27831
type: Resource
type: NamedIndividual
has db xref: nlx_157798
IAO_0000115: Curated data set from gene expression profiles of 29 unique samples from uveal melanoma patients that were measured on Affymetrix microarray. In addition, expression of syntenin-1 was measured by RT-PCR and this data is also available in the study.

GSE8650
type: Resource
type: NamedIndividual
has db xref: nlx_157799
IAO_0000115: Curated data set from analyzed gene expression profiles in 19 pediatric patients with SoJIA during the systemic phase of the disease (fever and/or arthritis), 25 SoJIA patients with no systemic symptoms (arthritis only or no symptoms), 39 healthy controls, 94 pediatric patients with acute viral and bacterial infections (available under GSE6269), 38 pediatric patients with Systemic Lupus Erythematosus (SLE), and 6 patients with a second IL-1 mediated disease known as PAPA syndrome.

GSE13732
type: Resource
type: NamedIndividual
has db xref: nlx_157800
IAO_0000115: Curated data set from a study that developed biomarkers that may predict development of Clinically Isolated Syndrome (CIS) into a full multiple sclerosis. Expression data was taken from 37 CIS patients and 28 healthy controls at baseline. 34 CIS patients and 10 healthy controls were resampled at a second time point, approximately one year later. Patients were followed clinically for up to two years to determine the TTC (time to conversion to MS).

GSE24060
type: Resource
type: NamedIndividual
has db xref: nlx_157801
IAO_0000115: Curated data set from a gene expression profiling study investigating monozygotic twin pairs with various systemic autoimmune diseases. RNA microarray analyses (Agilent Human 1A(V2) 20K oligo arrays) quantified differential gene expression in blood from 20 monozygotic (MZ) twin pairs, to minimize polymorphic gene effects, discordant for SAID (six with systemic lupus erythematosus (SLE), six rheumatoid arthritis (RA), eight idiopathic inflammatory myopathies (IIM)) and 40 unrelated matched controls.

GSE17755
type: Resource
type: NamedIndividual
has db xref: nlx_157802
IAO_0000115: Curated data set from a study that contains a gene expression profile of peripheral blood cells (PBMCs) isolated from patients (248 in total) with rheumatoid arthritis (RA)/ systemic lupus erythematosus (SLE)/ polyarticular type juvenile idiopathic arthritis (polyJIA)/ Systemic onset juvenile idiopathic arthritis (sJIA) vs healthy children (HC) and healthy individual (HI).

GSE13168
type: Resource
type: NamedIndividual
has db xref: nlx_157803
IAO_0000115: Curated data set from a study that assessed the effects of epidermal growth factor and interleukin 1-beta stimulation, and the modulatory effects of glucocorticoids treatment and protein kinase A inhibition, on the airway smooth muscle transcriptome by microarray analysis. The samples from 4 donors were subjected to different stimulations by Il-1b and EGF (or both) with or without pre-treatment with fluticasone, and data was collected at different timepoints.

RINS
type: Resource
type: NamedIndividual
has db xref: OMICS_00223
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. An intersection-based pathogen detection workflow that utilizes a user-provided custom reference genome set for identification of nonhuman sequences in deep sequencing datasets. This is a package recommended for advanced users only.

International Stem Cell Registry
type: Resource
type: NamedIndividual
has db xref: nlx_157804
abbrev: ISCR
IAO_0000115: A registry of stem cell lines that provides a searchable database that includes published and validated unpublished information on human embryonic (hESC) and disease-specific induced pluripotent (iPS) stem cell lines. The Registry will include information on cell lines from non-profit institutions, academic centers, stem cell banks and industry based in the United States and abroad. The International Stem Cell Registry is developed in partnership with and funded by the Massachusetts Life Sciences Center. The work of the registry is made possible by the MLSC and important collaborators, including the Harvard Stem Cell Institute.

Seattle Longitudinal Study
type: Resource
type: NamedIndividual
has db xref: nlx_157807
synonym: Seattle Longitudinal Study (SLS) of Adult Cognitive Development
synonym: Seattle Longitudinal Study of Adult Cognitive Development
abbrev: SLS
IAO_0000115: Data set from an ongoing, longitudinal-sequential study of adult-cognitive development, which began in 1956, that focuses on individual differences in age-related changes and differences across cohorts. The general purpose of the study is to examine the changes in intelligence and various abilities throughout adulthood. The data provide a normative base to determine the ages of detectable decrements in ability and the magnitudes of the decrements. The study also seeks to examine patterns of generational differences and age-related differences and to determine the effects of educational intervention on intellectual decline. This study is a mixed cross-sectional, longitudinal, and time-lag design. Included are family studies of cognitive similarity, prospective studies of early signs of dementia via psychological and genetic markers, as well as the investigation of personality and demographic variables that affect cognitive change in adults from young adulthood to advanced old age. Questionnaire topics include health behavior, behavioral rigidity, family environment, Life Complexity Inventory, CES-D Depression, and cognitive and neuropsychology batteries. Group Health Cooperative of Puget Sound Medical Records and Pharmacy Records. * Dates of Study: 1956-Present * Study Features: Longitudinal * Sample Size: 6,000+

Speech Language Disorders Database
type: Resource
type: NamedIndividual
has db xref: nlx_157808
synonym: Speech / Language Disorders Database
synonym: Speech/Language Disorders Database
abbrev: SLDB
IAO_0000115: Curated lists of genes associated to speech / language phenotypes and structural or functional abnormalities observed in patient populations. Entrez ID gene information, as well as gene expression profiles from the Allen Brain Atlas are available. You can also download expression data for a given gene in JSON or XML format.

Global Assessment of Functioning
type: Resource
type: NamedIndividual
has db xref: nlx_157810
synonym: Global Assessment of Functioning (GAF) Scale
abbrev: GAF
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE.Documented on October 6th, 2022. Assessment scale that considers psychological, social, and occupational functioning (how well they handle various problems in life) on a hypothetical continuum of mental health-illness. This does not include impairment in functioning due to physical (or environmental) limitations. The score received is usually given as a range (0-100) to patients. Scoring: * 91-100 No Symptoms * 81-90 Absent/Minimal Symptoms * 71-80 Symptoms are Present * 61-70 Mild Symptoms * 51-60 Moderate Symptoms * 41-50 Serious Symptoms * 31-40 Some Impairment * 21-30 Influenced behavior by Delusions or Hallucinations * 11-20 Some Danger of Hurting Self or Others * 1-10 Persistent Danger of Hurting Self or Others * 0 Inadequate Information on Patient

Brief Psychiatric Rating Scale
type: Resource
type: NamedIndividual
has db xref: nlx_157811
abbrev: BPRS
IAO_0000115: Assessment scale to measure the psychiatric symptoms of patients who might have psychiatric symptoms including depression, anxiety, hallucinations, and strange or unusual behaviors. The symptoms of the patient are rated between 1 and 7 and then the 18-24 items/symptoms are scored and combined to create the final score of the patient. This scale is similar to the PANSS, SANS, and SAPS.

Linked Neuron Data
type: Resource
type: NamedIndividual
has db xref: nlx_157812
synonym: Linked Neuron Data (LND)
abbrev: LND
IAO_0000115: Neuroscience data and knowledge from multiple scales and multiple data sources that has been extracted, linked, and organized to support comprehensive understanding of the brain. The core is the CAS Brain Knowledge base, a very large scale brain knowledge base based on automatic knowledge extraction and integration from various data and knowledge sources. The LND platform provides services for neuron data and knowledge extraction, representation, integration, visualization, semantic search and reasoning over the linked neuron data. Currently, LND extracts and integrates semantic data and knowledge from the following resources: PubMed, INCF-CUMBO, Allen Reference Atlas, NIF, NeuroLex, MeSH, DBPedia/Wikipedia, etc.

Signalway
type: Organization
type: NamedIndividual
has db xref: nlx_152462
synonym: Signalway Antibody Co. Ltd
abbrev: SAB
IAO_0000115: An Antibody supplier

eBioscience
type: Organization
type: NamedIndividual
has db xref: nlx_152349
IAO_0000115: An Antibody supplier

DBpedia
type: Resource
type: NamedIndividual
has db xref: nlx_157815
IAO_0000115: Data set of a crowd-sourced community effort to extract structured information from Wikipedia and make this information available on the Web. DBpedia allows you to ask sophisticated queries against Wikipedia, and to link the different data sets on the Web to Wikipedia data. It is hoped that this work will make it easier for the huge amount of information in Wikipedia to be used in some new interesting ways. Furthermore, it might inspire new mechanisms for navigating, linking, and improving the encyclopedia itself. The project extracts knowledge from 111 different language editions of Wikipedia. The DBpedia project maps Wikipedia infoboxes from 27 different language editions to a single shared ontology consisting of 320 classes and 1,650 properties. The mappings are created via a world-wide crowd-sourcing effort and enable knowledge from the different Wikipedia editions to be combined. The project publishes regular releases of all DBpedia knowledge bases for download and provides SPARQL query access to 14 out of the 111 language editions via a global network of local DBpedia chapters. In addition to the regular releases, the project maintains a live knowledge base which is updated whenever a page in Wikipedia changes. DBpedia sets 27 million RDF links pointing into over 30 external data sources and thus enables data from these sources to be used together with DBpedia data. Several hundred data sets on the Web publish RDF links pointing to DBpedia themselves and thus make DBpedia one of the central interlinking hubs in the Linked Open Data (LOD) cloud.

OpenLink Software
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_157816
synonym: OpenLink Group Limited
abbrev: OpenLink
IAO_0000115: An technology innovator in database and application server software that has been a long time developer of database and semantic repository technologies on both single servers and clusters. This, combined with OpenLink's experience with SQL, gives an all round view of performance across many environments and workload profiles, from transactions to decision support or search. OpenLink also has extensive experience in developing scale-out parallel database technology. The cross-platform product portfolio addresses challenges such as: Universal Data Access, Data Virtualization & Management, Personal & Enterprise Data Spaces, and Implementation & Support.

Adult ADHD Self-Report Scale
type: Resource
type: NamedIndividual
has db xref: nlx_157817
synonym: Adult ADHD Self-Report Scale (ASRS-v1.1) Symptom Checklist
synonym: Adult ADHD Self-Report Scale Symptom Checklist
abbrev: ASRS
IAO_0000115: A self reporting scale to assess if adult patients are suffering from symptoms of attention deficit-hyperactivity disorder (ADHD). The Symptom Checklist is an instrument consisting of the eighteen DSM-IV-TR criteria. Six of the eighteen questions were found to be the most predictive of symptoms consistent with ADHD. These six questions are the basis for the ASRS v1.1 Screener and are also Part A of the Symptom Checklist. Part B of the Symptom Checklist contains the remaining twelve questions.

Hamilton Anxiety Rating Scale
type: Resource
type: NamedIndividual
has db xref: nlx_157820
synonym: Hamilton Anxiety Rating Scale (HAM-A)
abbrev: HAM-A
IAO_0000115: Assessment scale to assess the severity of symptoms of anxiety in adults, adolescents and children. The scale consists of 14 items, each defined by a series of symptoms, and measures both psychic anxiety (mental agitation and psychological distress) and somatic anxiety (physical complaints related to anxiety). Although the HAM-A remains widely used as an outcome measure in clinical trials, it has been criticized for its sometimes poor ability to discriminate between anxiolytic and antidepressant effects, and somatic anxiety versus somatic side effects. The HAM-A does not provide any standardized probe questions. Despite this, the reported levels of inter-rater reliability for the scale appear to be acceptable. The scale has been translated into: Cantonese for China, French and Spanish. An IVR version of the scale is available from Healthcare Technology Systems.

Hospital Anxiety and Depression Scale
type: Resource
type: NamedIndividual
has db xref: nlx_157821
synonym: Hospital Anxiety and Depression Scale (HADS)
abbrev: HADS
IAO_0000115: Assessment scale commonly used in hospitals to determine the anxiety and depression levels that a patient is experiencing. It contains 14 items, 7 of which are questions about anxiety and the other 7 are about depression.

Generalized Anxiety Disorder 7
type: Resource
type: NamedIndividual
has db xref: nlx_157822
synonym: Generalized Anxiety Disorder 7 Item
synonym: Generalized Anxiety Disorder 7 Item (GAD-7)
synonym: Generalized Anxiety Disorder 7 Item Scale
abbrev: GAD-7
IAO_0000115: A seven item assessment to measure the severity of a patient's anxiety. The test is self administered and cannot be used to replace a proper clinical assessment and additional evaluations.

Panic and Agoraphobia Scale
type: Resource
type: NamedIndividual
has db xref: nlx_157823
synonym: Panic and Agoraphobia Scale (PAS)
abbrev: PAS
IAO_0000115: Assessment scale to measure the severity of illness in patients with panic disorder (with or without agoraphobia). It is available in both clinician-administered and self-rating formats. It contains 5 sub-scales: panic attacks, agoraphobic avoidance, anticipatory anxiety, disability, and functional avoidance (health concerns). It rates the severity of symptoms over the past week.

Master Drug Data Base Clinical Drugs
type: Resource
type: NamedIndividual
has db xref: nlx_157466
abbrev: MDDB
IAO_0000115: Ontology of master drug data base, 2009_08_05

Brandeis University; Massachusetts; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100007864
has db xref: grid.253264.4
has db xref: ISNI:0000 0004 1936 9473
has db xref: nlx_50198
has db xref: Wikidata:Q49119
IAO_0000115: Private research university located in the Boston suburb of Waltham, Massachusetts. Founded in 1948 as a non-sectarian, coeducational institution sponsored by the Jewish community, Brandeis was established on the site of the former Middlesex University.

NIH Blueprint for Neuroscience Research
type: Resource
type: NamedIndividual
has db xref: nif-0000-00219
synonym: Neuroscience Blueprint
abbrev: Blueprint
abbrev: NIH Blueprint
IAO_0000115: Collaborative framework that includes the NIH Office of the Director and the 14 NIH Institutes and Centers that support research on the nervous system. By pooling resources and expertise, the Blueprint identifies cross-cutting areas of research, and confronts challenges too large for any single Institute or Center. The Blueprint makes collaboration a day-to-day part of how the NIH does business in neuroscience, complementing the basic missions of Blueprint partners. During each fiscal year, the partners contribute a small percentage of their funds to a common pool. Since the Blueprint's inception in 2004, this pool has comprised less than 1 percent of the total neuroscience research budget of the partners. In 2009, the Blueprint Grand Challenges were launched to catalyze research with the potential to transform our basic understanding of the brain and our approaches to treating brain disorders. * The Human Connectome Project is an effort to map the connections within the healthy brain. It is expected to help answer questions about how genes influence brain connectivity, and how this in turn relates to mood, personality and behavior. The investigators will collect brain imaging data, plus genetic and behavioral data from 1,200 adults. They are working to optimize brain imaging techniques to see the brain's wiring in unprecedented detail. * The Grand Challenge on Pain supports research to understand the changes in the nervous system that cause acute, temporary pain to become chronic. The initiative is supporting multi-investigator projects to partner researchers in the pain field with researchers in the neuroplasticity field. * The Blueprint Neurotherapeutics Network is helping small labs develop new drugs for nervous system disorders. The Network provides research funding, plus access to millions of dollars worth of services and expertise to assist in every step of the drug development process, from laboratory studies to preparation for clinical trials. Project teams…

Panic Disorder Severity Scale - Self-Report
type: Resource
type: NamedIndividual
has db xref: nlx_157825
synonym: Panic Disorder Severity Scale (PDSS) Self-report
synonym: Panic Disorder Severity Scale - Self rated
abbrev: PDSS-SR
IAO_0000115: A self-administered assessment used to detect possible symptoms of panic disorder and suggest the need for a formal diagnostic assessment. It consists of seven items (which are rated from 0-4). The items assess panic frequency, distress during panic, panic-focused anticipatory anxiety, phobic avoidance of situations, phobic avoidance of physical sensations, impairment in work functioning, and impairment in social functioning. The overall assessment is made by a total score, which is calculated by summing the scores for all seven items. The total scores range from 0 to 28. The PDSS-SR is used for screening and the scores 9 and above suggest the need for a formal diagnostic assessment. (Adapted from Wikipedia)

PTSD Symptom Scale - Self-Report
type: Resource
type: NamedIndividual
has db xref: nlx_157826
abbrev: PSS-SR
IAO_0000115: A 17 item self-reported questionnaire to assess the symptoms of posttraumatic stress disorder (PTSD) during the past 2 weeks. The 17 questions all describe symptoms of PTSD which patients rate (by severity) between 0-3, 0 meaning not at all or only once and 3 meaning almost all the time or at least five times a week. The end scores range from 0-51. Scoring: * 0-13 Likelihood of Little to No PTSD * 13-51 Likelihood of PTSD (Higher Score = More Severe)

Social Phobia Inventory
type: Resource
type: NamedIndividual
has db xref: nlx_157827
abbrev: SPIN
IAO_0000115: A 17-item self-administered assessment questionnaire developed by the Psychiatry and Behavioral Sciences Department at Duke University effective in screening for and measuring the severity of social anxiety disorder. Each question is answered with one of 5 responses ranging from Not at All to Extremely. Each response is assigned a score and then totaled at the end. Scoring: * 0-20 Little or No Anxiety * 21-30 Mild Anxiety * 31-40 Moderate Anxiety * 41-50 Severe Anxiety * 51-68 Very Severe Anxiety

Polycystic Kidney Disease Outcomes Consortium
type: NamedIndividual
has db xref: nlx_157909
synonym: PKD Consortium
synonym: PKD Outcomes Consortium
synonym: Polycystic Kidney Disease (PKD) Outcomes Consortium
abbrev: PKDOC
IAO_0000115: Consortium to develop evidence supporting the use of imaging Total Kidney Volume (TKV) as a prognostic biomarker that predicts the progression of Autosomal Dominant Polycystic Kidney Disease (ADPKD) to select patients likely to respond to therapy into clinical trials. It aims to replace the currently used measurement of glomerular filtration rate (GFR). Scientists will use the data collected to develop a disease progression model that will evaluate the relationship between TKV and the known complications of ADPKD, including rate of loss of kidney function, hypertension, gross hematuria, kidney stones, urinary tract infections, development of end-stage renal disease, and mortality. These analyses will be used to support the regulatory qualification of TKV as an accepted measure for assessing the progression of ADPKD in clinical trials in which new therapies are tested. PKDOC has the following goals: # Develop standard clinical data elements and definitions that are specific to ADPKD # Create a database of aggregated data from existing multiple, longitudinal, and well-characterized research registries maintained over decades by the leading institutions in ADPKD clinical investigation # Advance and harmonize the missions of regulatory agencies by creating tools that help with the evaluation of new pharmaceutical compounds # Develop a quantitative disease progression model to examine the linkage between TKV and disease outcomes

Trauma Screening Questionaire
type: Resource
type: NamedIndividual
has db xref: nlx_157828
synonym: Trauma Screening Questionnaire (TSQ)
abbrev: TSQ
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented October 12, 2016. A brief self-report trauma screening tool, simple to administer and score, designed for trauma victims in general. This 10-items scale, all derived from the DSM-IV2 criteria, describes either a reexperiencing symptom of post-traumatic stress disorder (items 1 through 5) or an arousal symptom of PTSD (items 6 through 10). The result of the original study indicate that an excellent prediction of a PTSD diagnosis was provided by respondents endorsing at least 6x re-experiencing or arousal symptoms, for each sample of patients (rail crash survivors and crime victims). Scoring: 0-5 yes responses = Likelihood of No PTSD, 6-10 yes responses = likelihood of PTSD

Yale-Brown Obsessive Compulsive Scale
type: Resource
type: NamedIndividual
has db xref: nlx_157829
synonym: Yale-Brown Obsessive Compulsive Scale (Y-BOCS)
abbrev: Y-BOCS
IAO_0000115: Self-rating scale to assess the severity and type of symptoms in patients with obsessive-compulsive disorder (OCD). Each question is to be answered based on the average occurrence of each item over the past week. The first 5 questions relate to obsessive thoughts, the last 5 questions relate to compulsive behaviors. Scoring: * 07 Sub-Clinical * 815 Mild * 1623 Moderate * 2431 Severe * 3240 Extreme

Abbreviated Mental Test Score
type: Resource
type: NamedIndividual
has db xref: nlx_157830
synonym: Abbreviated Mental Test
abbrev: AMT
abbrev: AMTS
IAO_0000115: A 10 question assessment to assess elderly patients for the possibility of dementia. The test has utility across a range of acute and outpatient settings. It takes five minutes to administer and must include all 10 questions. A score of less than 7 or 8 suggests cognitive impairment. Scoring: * 7-10 (correct) No Cognitive Impairment * 6-0 (correct) Cognitive Impairment, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Clinical Dementia Rating
type: Resource
type: NamedIndividual
has db xref: nlx_157831
synonym: Global CDR Assignment Based On Box Scores
synonym: Global Clinical Dementia Rating (CDR) Based on CDR Box Scores
abbrev: CDR
IAO_0000115: A numeric scale used to quantify the severity of symptoms of dementia (i.e. its stage). Using a structured-interview protocol, a qualified health professional assesses a patient's cognitive and functional performance in six areas: memory, orientation, judgment and problem solving, community affairs, home and hobbies, and personal care. Scores in each of these are combined to obtain a composite score ranging from 0 through 3. (Adapted from Wikipedia)

General Practitioner Assessment of Cognition
type: Resource
type: NamedIndividual
has db xref: nlx_157832
synonym: GPCOG Screening Test
abbrev: GPCOG
IAO_0000115: Assessment test to screen a patient for cognitive impairment that takes less than four minutes for the cognitive test and less than two minutes for the informant interview. The cognitive test includes nine items: (1) time orientation, clock drawing: (2) numbering and spacing as well as (3) placing hands correctly, (4) awareness of a current news event and recall of a name and an address ( (5) first name, (6) last name, (7) number, (8) street, and (9) suburb). Each correct answer is valid one point leading to a maximum score of 9 (fewer points indicate more impairment). (Wikipedia) The informant interview asks six historical questions from an informant/next of kin who knows the patient well. He or she is asked to compare the patient's current function with his/her performance a few years ago. Areas that are covered in the informant interview include memory, word finding difficulties, trouble managing finances, difficulties managing medication independently and needing assistance with transportation. Scoring: * 9 No Significant Cognitive Impairment * 8-5 More Testing Required * 4-0 Cognitive Impairment

Informant Questionnaire on Cognitive Decline in the Elderly
type: Resource
type: NamedIndividual
has db xref: nlx_157833
synonym: Informant Questionnaire on Cognitive Decline in the Elderly (IQCODE)
abbrev: IQCODE
IAO_0000115: Assessment questionnaire used as a screening test for dementia that is filled out by a relative or other supporter who knows the patient for a minimum of 10 years to determine whether that person has declined in cognitive functioning. It lists 26 everyday situations where a person has to use their memory or intelligence. The questions on the test compare the patient''s state of mind to 10 years ago using the scale of: Much Improved A Bit Improved Not Much Change A Bit Change A Bit Worse and Much Worse. If the person is found to have significant cognitive decline, then this needs to be followed up with a medical examination to determine whether dementia is present. Scoring: * 0-3 No Cognitive Impairment * >3 Cognitive Impairment

Mini-Mental State Examination
type: Resource
type: NamedIndividual
has db xref: nlx_157834
synonym: Folstein Test
synonym: Mini-Mental State Examination (MMSE)
abbrev: MMSE
IAO_0000115: A 30 question assessment test to screen patients for cognitive impairment that is commonly used in medicine to screen for dementia. It is also used to estimate the severity of cognitive impairment and to follow the course of cognitive changes in an individual over time, thus making it an effective way to document an individual's response to treatment. It takes about 10 minutes and examines functions including arithmetic, memory and orientation.

Structured Clinical Interview for DSM-IV
type: Resource
type: NamedIndividual
has db xref: nlx_157838
abbrev: SCID
abbrev: SCID-I
abbrev: SCID-II
IAO_0000115: A diagnostic exam used to determine DSM-IV Axis I disorders (SCID-I) (major mental disorders) and Axis II disorders (SCID-II) (personality disorders). An Axis I SCID assessment with a psychiatric patient usually takes between 1 and 2 hours, depending on the complexity of the subject's psychiatric history and their ability to clearly describe episodes of current and past symptoms. A SCID with a non-psychiatric patient takes 1/2 hour to 1-1/2 hours. A SCID-II personality assessment takes about 1/2 to 1 hour. The instrument was designed to be administered by a clinician or trained mental health professional. (Adapter from Wikipedia)

Beck Hopelessness Scale
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_157839
synonym: Beck Hopelessness Scale (BHS)
abbrev: BHS
IAO_0000115: 20-item clinical assessment to measure key aspects of hopelessness: feelings about the future, loss of motivation, and expectations. It takes 5 to 10 minutes is self-administered or verbally administered by a trained administrator.

SignalChem
type: Organization
type: NamedIndividual
has db xref: grid.422212.5
has db xref: nlx_152461
IAO_0000115: An Antibody supplier

Edinburgh Postnatal Depression Scale
type: Resource
type: NamedIndividual
has db xref: nlx_157840
synonym: Edinburgh Postnatal Depression Scale (EPDS)
abbrev: EPDS
IAO_0000115: A 10 item assessment scale developed to identify women who have postpartum depression (PPD). Items of the scale correspond to various clinical depression symptoms, such as guilt feeling, sleep disturbance, low energy, anhedonia, and suicidal ideation. Overall assessment is done by total score, which is determined by adding together the scores for each of the 10 items. Higher scores indicate more depressive symptoms. The EPDS may be used within 8 weeks postpartum and it also can be applied for depression screening during pregnancy. (Adapted from Wikipedia) Scoring: * 0-9 Not Likely to Have Depression * 10-30 Likely to Have Depression

Hamilton Rating Scale for Depression
type: Resource
type: NamedIndividual
has db xref: nlx_157841
synonym: Hamilton Depression Rating Scale
abbrev: HAM-D
abbrev: HAM-D17
abbrev: HDRS
abbrev: HRSD
IAO_0000115: A multiple question assessment scale used to provide an indication of depression and serves as a way to evaluate recovery in patients. It is designed for adults and is used to rate the severity of their depression by probing mood, feelings of guilt, suicide ideation, insomnia, agitation or retardation, anxiety, weight loss, and somatic symptoms. It was designed to be administered by a trained professional using a semi-structured interview. Although Hamilton's original scale had 17 items, other versions were developed to include up to 29 items (HRSD-29).(Adapted from Wikipedia) It takes about 20 minutes to complete the interview and score the results. Scoring: * 0-7 Normal * 8-13 Mild * 14-18 Moderate * 19-22 Severe * > or = 23 Very Severe

Kutcher Adolescent Depression Scale
type: Resource
type: NamedIndividual
has db xref: nlx_157842
abbrev: KADS
IAO_0000115: A psychological self-rating scale developed by Dalhousie University professor of psychiatry Stan Kutcher, to assess the level of depression in adolescents. While there are some variations, the 11-item version of the KADS is the most commonly used and most thoroughly verified for efficacy in monitoring outcomes in adolescents who are receiving treatment for major depressive disorder. Its items are worded using standard and colloquial terminology, and responses are scored on a simple 4 choice scale. There are ten questions about depression symptom frequency that the patient rates on a straight 4 point scale according to the following choices: hardly ever, much of the time, most of the time, all the time, and one question relating to the severity of suicidal ideation. Scores on the test range from 0 to 33. Unlike some rating scales, there is no threshold for sub-clinical presentation, or ranges for mild, moderate, and severe symptoms. Higher scores simply indicate more severe current depression symptoms. (Adapted from Wikipedia)

Major Depression Inventory
type: Resource
type: NamedIndividual
has db xref: nlx_157843
abbrev: MDI
IAO_0000115: A 12 item self-report mood assessment developed by the World Health Organisation that is able to generate an ICD-10 or DSM-IV diagnosis of clinical depression in addition to an estimate of symptom severity. Scoring: * Mild depression: A score of 4 or 5 in two of the first three items. Plus a score of at least 3 on two or three of the last seven items. * Moderate depression: A score of 4 or 5 in two or three of the first three items. Plus a score of at least 3 on four of the last seven items. * Severe depression: A score of 4 or 5 in all of the first three items. Plus a score of at least 3 on five or more of the last seven items. * Major depression: The number of items is reduced to nine, as Item 4 is part of Item 5. Include whichever of the two items has the highest score (item 4 or 5). A score on at least five items is required, to be scored as follows: the score on the first three items must be at least 4, and on the other items at least 3. Either Item 1 or 2 must have a score of 4 or 5.

Tocris Bioscience
type: Organization
type: NamedIndividual
has db xref: nlx_152479
IAO_0000115: An Antibody supplier

Montgomery-Asberg Depression Rating Scale
type: Resource
type: NamedIndividual
has db xref: nlx_157844
synonym: Montgomery����??����?sberg Depression Rating Scale
abbrev: MADRS
IAO_0000115: A ten-item diagnostic questionnaire which psychiatrists use to measure the severity of depressive episodes in patients with mood disorders. Higher MADRS score indicates more severe depression, and each item yields a score of 0 to 6. The overall score ranges from 0 to 60. The questionnaire includes questions on the following symptoms: 1. Apparent sadness 2. Reported sadness 3. Inner tension 4. Reduced sleep 5. Reduced appetite 6. Concentration difficulties 7. Lassitude 8. Inability to feel 9. Pessimistic thoughts 10. Suicidal thoughts. Scoring: * 0-6 Normal/Symptom Absent * 7-19 Mild Depression * 20-34 Moderate Depression * >34 Severe Depression (Adapted from Wikipedia)

Cubist Pharmaceuticals
type: Organization
type: NamedIndividual
has db xref: grid.417686.a
has db xref: ISNI: 0000 0004 0408 8804
has db xref: nlx_158092
has db xref: Wikidata: Q5192265
synonym: Cubist Pharmaceuticals Inc.
abbrev: CBST
abbrev: Cubist
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 27th, 2023. Cubist Pharmaceuticals was American biopharmaceutical company that targeted pathogens like MRSA. Company employed 638 people, mostly in Lexington, MA. On 8 December 2014, Merck acquired Cubist.

Zung Self-Rating Depression Scale
type: Resource
type: NamedIndividual
has db xref: nlx_157845
synonym: Zung Self-Rating Depression Scale (SDS)
abbrev: SDS
IAO_0000115: A self-rating scale to assess the level of depression for patients diagnosed with depressive disorder. There are 20 items on the scale that rate the rating affective, psychological and somatic symptoms associated with depression. There are ten positively worded and ten negatively worded questions. Each question is scored on a scale of 1 through 4 (based on these replies: a little of the time, some of the time, good part of the time, most of the time). Scores on the test range from 20 through 80. The scores fall into four ranges: Scoring: * 20-44 Normal Range * 45-59 Mildly Depressed * 60-69 Moderately Depressed * 70 and above Severely Depressed The Zung Self-Rating Depression Scale has been translated into many languages, including Arabic, Azerbaijani, Dutch, German, Portuguese, and Spanish. (Adapted from Wikipedia)

Anorectic Behavior Observation Scale
type: Resource
type: NamedIndividual
has db xref: nlx_157846
synonym: Anorectic Behavior Observation Scale (ABOS)
abbrev: ABOS
IAO_0000115: A thirty-item diagnostic scale devised to be answered by the parents, spouse or other family member of an individual suspected of having an eating disorder. The questions address three factors; unusual eating behavior, bulimic-type behavior and hyperactivity. The ABOS however does not address the frequency of the observed behavior. The ABOS is scored on a range of from 0-60. There are three possible answers provided per question, each assigned a numerical value: two points for yes, zero for no, and one for don't know. (Adapted from Wikipedia) Scoring: * 0-10 Non-Anorexic * 11-20 Retest Required in 2 Months * 21-30 Anorexic Eating Detected, More Testing Required * 31-60 Severe Anorexia, Seek Professional Guidance

Binge Eating Scale
type: Resource
type: NamedIndividual
has db xref: nlx_157847
abbrev: BES
IAO_0000115: A 16 item questionnaire used to assess the presence of binge eating behavior indicative of an eating disorder that was devised specifically for use with obese individuals. The questions are based upon both behavioral characteristics (e.g., amount of food consumed) and the emotional, cognitive response, guilt or shame. Each question has 3-4 separate responses assigned a numerical value. The score range is from 0-46: * < 17 Non-Binging * 18-26 Moderate Binging * 27 and greater Severe Binging (Adapted from Wikipedia)

Eating Attitudes Test
type: Resource
type: NamedIndividual
has db xref: nlx_157848
synonym: Eating Attitudes Test - 26 Item
abbrev: EAT
abbrev: EAT-26
IAO_0000115: A widely used standardized self-report measure of symptoms and concerns characteristic of eating disorders. The original 40-item version was developed for a study to examine socio-cultural factors in the development and maintenance of eating disorders. A 26-item refinement of the original test has been made and it has been translated into many different languages and used in hundreds of studies. The EAT-26 has been useful as a screening tool to assess eating disorder risk in high school, college and other special risk samples such as athletes. It can be used in a non-clinical as well as a clinical setting not specifically focused on eating disorders. It can be administered in group or individual settings and is designed to be administered by mental health professionals, school counselors, coaches, camp counselors, and others with interest in gathering information to determine if an individual should be referred to a specialist for evaluation for an eating disorder. It is intended primarily for adolescents and adults. The EAT-26 should be used as the first step in a two-stage screening process. According to this methodology, individuals who score 20 or more on the test should be interviewed by a qualified professional to determine if they meet the diagnostic criteria for an eating disorder. The tests are rated on a six-point scale in response to how often the individual engages in specific behaviors. (adapted from Wikipedia)

Eating Disorder Inventory
type: Resource
type: NamedIndividual
has db xref: nlx_157849
abbrev: EDI
IAO_0000115: A self-report questionnaire used to assess the presence of eating disorders, anorexia nervosa, bulimia nervosa, and eating disorder not otherwise specified including Binge Eating Disorder (BED). The original questionnaire consisted of 64 questions, divided into eight subscales. There have been two subsequent revisions by Garner; Eating disorder inventory-two (EDI-2) and Eating disorder inventory-three (EDI-3). (Adapted from Wikipedia) The EDI-3 consists of 91 items organized into 12 primary scales: Drive for Thinness, Bulimia, Body Dissatisfaction, Low Self-Esteem, Personal Alienation, Interpersonal Insecurity, Interpersonal Alienation, Interoceptive Deficits, Emotional Dysregulation, Perfectionism, Asceticism, and Maturity Fears.

Sino Biological
type: Organization
type: NamedIndividual
has db xref: nlx_152463
synonym: Sino Biological Inc.
IAO_0000115: An Antibody supplier

Critical Path to TB Drug Regimens
type: NamedIndividual
has db xref: nlx_157981
synonym: Critical Path to Tuberculosis Drug Regimens
abbrev: CPTB
IAO_0000115: A collaboration of international pharmaceutical companies, public health experts, civil society organizations, and U.S., European, and other regulatory authorities to speed the development of new and improved drug regimens for tuberculosis (TB). Its goals include creating innovative tools, including TB data standards and databases. The Initiative is built around four operating arms: Regulatory Science Consortium, Drug Development Coalition, Research Resources Group, and Drug Susceptibility Testing Group. The focus of the consortium is to: * Develop and integrate data standards * Qualify biomarkers through the Food and Drug Administration (FDA) / European Medicines Authority (EMA) * Develop quantitative disease progression (natural history) models * Create disease response metrics, develop target product profiles and supporting assays, and * Develop new pharmacokinetic/dynamic measures of drug interactions Accomplishments include: * Engaged the FDA, which has released updated regulatory guide-lines for developing new TB drug regimens with efforts to create a more favorable environment for combination regimen development * TB Alliance launched the first-ever clinical trial of a novel combination drug regimen for TB, validating the approach to regimen development set forth by CPTR, and is moving to a phase III clinical trial named STAND. * Developed and published TB data standards in collaboration with the Clinical Data Interchange Standards Consortium (CDISC). * Expanded scope to include the CPTR Rapid Drug Susceptibility Testing (RDST) Consortium and an expanded Modeling and Simulation development program. * Pursued several regulatory pathways with the FDA for the Hollow Fiber System Model for TB (HFS-TB). * Submitted a dossier to the EMA on the HFS-TB for qualification opinion consideration. * Submitted a "briefing book" to the FDA via the pre-IND process to review CPTR's data analysis plan and data inventory for liquid culture, with emphasis on time-to-positivity, …

Altman Self-Rating Mania Scale
type: Resource
type: NamedIndividual
has db xref: nlx_157850
synonym: Altman Self-Rating Mania Scale (ASRM)
abbrev: ASRM
IAO_0000115: A 5-item self-reported diagnostic scale used to assess the presence and severity manic and hypomanic symptoms, most commonly in patients diagnosed with bipolar disorder. It assesses differences in normal or baseline levels in five subjective and behavioral areas: positive mood, self-confidence, sleep patterns, speech patterns / amount of sleep, and motor activity. Scores above a 5 are indicative of mania, or hypomania, with the severity of symptoms increasing with higher scores. Examining score changes over time is also used to determine the efficacy of a particular treatment in a clinical setting and to qualify whether the severity a manic episode is increasing or decreasing. (Adapted from Wikipedia) Scoring: * 0-5 Normal * 6-25 Probable Manic or Hypomanic Condition, Further Testing Recommended

Young Mania Rating Scale
type: Resource
type: NamedIndividual
has db xref: nlx_157851
synonym: Young Mania Rating Scale (YMRS)
abbrev: YMRS
IAO_0000115: An eleven-item, multiple-choice diagnostic questionnaire which psychiatrists use to measure the severity of manic episodes in patients. The scale was originally developed for use in the evaluation of adult patients who were suffering from bipolar disorder, but has since been modified for use in pediatric patients. A similar scale was then developed to allow clinicians to interview parents about their children's symptoms, in order to ascertain a better diagnosis of mania in children. Clinical studies have demonstrated the effectiveness of the parent version of the scale. The scale provided is in a slightly reworded form as a self-assessment. This may not be as accurate when self-administered, as people suffering from mania are often unable to properly assess relevant outward symptoms.

Narcissistic Personality Inventory
type: Resource
type: NamedIndividual
has db xref: nlx_157853
abbrev: NPI
IAO_0000115: A test to measure narcissism as a personality trait in social psychological research. Although there are several versions, a forty-item forced-choice version (Raskin & Terry 1988) is the one most commonly employed in current research. It is based on the DSM-III clinical criteria for narcissistic personality disorder (NPD), although it was designed to measure these features in the general population. Thus, the NPI is often said to measure normal or subclinical (borderline) narcissism (i.e., in people who score very high on the NPI do not necessarily meet criteria for diagnosis with NPD). Raskin and Terry (1988) identified seven factors of the NPI (i.e., Authority, superiority, exhibitionism, entitlement, vanity, exploitativeness and self-sufficiency), mapping roughly onto the DSM criteria for NPD. Since then, several studies have further examined the factor structure of the NPI with varying results. It should take most people five to ten minutes to complete.

CAGE Questionnaire
type: Resource
type: NamedIndividual
has db xref: nlx_157854
synonym: CAGE Alcohol Questionnaire
IAO_0000115: 4-item questionnaire, where the name is an acronym of its four questions, that can indicate potential problems with alcohol abuse and has been extensively validated for use in identifying alcoholism. It has been determined that CAGE test scores >=2 had a specificity of 76% and a sensitivity of 93% for the identification of excessive drinking and a specificity of 77% and a sensitivity of 91% for the identification of alcoholism. The most important question in the questionnaire is the use of a drink as an Eye Opener, so much so that some clinicians use a yes to this question alone as a positive to the questionnaire; this is due to the fact that the use of an alcoholic drink as an Eye Opener denotes abuse since the patient is going through withdrawal in the morning, hence the need for a drink as an Eye Opener.(Adapted from Wikipedia) Scoring: * 2 (or more) yes responses indicates the possibility of alcoholism

Standardized Mini-Mental State Examination
type: Resource
type: NamedIndividual
has db xref: nlx_157856
synonym: Standardised Mini-Mental Examination
synonym: Standardized Mini-Mental State Examination (SMMSE)
abbrev: SMMSE
IAO_0000115: Assessment test imposing strict guidelines for administration and scoring to improve the reliability of the Mini-Mental State Examination (MMSE), a screening test for the purpose of evaluating cognitive impairment in older adults.

Social Environment and Biomarkers of Aging Study in Taiwan
type: Resource
type: NamedIndividual
has db xref: nlx_157859
synonym: SEBAS in Taiwan
synonym: Social Environment and Biomarkers of Aging Study (SEBAS) in Taiwan
abbrev: SEBAS
IAO_0000115: Data sets of information regarding the health and well-being of older persons in Taiwan (from 2000 and 2006), in particular the relationship between life challenges and mental and physical health, the impact of social environment on the health and well-being of the elderly, and biological markers of health and stress. The study collected self-reports of physical, psychological, and social well-being, plus extensive clinical data based on medical examinations and laboratory analyses. Examination of health outcomes included chronic illnesses, functional status, psychological well-being, and cognitive function. Questions regarding life challenges focused on perceived stress, economic difficulties, security and safety, and the consequences of a major earthquake. Biological markers were used to identify cardiovascular risk factors, metabolic process measures, immune-system activity, the hypothalamic-pituitary adrenal axis, and sympathetic nervous system activity. The study design consists of face-to-face interviews with participants drawn from a random sub-sample of participants from 27 PSUs from the 1999 Survey of Health and Living Status of the Middle Aged and Elderly in Taiwan. Hospital visits and blood and urine specimens also were collected. A second wave of SEBAS was conducted in 2006 using a similar protocol to SEBAS 2000, but with the addition of performance assessments conducted by the interviewers at the end of the home interview. * Dates of Study: -2000, 2006 * Study Features: Longitudinal, International, Anthropometric Measures * Sample Size: 27 PSUs

Consortia-pedia
type: Resource
type: NamedIndividual
has db xref: nlx_157863
synonym: Consortiapedia
IAO_0000115: Project that aims to provide structure and clarity to the research-by-consortium model, presenting both the consortia framework and partnership components in an effort to guide and inform emerging and existing collaborative efforts. Their goal is to ensure that research-by-consortium efforts are at their highest performance and achieving the best possible outcomes. A consortium will thrive if its leadership and governance structure is able to define a mission that's shared by all stakeholders and articulate the desired outcomes of the effort early in the process. For collaborative efforts to move forward, consortia must recognize and leverage the unique strengths and resources that each partner can contribute and bring to fruition. They have found that managing expectations and establishing transparency measures are essential to building trust among all participating stakeholders. Transparency curbs potential conflicts of interest and creates a culture that allows for open sharing of data and a responsible approach to intellectual property negotiations. They found that for collaborations in the medical research and development ecosystem to be effective and sustainable, they must be driven by the ultimate goal of delivering a medical solution that could improve or save lives. Through the project, they are creating several tools for the biomedical research community: * Framework report: This series of reports analyzes a diversity of existing consortia to understand the operational management and framework used to initiate and manage these complex collaborations. * Consortium database * Landscape analysis trends and intended output * Educational webinars and spotlights

Academic Drug Discovery Consortium
type: NamedIndividual
has db xref: nlx_157873
has db xref: SciRes_000146
synonym: Academic Drug Discovery Consortium (ADDC)
abbrev: aD2c
abbrev: ADDC
IAO_0000115: A collaborative network among university-led drug discovery centers and programs to allow scientists to exchange technical expertise on drug discovery and development strategies as well as form partnerships with each other, biopharma companies, and drug discovery-focused contract service organizations and consultants. The website will also serve as a repository for drug discovery events, educational material, job postings, and partnership opportunities. Through active member participation this website will become a valuable tool for every scientist working in the drug discovery arena. In addition, involvement of members will enable them to effectively advocate to the NIH and other funding agencies to increase the awareness of the growing number of academic drug discovery scientists and their success as well as their needs.

elements of morphology
type: Resource
type: NamedIndividual
has db xref: nlx_157874
synonym: Elements of Morphology: Human Malformation Terminology
synonym: Human Malformation Terminology
IAO_0000115: Data set of standardized terms used to describe human morphology including definitions of terms for the craniofacies in general, the major components of the face, and the hands and feet. This provides a uniform and internationally accepted terms to describe the human phenotype.

Collaborative Chronic Care Network
type: NamedIndividual
has db xref: nlx_157875
synonym: C3N Project
abbrev: C3N
IAO_0000115: Project designing, prototyping, optimizing, and evaluating a learning health system to improve clinical practice, patient self-management, and disease outcomes of patients with chronic illness. This open, peer production system combines the collective input of patients, clinicians and researchers. It combines large clinical data registries with patient entered data and makes them accessible and interactive. A platform allows researchers to design, test and implement new knowledge and innovations in patient care. To test their platform approach, C3N is working on a model of treating children with Inflammatory Bowel Disease using the ImproveCareNow Network of pediatric clinics. Following this demonstration phase, the goal is to apply the social, scientific and technical platform to transform the care of a variety of chronic illnesses. The C3N effort has the following goals: # Deploy and optimize an integrated set of engagement tools to make it easier for patients and care providers to collect and use the right information during the clinical encounter and in between visits. # Prototype novel interventions to re-design care delivery by promoting the development of tools for real-time and dynamic population management, "just-in time" scheduling of visits, virtual clinic visits, and measuring the impact of these interventions on health, care, and cost. # Pilot and deploy patient-focused technology to improve the flow of data between patients, clinicians and scientists to enable faster learning and improvement.

PSTC Nephrotoxicity Biomarkers
type: Resource
type: NamedIndividual
has db xref: nlx_157890
synonym: Predictive Safety and Testing Consortium Drug-induced Nephrotoxicity Biomarkers
synonym: PSTC NWG Drug-induced Nephrotoxicity Biomarkers
IAO_0000115: Urinary kidney biomarkers (KIM-1, albumin, total protein, 2-microglobulin, cystatin C, clusterin and trefoil factor-3) that are considered acceptable biomarkers for the detection of acute drug-induced nephrotoxicity in rats and can be included along with traditional clinical chemistry markers and histopathology in toxicology studies. These biomarkers may be used voluntarily as additional evidence of nephrotoxicity in nonclinical safety assessment studies to complement the standard data (BUN and sCr). In ROC analyses, some of these biomarkers showed better sensitivity and specificity than BUN and sCr relative to histopathological alterations considered to be the gold standard when tested with a limited number of nephrotoxicant and control compounds.

Center for Integration of Medicine and Innovative Technology
type: NamedIndividual
has db xref: nlx_157880
synonym: Center for Integration of Medicine & Innovative Technology
synonym: Center for Integration of Medicine and Innovative Technology (CIMIT)
abbrev: CIMIT
IAO_0000115: A non-profit consortium of Boston academic medical centers and universities (and growing) to accelerate the healthcare innovation cycle by fostering interdisciplinary, inter-institutional collaboration among experts in translational research, medicine, science, engineering, healthcare implementation and entrepreneurship in concert with industry, foundations and government to rapidly improve patient care. It concentrates on early stage, high-risk ideas, projects and supports them through to a commercial exit from academia. It provides innovators with resources to explore, develop and implement novel technological solutions for today's most urgent healthcare problems. CIMIT is dedicated to helping develop medical technology that will help both military and civilian patients.

Quebec Consortium for Drug Discovery
type: NamedIndividual
has db xref: nlx_157881
abbrev: CQDM
IAO_0000115: Consortium to identify, fund and support breakthrough technologies that will significantly enhance biopharmaceutical R&D productivity and accelerate the development of new safe and efficacious drugs. CQDM is a neutral ground that brings patient groups, academia, governments, biotech and the pharma industry together to work collaboratively on complex medical challenges. Projects supported by the consortium are highly relevant to the pharmaceutical sector and typically address: * Opportunity for new therapeutic approaches and research * Safe and effective new drug development * Enhancing the efficacy of already existing drugs * Reducing costs, time and risks associated with the discovery and development of new drugs Funded projects typically involve multidisciplinary collaborations between research teams that represent both the academic and the private sector, who are mentored by industry scientists provided by the consortium sponsors.

eTOX
type: NamedIndividual
has db xref: nlx_157882
IAO_0000115: Project to develop a drug safety database from the pharmaceutical industry legacy toxicology reports and public toxicology data; innovative in silico strategies and novel software tools to better predict the toxicological profiles of small molecules in early stages of the drug development pipeline. The project is creating this pharmaco-toxicological database with an aim to: * Reduce the number of animal tests * Decrease the attrition rates of new drug candidates * Increase the success rate of new molecular entities becoming drugs * Improve the safety of drugs on the market The project consists of three different systems, * eTOX VITIC Database a unified database containing all confidential and non-confidential data collected in eTOX (historical data from the pharmaceutical industry) * ChOX Database a unified database containing public data (literature and public database) * eTOXsys Query and Prediction System an interface providing a uniform access to the two databases (VITIC and ChOX) and to all developed prediction models and systems

I-SPY 2 TRIAL
type: NamedIndividual
has db xref: nlx_157884
synonym: Investigation of Serial Studies to Predict Your Therapeutic Response With Imaging And moLecular Analysis 2
synonym: ISPY-2 Clinical Trials
abbrev: I-SPY2
abbrev: I-SPY 2
abbrev: ISPY2
IAO_0000115: A collaboration to test an adaptive clinical trial model that would assess the efficacy of a candidate therapeutic earlier than traditional clinical trials, potentially enabling drugs to be developed and approved using fewer patients, less time and fewer resources. This trial focuses on women with newly diagnosed locally advanced breast cancer to test whether adding investigational drugs to standard chemotherapy is better than standard chemotherapy alone. It uses genetic and biological markers from individual patients' tumors to screen several promising new treatments simultaneously and allows doctors to quickly measure the effectiveness of the treatment prior to removing the tumor. The experimental adaptive trial design uses patient outcomes to immediately inform treatment options for subsequent trial participants. The trial has 5 components that differentiate it from conventional clinical trial models. # I-SPY2 uses tissue and imaging biomarkers from individual cancer patients' tumors to determine eligibility, guide/screen promising new treatments and identify which treatments are most effective in specific tumor subtypes. # The trial's adaptive design allows the Team to learn as they go, enabling researchers to use data from patients early in the trial to guide decisions about which treatments might be more useful for patients who enter the trial earlier. I-SPY2 provides a scientific basis for researchers to eliminate ineffective treatments and graduate effective treatments more quickly. # The neoadjuvant treatment approach - in which chemotherapy is given to patients prior to surgery - allow the team to evaluate tumor response with MRI before removal. This approach is safe as treating after surgery, allowing tumors to shrink, and more importantly, it enables critical learning early on about how well treatments work. # The ability for the team to screen multiple drug candidates developed by multiple companies. New agents will be selected and added as those used i…

Drug Development Tools Qualification Programs
type: Resource
type: NamedIndividual
has db xref: nlx_157888
synonym: Drug Development Tools (DDT) Qualification Programs
abbrev: DDT Qualification Programs
IAO_0000115: To support Drug Development Tools development efforts, FDA established qualification programs for animal models for use under Animal Rule, biomarkers, and clinical outcome assessments. DDTs are methods, materials, or measures that have potential to facilitate drug development. Examples of DDTs may include, but are not limited to biomarker2 used for clinical trial enrichment, clinical outcome assessment used to evaluate clinical benefit, and animal model used for efficacy testing of medical countermeasures under regulations commonly referred to as Animal Rule3.

Hungarian Neurological-Psychiatric Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_13478
synonym: Hungarian Neurological - Psychiatric Biobank
synonym: Hungarian Neurological - Psychiatric Biobank - NEPSYBANK
abbrev: NEPSYBANK
IAO_0000115: The Hungarian Society of Clinical Neurgenetics established a nationwide collaboration for prospective collection of human biological materials and databases from patient with neurological and psychiatric diseases. The basic triangle of the NEPSYBANK is the sample, the information and the study management. The present participants of the NEPSYBANK are the Department of Neurology and Psychiatry of the four Medical Universities (in Budapest, Debrecen, Pecs, Szeged) and the National Institute of Psychiatry and Neurology in Budapest. The NEPSYBANK is a disease based biobank collecting both phenotypical and environmental data and biological materials such as DNA/RNA, whole blood, plasma, cerebral spinal fluid, muscle / nerve / skin biopsy, brain, and fibroblast. The target of the diseases is presently (Phase I): stroke syndromes, dementias, movement disorders, motoneuron diseases, epilepsy, multiple sclerosis, schizophrenia, alcohol addiction. In the near future (Phase II.) it is planned to enlarge the scale with headaches, disorders of the peripheral nerves, disorders of neuromuscular transmission, disorders of skeletal muscle, depression, anxiety. DNA/RNA is usually extracted from whole blood, but occasionally different tissues such as muscle, brain etc. can be used as well. The extracting procedures differ among the institutes, but in all cases the concentration and the quality of the DNA/RNA must be registered in the database. Participating institutional biobanks have committed themselves to follow common quality standards, which provide access to samples after prioritization on scientific grounds only. In every case the following data are registered. 1. General data: main bank categories, age, sex, ethnicity, body height, body weight, economic stats, education, type of place of living, marital status, birth complications, alcohol, drugs, smoking. 2. Sample properties (sample ID, type of sample, date of extraction, concentration, and level of purity). General patient …

ILSI HESI Drug-induced Nephrotoxicity Biomarkers
type: Resource
type: NamedIndividual
has db xref: nlx_157892
synonym: HESI Drug-induced Nephrotoxicity Biomarkers
synonym: ILSI / HESI Nephrotoxicity Working Group Drug-induced Nephrotoxicity Biomarkers
synonym: International Life Sciences Institute / Health and Environmental Sciences Institute Nephrotoxicity Working Group Drug-induced Nephrotoxicity Biomarkers
abbrev: HESI Nephrotoxicity Biomarkers
IAO_0000115: Urinary kidney biomarkers, Clusterin and Renal Papillary Antigen-1 (RPA-1), that sponsors may use to determine more conservative NOAELs for estimating starting doses in the initial human clinical trial of a drug that displays nonclinical nephrotoxicity as determined by histopathology. When tested with a limited number of nephrotoxic compounds, the Receiver Operating Characteristic (ROC) analyses showed that urinary clusterin and renal papillary antigen-1 (RPA-1) have better sensitivity and specificity than BUN and creatinine for the detection of specific kidney pathologies in male rats. Clusterin and RPA-1 provide additional and complementary information to BUN, serum creatinine (sCr), and histopathology for the detection of acute drug-induced nephrotoxicity in safety assessment studies.

O'Brien Reagan York and Jacobsen Drug-induced Cardiotoxicity Biomarkers
type: Resource
type: NamedIndividual
has db xref: nlx_157893
abbrev: O'Brien et al Cardiotoxicity Biomarkers
IAO_0000115: Serum / plasma biomarkers, Cardiac troponins T (cTnT) and I (cTnI), in safety assessment studies for rats, dogs, and monkeys are qualified biomarkers for the following contexts of use: # When there is previous indication of cardiac structural damage with a particular drug, cardiac troponin testing can help estimate a lowest toxic dose or a highest non-toxic dose to help choose doses for human testing. In this case, cardiac troponins may serve as a clinical chemistry correlate to the histology. For example, in a safety assessment study, lower doses without increases in cardiac troponins may be used to support a no observed effect level (NOEL) identified by histology. # When there is known cardiac structural damage with a particular pharmacologic class of a drug and histopathologic analyses do not reveal structural damage, circulating cardiac troponins may be used to support or refute the inference of low cardiotoxic potential. # When unexpected cardiac structural toxicity is found in a nonclinical study, the retroactive (reflex) examination of serum or plasma from that study for cardiac troponins can be used to help determine a no observed adverse effect level (NOAEL) or lowest observed adverse effect level (LOAEL). The results of this testing may support inclusion of cardiac troponin testing in subsequent safety assessment studies.

Exacerbations of Chronic Pulmonary Disease Tool
type: Resource
type: NamedIndividual
has db xref: nlx_157894
synonym: Exacerbation of Chronic Pulmonary Disease Tool Patient Reported Outcome (EXACT-PRO) Instrument
synonym: Exacerbation of Chronic Pulmonary Disease Tool Patient Reported Outcome Instrument
synonym: Exacerbations of Chronic Pulmonary Disease Tool (EXACT)
synonym: EXACT-PRO
abbrev: EXACT
IAO_0000115: An electronically administered patient-reported outcome (PRO) measure that is a qualified measure of symptoms of acute bacterial exacerbation of chronic bronchitis in patients with chronic obstructive pulmonary disease (ABECB-COPD), for use in phase 2 trials. Refer to the proposed context of use, http://www.fda.gov/downloads/Drugs/DevelopmentApprovalProcess/DrugDevelopmentToolsQualificationProgram/UCM399682.pdf. Its intent to quantify frequency, severity, and duration of acute exacerbations in clinical trials of COPD including those with chronic bronchitis. It is designed as an electronic diary made up of fourteen items to be completed by the patient each evening just prior to bedtime. (An item-reduction statistical analysis narrowed the questions from 23 to 14.) For more information see, http://www.fda.gov/downloads/Drugs/DevelopmentApprovalProcess/DrugDevelopmentToolsQualificationProgram/UCM386248.pdf

Medaka Fish Anatomy and Development Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157469
abbrev: MFO
IAO_0000115: A structured controlled vocabulary of the anatomy and development of the Japanese medaka fish, Oryzias latipes.

European Multicenter Study about Spinal Cord Injury
type: Resource
type: NamedIndividual
has db xref: nlx_157896
abbrev: EMSCI
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. A clinical spinal cord injury network that provides a database of clinical assessment data from spinal cord injured patients. The EMSCI assessment scheme currently consists of the so called core sets: neurological (ISNCSCI), functional (10MWT, 6MWT, TUG, WISCI2) measurements and independence measures (SCIM3). Additional assessments are: neurophysiology (MEP, SSEP, NCV), pain, hand function and an urodynamics.

MMRF CoMMpass Study
type: NamedIndividual
has db xref: nlx_157899
synonym: Multiple Myeloma Research Foundation (MMRF) - CoMMpass Study
synonym: Relating Clinical Outcomes in MM to Personal Assessment of Genetic Profile
synonym: Relating Clinical Outcomes in Multiple Myeloma to Personal Assessment of Genetic Profile Study
abbrev: CoMMpass
IAO_0000115: A personalized medicine initiative to discover biomarkers that can better define the biological basis of multiple myeloma to help stratify patients. This effort hopes to obtain samples from approximately 1,000 multiple myeloma patients and follow them over time to identify how a patient's genetic profile is related to clinical progression and treatment response. As a partnership between 17 academic centers, 5 pharmaceuticals and the Department of Veterans Affairs, the goal of this eight year study is to create a database that can accelerate future clinical trials and personalized treatment strategies. MMRF's CoMMpass Study has the following goals: * Create a guide to which treatments work best for specific patient subgroups. * Share data with researchers to accelerate drug development for specific subtypes of multiple myeloma patients. In order to facilitate discoveries and development related to targeted therapies, the comprehensive data from CoMMpass is placed in an open-access research portal. The data will be part of the Multiple Myeloma Research Foundation's (MMRF) Personalized Medicine Platform combines CoMMpass data with those collected from MMRF's Genomics Initiative. It is hoped that the longitudinal data, combined with the annotated bio-specimens will help provide insights that can accelerate personalized therapies.

Multiple Myeloma Genomics Portal
type: Resource
type: NamedIndividual
has db xref: nlx_157900
synonym: MMRC Multiple Myeloma Genomics Portal
abbrev: MMGP
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. Database providing access and limited analysis to the MMGP portal data sets. These include the MMRC funded reference array comparative genomic hybridization (aCGH) and gene expression data and additional public multiple myeloma datasets. The MMGP will be updated with new features such as additional data and analysis tools as they become available.

Myelin Repair Foundation
type: Organization
type: NamedIndividual
has db xref: grid.429475.9
has db xref: nlx_157901
has db xref: Wikidata: Q6947290
abbrev: MRF
IAO_0000115: A non-profit foundation that funds basic research and is focused on accelerating the development of myelin repair therapeutics for multiple sclerosis. They have defined a 15-year research plan to develop a drug or drugs and believes its Accelerated Research Collaborative (ARC) model can subsequently be used to accelerate the treatment for all diseases. The ARC framework coordinates and manages the entire therapeutic development continuum from discovery biology to FDA approval. The model works by coordinating multi-disciplinary basic research from academic and government laboratories, systematically validating and derisking potential compounds/targets, and collaborating with pharma partners to increase the probability of successful programs.

Observational Medical Outcomes Partnership
type: NamedIndividual
has db xref: nlx_157903
synonym: Observational Medical Outcomes Partnership (OMOP)
abbrev: OMOP
IAO_0000115: Initiative to improve the safety of drugs on the market that utilized information drawn from patient medical record databases and health insurance claims to develop and test methods to detect and evaluate drug safety issues over time. The OMOP pilot project focused on the following objectives: * Defining and evaluating analytical methods that can be used to identify associations between drugs and health-related conditions. * Developing tools for organizing access to and evaluating the usefulness of multiple observational datasets. * Study how information from analyses of observational data can be used to inform ongoing pharmacovigilence efforts. The software tools - packaged as the OMOP Web RL Platform was developed and made available to the public, https://github.com/OMOP . In addition to these data tools, this collaborative research effort discovered methods for using data to reliably identify correlations between individual medical interventions and specific health outcomes. These insights are being used to help inform the FDA Sentinel Initiative as part of the Innovation in Medical Evidence Development and Surveillance (IMEDS) program. The achievements of the program include: * Establishment of a common data model and creation of data characterization tools, and vocabulary mappings * Implementation of Health Outcome of Interest definitions, including a program to implement these definitions as part of the Regularized Identification of Cohorts (RICO) * Release of 14 analysis methods to evaluate the performance of methods and data in identifying drug safety issues

Medical Diagnostic Categories - Diagnosis Related Groups
type: Resource
type: NamedIndividual
has db xref: nlx_157470
abbrev: MDCDRG
IAO_0000115: Ontology of Medical Diagnostic Categories-Diagnosis Related Groups

Project Data Sphere
type: Resource
type: NamedIndividual
has db xref: DOI:10.17616/R31NJMJB
has db xref: DOI:10.34949
has db xref: nlx_157911
has db xref: r3d100010760
synonym: DataSphere
synonym: Project Data Sphere Initiative
synonym: Project Data Sphere LLC
synonym: Project DataSphere
abbrev: PDS
IAO_0000115: Initiative to advance oncology research by enabling collaborative sharing of historical oncology clinical trial data through a universal platform (database). The initiative aims to network all stakeholders in the cancer community researchers, industry, academia, advocacy, and other organizations to share insights and collaborate on issues that could not be solved individually. To do this, they have made efforts to address issues of data privacy, security, intellectual property, resources, and incentives as part of its effort to maximize participation. Data contributions include control arms of clinical trials, and the platform uses data-security precautions and analytics to pool multiple studies associated with the same diagnosis in a manner that seeks to protect the privacy of patients and the security of the data contributed.

Predictive Safety Testing Consortium
type: Resource
type: NamedIndividual
has db xref: nlx_157912
abbrev: PSTC
IAO_0000115: A public-private partnership to identify new and improved translational safety testing methods for use in nonclinical and clinical studies and submit them for formal regulatory qualification by the FDA (Food and Drug Administration), EMA (European Medicines Agency), and PMDA (Japanese Pharmaceutical and Medical Devices Agency). The current 19 corporate members of the consortium share internal experience with nonclinical and clinical safety biomarkers in six working groups: cardiac hypertrophy, nephrotoxicity, hepatotoxicity, skeletal myopathy, testicular toxicity, and vascular injury. The ultimate goal of the consortium is to improve the current approach to drug safety testing and offer assurance to the drug developers that these approaches will be accepted by the regulatory authorities in their drug development programs. Through PSTC, members are able to share their expertise, resources, data, and internally developed approaches in a neutral, precompetitive, confidential environment. There are more than 250 participating scientists and C-Path serves as the trusted third party, leading the collaborative process by collecting and summarizing the data, and leading the interactions with global health authorities.

TransCelerate BioPharma
type: Organization
type: NamedIndividual
has db xref: nlx_157913
synonym: TransCelerate BioPharma Inc.
abbrev: TransCelerate
IAO_0000115: Non-profit research organization aiming to accelerate drug development by increasing the quality and efficiency of clinical studies through the development of shared tools, methods, and platforms. Consortium partnerships are limited to pharmaceutical and biotechnology companies with research & development operations, although there are collaborations with external organizations such the Clinical Data Interchange Standards Consortium (CDISC). Its current focus is to collaborate on: * Standardizing risk-based monitoring * Development of methods to qualify and train clinical trial sites * Development of a common investigator web portal * Development of clinical data standards on efficacy, and methods for comparator drug trials It currently has 5 projects: # Standardized Approach for High-Quality, Risk-Based Monitoring program aims to develop an industry-wide standard and approach for risk-based monitoring of clinical trials in order to enhance patient safety and ensure the quality of clinical trial data. # Shared Site Qualification and Training program aims to standardize GCP training and site qualification credentials in order to realize efficiencies and accelerate study start-up timelines. # Common Investigator Site Portal is a platform designed to streamline investigator and site access through harmonized delivery of content and services. # Data Standards project is a partnership with CDISC to develop industry-wide data standards in priority therapeutic areas to support the exchange and submission of clinical research and meta-data, improving patient safety and outcomes. # Comparator Drugs project aims to establish reliable, rapid sourcing of quality products for use in clinical trials through a comparator supply model enabling accelerated trial timelines and enhanced patient safety.

Alsace BioValley
type: Resource
type: NamedIndividual
has db xref: nlx_157915
abbrev: Alsace
IAO_0000115: A French world-class cluster dedicated to therapeutic innovations, it is the one-stop contact to optimize any R&D development or business project in Europe, both in drug development and medical technologies. Located in Alsace region, part of the famous French-German-Swiss BioValley and with a unique concentration of international life sciences & healthcare players, Alsace BioValley helps any Life Sciences & Healthcare companies interested in new projects and partnerships in Europe: * to search outstanding scientific or industrial partners to develop very innovative R&D projects * to find the best innovative technology, patent or scientific expertise * to set up and locate in Alsace region

Business-Led Networks of Centres of Excellence
type: Resource
type: NamedIndividual
has db xref: nlx_157917
synonym: Business-Led Networks of Centres of Excellence Program
abbrev: BL-NCE
IAO_0000115: Funds large-scale collaborative research networks that bring a wide range of research expertise to bear on specific challenges identified by an industrial sector. Led by a not-for-profit consortium of industrial partners, networks enhance private sector innovation by blending academic expertise with the private sector''s drive to respond to real-world challenges. BL-NCEs increase private sector investments in Canadian research, support training of skilled researchers, and accelerate the transfer of ideas from the laboratory into solutions needed by the private sector.

Accelerating Medicines Partnership Autoimmune Diseases of Rheumatoid Arthritis and Lupus
type: Resource
type: NamedIndividual
has db xref: nlx_157975
synonym: Accelerating Medicines Partnership - Arthritis
synonym: Accelerating Medicines Partnership - Autoimmune
synonym: Accelerating Medicines Partnership - Autoimmune Diseases
synonym: Accelerating Medicines Partnership - Autoimmune Diseases of Rheumatoid Arthritis and Lupus
synonym: AMP Autoimmune Diseases of Rheumatoid Arthritis and Lupus
synonym: AMP RA/SLE Program
synonym: AMP Rheumatoid arthritis and lupus
abbrev: AMP Autoimmune
abbrev: AMP RA/SLE
IAO_0000115: The autoimmune disease arm of the Accelerating Medicine Partnership (AMP), which aims to identify and validate the most promising biological targets of disease for new diagnostic and drug development, that is focused on rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). They seek to identify shared common flaws in inflammation, particularly those that are shared with a larger number of autoimmune disorders which can cause severe disability, greatly affect quality of life, and are associated with an increased risk of death. This project aims to reveal biomarkers and biological targets for drug development, matching existing drugs to patients with specific molecular profiles who are most likely to benefit. The research plan proposes a 5 year process. Year one will include startup activities such as validation of tissue acquisition processes and analytic technologies, and the development of operating procedures. The second year will focus on identification of disease specific pathways by comparing data from patients and healthy individuals. Years 3-5 will expand the scale to include comparisons of different subsets of patients with RA or lupus to allow molecularly based patient stratification for precise treatment. The final 12 months (2019) will also include preliminary target validation. The data will be made publicly available through an internet-based information portal.

Karma
type: Resource
type: NamedIndividual
has db xref: nlx_157923
synonym: Karma - A Data Integration Tool
synonym: Karma A Data Integration Tool
IAO_0000115: An information integration software tool that enables users to integrate data from a variety of data sources including databases, spreadsheets, delimited text files, XML, JSON, KML and Web APIs. Users integrate information by modeling it according to an ontology of their choice using a graphical user interface that automates much of the process. Karma learns to recognize the mapping of data to ontology classes and then uses the ontology to propose a model that ties together these classes. Users then interact with the system to adjust the automatically generated model. During this process, users can transform the data as needed to normalize data expressed in different formats and to restructure it. Once the model is complete, users can publish the integrated data as RDF or store it in a database.

Lyonbiopole
type: Resource
type: NamedIndividual
has db xref: nlx_157924
synonym: Lyon Biopole
synonym: Lyonbiop��le
IAO_0000115: A worldwide competitiveness cluster centered on pharmaceutical activities including the fight against human and animal infectious diseases and cancers. Designed as a tool interface and public / private approximation, the division has implemented measures to encourage collaborative R & D, help in setting up projects and find funding, increase strategic and financial partnerships for economic development and international companies, provide access to reception areas, technological shared platforms such as the Infectious Diseases Center Lyonbiop��le. It aims to strengthen the competitiveness of the sector health and the attractiveness of the Rh��ne-Alpes area, mainly on the Lyon-Grenoble axis. (adapted from the translated Wikipedia)

Ontario Centres of Excellence
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100009011
has db xref: grid.440046.2
has db xref: ISNI: 0000 0004 0577 2202
has db xref: nlx_157928
synonym: Ontario Centers of Excellence
abbrev: OCE
IAO_0000115: Organization that drives the development of Ontario's economy by helping create new jobs, products, services, technologies and businesses by bridging academia and industry. The program suite covers almost all stages of business development and career advancement, covering three key areas: Industry-Academic R&D Collaboration; Commercialization; and Entrepreneurship. Other key initiatives are the IBM Smart Computing Initiative and Colleges Ontario Network for Industry Innovation (CONII). In partnership with industry, OCE co-invests to commercialize innovation originating in the province's publicly funded colleges, universities and research hospitals. They also support and invest in early-stage projects, where the probability of commercial success and potential total return on innovation are substantial. Another expanding focus for OCE is the development of the next generation of innovators through their entrepreneurship fellowships and programs for students and youth across Ontario. Their efforts are focused on sectors of the economy with the greatest potential to drive Ontario's future prosperity and global competitiveness: energy and environment (including water); advanced manufacturing; advanced health technologies; and information, communications technologies and digital media. A trusted partner of government in program delivery, they are committed to advancing a whole-of-government approach as a means of streamlining funding application processes for companies and entrepreneurs.

Identifiers.org
type: Resource
type: NamedIndividual
has db xref: biotools:identifiers.org
has db xref: nlx_157931
IAO_0000115: A system providing resolvable persistent Uniform Resource Identifiers (URIs) used to identify data for the scientific community, with a current focus on the Life Sciences domain. The provision of resolvable identifiers (URLs) fits well with the Semantic Web vision, and the Linked Data initiative. It provides direct access to the identified data using one chosen physical location (or resource). If more than one physical locations providing the data are recorded in the Registry, then you can access them via the top banner or by using a profile.

Charles Stark Draper Laboratory
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100006353
has db xref: grid.417533.7
has db xref: ISNI: 0000 0004 0634 6125
has db xref: nlx_157942
has db xref: Wikidata: Q2876029
synonym: Draper Laboratory
synonym: The Charles Stark Draper Laboratory Inc
abbrev: Draper
IAO_0000115: A not-for-profit research and development laboratory focused on the design, development, and deployment of advanced technological solutions for the nation's most challenging and important problems in security, space exploration, healthcare, and energy. Their expertise includes the areas of guidance, navigation, and control systems; fault-tolerant computing; advanced algorithms and software solutions; modeling and simulation; and MEMS and multichip module technology. With a strong commitment to delivering working solutions to their sponsors, they apply their expertise to a variety of domains, including autonomous air, land, sea, and space systems; information integration; distributed sensors and networks; precision-guided munitions; and biomedical engineering; chemical/biological defense; and energy system modeling and management. When appropriate for the needs of their sponsors, they will work with commercial partners to transition their technology to commercial production.

Ovation
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_158031
has db xref: SciRes_000172
abbrev: Ov
IAO_0000115: A dropbox like model cloud-based, commercial data management and collaboration system designed specifically for research scientists. It helps manage and annotate data, track provenance and share this with colleagues.

Mar Institute of Medical Research Foundation
type: Resource
type: NamedIndividual
has db xref: nlx_157957
synonym: Fundacio Institut Mar d'Investigacions Mediques
synonym: Fundació Institut Mar d'Investigacions Médiques
synonym: Fundación Instituto Mar de Investigaciones Médicas
synonym: IMIM Foundation
abbrev: FIMIM
IAO_0000115: A private non-profit independent organization that supports and manages research at the Municipal Institute for Medical Research (IMIM) in Barcelona. Its main roles include managing and monitoring research projects and grant requests, promoting quality research, ensuring the observance of ethical principles of professional practice, disseminating the results of research activities, and encouraging specialized teaching and continuous training by and for professionals in the field of Health Sciences. The Foundation is responsible for managing the Institute's resources, and plays an especially relevant role in managing European projects, services abroad and grants for research projects and cooperative research networks from the Carlos III Health Institute. The expertise of the Project Office team covers: project management; financial management; legal assessment; exploitation and intellectual property rights management; knowledge management; validation and assessment; business planning; and training, dissemination and communication strategies design and implementation.

TED
type: Resource
type: NamedIndividual
has db xref: nlx_157959
IAO_0000115: A nonprofit devoted to spreading ideas, usually in the form of short, powerful talks (18 minutes or less). TED began as a conference where Technology, Entertainment and Design converged, and today covers almost all topics - from science to business to global issues - in more than 100 languages. Meanwhile, independently run TEDx events help share ideas in communities around the world.

ABIRISK
type: NamedIndividual
has db xref: nlx_157967
synonym: ABIRISK Project
synonym: Anti-Biopharmaceutical Immunization: Prediction and Analysis of Clinical Relevance to Minimize the Risk
IAO_0000115: A consortium that seeks to provide an integrated approach to anti-drug immunization by evaluating immunogenicity in hemophilia A, multiple sclerosis, and inflammatory diseases, and exploring new tools for protein drug immunogenicity. The data collected will be pooled in a single immunogenicity databank and will be standardized and used to develop models of anti-drug antibodies. By examining the correlation between patient and clinical factors and the incidence of immunogenicity, it hopes to reduce the regulatory and resource burdens of immunogenicity testing. The objectives of the consortium are: # Access to large cohorts of patients treated with marketed biopharmaceutical products # Complementary expertise for anti-drug antibodies (ADA) assays; standardization and characterization of ADA # Novel integrated approaches to characterize anti-drug lymphocyte responses # Development and validation of innovative prediction tools # Collection and integration of immunogenicity-related data and clinical relevance of ADA ABIRISK is grouped into five working projects, which communicate with one another and provide each other with results and data for analysis. The five working projects are: ADA assay development and validation and cohort management; cellular characterization and mechanisms of the AD immune response; evaluation and development of technologies for predicting immunogenicity; establishment of database, data analyses and integration; and project management and communication.

Advanced Immunization Technologies
type: NamedIndividual
has db xref: nlx_157968
synonym: Advanced Immunization Technologies (ADITEC)
abbrev: ADITEC
IAO_0000115: A consortium that aims to accelerate the development of immunization technologies for the next generation of human vaccines. The goals are to characterize the mode of action and conduct comparative effectiveness studies of: adjuvants, vectors, formulations, delivery devices, routes of immunization, homologous and heterologous primeboost schedules, on vaccine efficacy. As part of these clinical trials, the consortium will also investigate the impact of host factors such as age, gender, genetics and pathologies. The consortium hopes to use insights gained from their projects to advance the development of next-generation vaccines, using tools such as standardized animal models to select promising immunization technologies. The intended outcome of this partnership is to improve the vaccine development process by advancing: basic research, new technology development, and clinical trial methods. Scientific objectives: # Development of adjuvants, vectors, formulations, and delivery devices # Selection of candidates, routes of immunization, and prime-boost combinations in animal models # Assessment of the impact of host factors in response to vaccination # Development of concepts and tools from human immunization # Development of concepts and tools to address regulatory and ethical issues posed by novel immunization technologies # Creation of an internationally recognized training program for translational immunology and vaccinology. Data is shared across the research partners within and between the different workstreams. Additionally, the consortium has plans to create a clinical database that combines phenotypic and clinical information to study the immune response to influenza vaccination at a population level, in an effort to advance studies into the effects of genetic background, gender, and disease on vaccine response.

Accelerating Medicines Partnership - Alzheimers
type: NamedIndividual
has db xref: nlx_157974
synonym: Accelerating Medicines Partnership - Alzheimer's
synonym: Accelerating Medicines Partnership - Alzheimer's Disease
synonym: Accelerating Medicines Partnership Alzheimer's Disease
abbrev: AMP Alzheimer's
abbrev: AMP Alzheimer's Disease
IAO_0000115: The Alzheimer's disease arm of the Accelerating Medicines Partnership (AMP) that will identify biomarkers that can predict clinical outcomes, conduct a large scale analysis of human AD patient brain tissue samples to validate biological targets, and to increase the understanding of molecular pathways involved in the disease to identify new potential therapeutic targets. The initiative will deposit all data in a repository that will be accessible for use by the biomedical community. The five year endeavor, beginning in 2014, will result in several sets of project outcomes. For the biomarkers project, tau imaging and EEG data will be released in year two, as baseline data becomes available. Completed data from the randomized, blinded trials will be added after the end of the five year studies. This will include both imaging data and data from blood and spinal fluid biomarker studies. For the network analysis project, each project will general several network models of late onset AD (LOAD) and identify key drivers of disease pathogensis by the end of year three. Years four and five will be dedicated to validating the novel targets and refining the network models of LOAD, including screening novel compounds or drugs already in use for other conditions that may have the ability to modulate the likely targets.

Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D)
type: Resource
type: NamedIndividual
has db xref: nlx_157976
has db xref: SCR_014533
synonym: Accelerating Medicines Partnership Type 2 Diabetes
synonym: Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal
synonym: AMP
synonym: AMP Diabetes
synonym: AMP T2D
synonym: AMP Type 2 Diabetes
synonym: AMP-T2D
synonym: T2D
synonym: The AMP-T2D Knowledge Portal
synonym: Type 2 Diabetes Knowledge Portal
abbrev: T2DKP
IAO_0000115: Portal and database of DNA sequence, functional and epigenomic information, and clinical data from studies on type 2 diabetes and analytic tools to analyze these data. .Provides data and tools to promote understanding and treatment of type 2 diabetes and its complications. Used for identifying genetic biomarkers correlated to Type 2 diabetes and development of novel drugs for this disease.

Shenandoah Biotechnology
type: Organization
type: NamedIndividual
has db xref: nlx_152459
synonym: Shenandoah Biotechnology Inc
synonym: Shenandoah Biotechnology Inc.
IAO_0000115: An Antibody supplier

BioVacSafe
type: NamedIndividual
has db xref: nlx_157978
synonym: Biomarkers for Enhanced Vaccine ImmunoSafety
synonym: Biomarkers for Enhanced Vaccine Safety
synonym: Biomarkers for enhanced vaccines immunosafety
synonym: BioVacSafe - Biomarkers for enhanced vaccines immunosafety
synonym: BioVacSafe Project
synonym: Biovacsafe.eu
IAO_0000115: Project focused on developing cutting edge tools to speed up and improve the testing and monitoring of vaccine safety, both before and after release to the market. The three specific objectives of the project are: * the characterization of early inflammation induced by vaccines currently on the market and the identification and validation of biomarkers of early inflammation and allergic responses; * the identification and validation of early biomarkers of autoimmunity and their use to help identifying population at risk of developing autoimmunity; * the analysis of the incidence and epidemiology of autoimmune disease in the general population and the link to genetic background or previous events in the life of patients, including severe effects, such as anaphylactic shock.

Be The Cure
type: NamedIndividual
has db xref: nlx_157979
synonym: Be The Cure For Rheumatoid Arthritis
abbrev: BTCure
IAO_0000115: Consortium bringing together academic and industry researchers to advance the understanding of disease causing factors and disease progression in Rheumatoid Arthritis (RA), with a focus on accelerating the development of new drugs. The efforts under this consortium aim to develop: (1) animal models; (2) human biobanks, databases and technologies; (3) research network to address critical biologic and clinical questions; (4) community to network patients and companies. The focus will be the development of new diagnostic methods to discover the early forms of RA as well as tools to separate the different forms of RA, where different molecular mechanisms are involved and where different therapies may be required. The ultimate goal for therapeutic development is to identify the disease-causing molecular events early in the disease and then influence immunity and inflammation so that functional deterioration is halted, immunity is re-regulated and the disease is cured. Samples from biobanks will be analysed in vitro and models will be aligned with different variants of human arthritis. In addition, new models will be established using similar molecular pathways as the relevant human arthritis subsets, leading to the understanding of the etiology and early pathology of the disease for a program aimed at early and curative treatment of RA and RA-like diseases. A major focus of these efforts will be to understand and subsequently alter the adaptive immune reactions in patients from a disease-inducing mode into either a protective mode against the disease or become asymptomatic.

California Integrated Data Exchange
type: NamedIndividual
has db xref: nlx_157980
abbrev: Cal INDEX
IAO_0000115: A three-year consortium that brings together insurers and health care providers to share information from approximately 9 million patients, with a goal that insights from the data will bring down healthcare costs and improve outcomes. It aims to be one of the largest health information exchanges in the country, with the goal of better connecting the vast, often disparate healthcare landscape across California. The database that will house patient data will be overseen by Orion Health, an independent eHealth software company. The information will only be used for clinical purposes. Academic research institutions can apply to use the Cal INDEX de-identified data for research to benefit the public good, such as population health initiatives. Cal INDEX has five main goals: * Improve the quality of care by providing clinicians with a unified statewide source of integrated patient information * Provide patients with a seamless transition between health plans or across various healthcare professionals and hospitals * Improve efficiency and reduce the cost of healthcare * Encourage healthcare technology innovation * Improve public health by providing de-identified data for medical research. Cal INDEX plans to launch at the end of 2014 with approximately 9 million health information records from combined members of Dignity Health and Blue Shield of California and Anthem Blue Cross. Cal INDEX is open to any health data contributor. Cal INDEX will establish a bi-directional data interface with providers to exchange data with EMRs and other hospital and office-based systems.

Seven Hills Bioreagents
type: Organization
type: NamedIndividual
has db xref: nlx_152458
IAO_0000115: An Antibody supplier

Coca-Cola Company
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100004367
has db xref: grid.451378.c
has db xref: ISNI: 0000 0004 0504 2170
has db xref: nlx_158091
has db xref: Wikidata: Q3295867
synonym: Coca-Cola
synonym: KO
synonym: The Coca-Cola Company
IAO_0000115: An American multinational beverage corporation and manufacturer, retailer and marketer of nonalcoholic beverage concentrates and syrups, which is headquartered in Atlanta, Georgia. (Wikipedia) It is the world's largest beverage company, refreshing consumers with more than 500 sparkling and still brands.

Nclamp - data acquisition software for electrophysiology
type: Resource
type: NamedIndividual
has db xref: nif-0000-00072
synonym: Nclamp
IAO_0000115: Data acquisition software that runs in conjunction with neuromatic. configured to work with Igor Pro on PC or Mac, instrutech or national instrument acquisition devices. Funded by The Medical Research Council (UK) Compatibility with WaveMetrics Igor Pro 5 and 6. Compatibility with Mac or PC. NIDAQ interfacing multifunction DAQ boards from National Instruments. Requires Igor NIDAQ Tools MX. ITC interfacing - data acquisition systems from InstruTech / Heka. Requires Igor ITC XOPs. Episodic acquisition (stim and sample). Continuous acquisition (currently for ITC users only). Online analysis, with ability to create your own analysis functions. Notes and Log Files which can be displayed within a table or notebook. Automatic saving of data and log folders to your hard drive. Flexible stimulus pulse generator with ability to use your own pulse waveforms. Instant accessibility to all of NeuroMatics and Igor Pros pre-existing data analysis functions.

Medical Dictionary for Regulatory Activities
type: Resource
type: NamedIndividual
has db xref: nlx_157471
abbrev: MEDDRA
IAO_0000115: Ontology of Medical Dictionary for Regulatory Activities Terminology (MedDRA)

St. John's College of Pharmacy and Allied Health Professions
type: Organization
type: NamedIndividual
has db xref: nif-0000-02067
synonym: St. John's University College of Pharmacy and Health Sciences
abbrev: St. Johns College of Pharmacy and Allied Health Professions
IAO_0000115: The College of Pharmacy and Allied Health Professions equips students with the education, training and support they need to meet the present and future demands professionals encounter as pharmacists, physician assistants, clinical laboratory scientists, toxicologists and radiologic technologists. The College is committed to helping students: * Focus on the responsibilities of public health and service * Appreciate the ever-changing character of the health professions * Enjoy a broad, general education * Pursue graduate study in specialized fields of interest Facilities Laboratory facilities in the College of Pharmacy and Allied Health Professions include state-of-the-art equipment used in pharmacology/toxicology, medicinal chemistry, industrial pharmacy and drug information. Our facilities include: GC-mass spectrophotometers; transmission and scanning electron microscopes; Mrs.; capillary GCs; preparative and analytical HPLCs; liquid scintillation and gamma counters; luminometers; dissolution apparatus; membrane potentiometers; atomic absorption spectrophotometers; polygraphs; high-speed and ultracentrifuges. In addition, we have sophisticated tissue-cultures laboratories, molecular pharmacology and molecular biology laboratories, as well as an AAALAC accredited animal facility. In addition to the main University computer, a fully equipped microcomputer laboratory is located adjacent to the main science complex.

Global Health Innovative Technology Fund
type: Organization
type: NamedIndividual
has db xref: grid.475132.6
has db xref: nlx_157983
abbrev: GHIT
abbrev: GHIT Fund
IAO_0000115: A consortium that focuses their efforts on discovering and developing new pharmaceutical drugs, vaccines (both preventive and therapeutic) and diagnostics against the infectious diseases that are prevalent in developing countries. The initial targets are those disorders designated by WHO as neglected tropical diseases prevalent in developing nations. The consortium aims to facilitate international partnerships that enable Japanese technology, innovations, and insights to play a more direct role in improving global health. Another goal of GHIT is to develop a new drug-discovery screening platform to assist the screening of compound libraries housed within Japanese companies and academic institutions. The vision is to have Japanese research organizations donate compounds, with the Fund reimbursing screening costs and leveraging screening programs of existing product-development partners.

Innovative Medicines Initiative
type: Organization
type: NamedIndividual
has db xref: grid.454814.8
has db xref: ISNI: 0000 0004 0577 0821
has db xref: nlx_157984
has db xref: Wikidata: Q1664196
abbrev: IMI
IAO_0000115: Initiative to improve health by speeding up the development of, and patient access to, innovative medicines, particularly in areas where there is an unmet medical or social need. It does this by initiating and managing consortia composed of the key players involved in healthcare research, including universities, the pharmaceutical and other industries, small and medium-sized enterprises (SMEs), patient organizations, and medicines regulators. IMI is a public-private partnership between the European Union and the European pharmaceutical industry, represented by the European Federation of Pharmaceutical Industries and Associations (EFPIA), with a timeframe separated into two phases (2008-2013, 2014-2024) that are each defined by unique research agendas. The first phase (2008 2013) had four pillars that defined the focus of its research agenda: * Predicting safety: evaluating the safety of a compound during the pre-clinical phase of the development process and the later phases in clinical development. * Predicting efficacy: improving the ability to predict how a drug will interact in humans and how it may produce a change in function. * Knowledge management: utilization of information and data for predicting safety and efficacy. * Education and training: closing existing training gaps in the drug development process. Some of the consortia managed under IMI focused on specific health issues while others focused on broader challenges in drug development. Additionally, IMI launched a number of education and training projects during its first phases. The goal of the second phase (IMI2, 2014-2024) is to develop next generation vaccines and drugs. The focus is on delivering the right prevention and treatment for the right patient at the right time. There is a strong focus on the development of new medicines with an emphasis on tools and methods that accelerate patient access to new medicines. IMI2's agenda can be defined by four axes of research: * target validation and biom…

MARCAR
type: NamedIndividual
has db xref: nlx_157986
synonym: bioMARkers and molecular tumor classification for non-genotoxic CARcinogenesis
synonym: MARCAR - towards novel biomarkers for cancer risk assessment
IAO_0000115: Consortium to identify early biological indicators (biomarkers) that can be used to predict the development of cancer, as an unintended and adverse response to a new drug. The use of these biomarkers that detect early carcinogenicity will hopefully accelerate drug development and increase patient safety. The project focuses on non-genotoxic carcinogenesis (NGC) specifically looking at the role of epigenetic effects that could be caused as unintended consequences of new drugs. Using a combination of molecular analysis technologies, the consortium combines expertise in the field of biomarkers, human and rodent cancer models, imaging, molecular profiling and bioinformatics. Participants will focus on liver tumors, the organ most affected by non-genotoxic carcinogenesis, during the preclinical safety evaluations of candidate-medicines. Their findings aim to facilitate tumor identification in other organs as well, in hopes of providing insights in the mechanisms of tumor growth. The main objectives of the consortium are to: * Identify early biomarkers for predicting which compounds have a potential for later cancer development * Improve the scientific basis for assessing carcinogenic potential of non-genotoxic (NGC) drugs * Identify the molecular response to NGC exposure that underpins development of early exposure biomarkers * Improve drug safety and the efficiency of drug development by advancing the development of alternative research methods

Oxford Nanopore Technologies
type: Organization
type: NamedIndividual
has db xref: nlx_158233
synonym: Oxford Nanopore Technologies Ltd
abbrev: Oxford Nanopore
IAO_0000115: Commercial organization developing a disruptive, proprietary technology platform for the direct, electronic analysis of single molecules. The instruments GridION and MinION are adaptable for the analysis of DNA, RNA, proteins, small molecules and other types of molecule. Consequently, the platform has a broad range of potential applications, including scientific research, personalized medicine, crop science and security / defence.

PyroBayes
type: Resource
type: NamedIndividual
has db xref: OMICS_01155
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. A base caller for pyrosequences from the 454 Life Sciences sequencing machines.

TI Pharma
type: NamedIndividual
has db xref: nlx_157987
synonym: Foundation Top Institute Pharma
synonym: Stichting Top Instituut Pharma
synonym: Top Industry Pharma
synonym: Top Institute Pharma
IAO_0000115: A not-for-profit organization that initiates and manages drug development consortia that involve the pharmaceutical industry, academia, and the Dutch Government. The aim of all their consortia is to conduct pre-competitive research while strengthening the Netherlands' international reputation for drug development. The consortia are focused on addressing therapeutic areas that are listed as priority areas by the World Health Organization including: autoimmune diseases, cardiovascular diseases, cancer, infectious diseases, and diseases of the brain. The consortia are also focused on enabling: therapeutic target discovery, validation, and animal models; lead selection and in-silico modeling; predictive drug disposition and toxicology; biomarkers and biosensors; drug formulation, delivery, and targeting; and, production technologies. TI Pharma consortia aim to improve the efficiency of the drug-development process, with a focus on advancing regulatory science. In addition to research, TI Pharma also has objectives to train and educate scientists in the Netherlands on the drug discovery and development processes, as well as on entrepreneurship. Participants include: all Dutch universities and academic medical centers, more than 30 industrial partners, small-to-medium sized companies, and representatives from the Dutch Medicines Evaluation Board (Netherlands regulatory body for drugs).

Stein Institute for Research on Aging
type: Resource
type: NamedIndividual
has db xref: nlx_157988
synonym: Center for Healthy Aging Stein Institute for Research on Aging
synonym: Sam and Rose Stein Institute for Research on Aging
synonym: UCSD Stein Institute for Research on Aging
abbrev: Stein Institute
IAO_0000115: Portal dedicated to the development and application of the latest advances in biomedical and behavioral science knowledge to issues of successful, healthy aging and the prevention and reduction of the burden of disability and disease in late life. Additionally, they provide numerous grants to junior faculty, as well as education programs for doctors and researchers through monthly Grand Rounds. From studying memory to identifying genes with important roles in aging, Stein Institute scientists are continuously pushing the boundaries of knowledge. One of their most promising ongoing projects is the Successful AGing Evaluation (SAGE) Study. SAGE is the only large-scale study on successful aging that considers the impact of positive psychological traits, such as resilience and wisdom, in addition to biological factors, providing a much more complete picture of older adults. Their monthly public lectures presented by renowned physicians and scientists are broadcast on UCSD-TV and have been viewed more than one billion times. This year they partnered with the Clinical and Translational Research Institute and the Osher Lifelong Learning Institute to organize Making Sense of Science, a course for older adults interested in science and health. In addition, They distribute a free monthly newsletter and work extensively with the community, participating in numerous events and conferences.

Stein Institute for Research on Aging News
type: Resource
type: NamedIndividual
has db xref: nlx_157989
abbrev: Stein Institute News
IAO_0000115: A list of articles published related to aging produced by the Center for Healthy Aging, Stein Institute for Research on Aging.

Stein Institute for Research on Aging Video Archive
type: Resource
type: NamedIndividual
has db xref: nlx_157990
abbrev: Stein Institute Videos
IAO_0000115: Videos and podcasts presenting the latest innovative research being conducted by the Stein Institute for Research on Aging medical faculty, with the aim of promoting healthy aging. Additionally, many of the public lectures from the Public Lecture Series are also available on UCSD-TV's website video on demand programming. The Lecture series allows affiliated faculty members of the Stein Institute for Research on Aging and other scientists from the UCSD School of Medicine, as well as individuals from surrounding academic and research institutions, to present the latest findings in their respective fields of expertise and share their present work with the general community. All of these lectures focus on topics related to healthy aging or age-related diseases.

UCSD-TV
type: Resource
type: NamedIndividual
has db xref: nlx_157991
synonym: UCSDTV
synonym: University of California San Diego Television
IAO_0000115: A University of California San Diego based station, including television, blogs, videos and podcasts, with access to people and events that impact both the campus community and the greater San Diego region. The station's non-commercial status gives it the autonomy to create content based strictly on relevance, interest and merit and is able to devote significant airtime to in-depth coverage of new ideas, key issues and emerging talent.

mzML
type: Resource
type: NamedIndividual
has db xref: nlx_158004
synonym: mzML Specification
IAO_0000115: Markup language for encoding raw spectrometer output. From 2005-2008 there has existed two separate XML formats for encoding raw spectrometer output: mzData developed by the PSI and mzXML developed at the Seattle Proteome Center at the Institute for Systems Biology. It was recognized that the existence of two separate formats for essentially the same thing generated confusion and required extra programming effort. Therefore the PSI, with full participation by ISB, has developed a new format by taking the best aspects of each of the precursor formats to form a single one. It is intended to replace the previous two formats. This new format was originally given a working name of dataXML. The final name is mzML.

University of Connecticut; Connecticut; USA
type: Organization
type: NamedIndividual
has db xref: Crossref Funder ID 100009073
has db xref: GRID grid.63054.34
has db xref: ISNI 0000 0001 0860 4915
has db xref: nlx_74010
has db xref: Wikidata Q49206
synonym: University of Connecticut
abbrev: UConn
IAO_0000115: University of Connecticut is a public land-grant research university system with its main campus in Storrs, Connecticut, United States. It was founded in 1881 as the Storrs Agricultural School, named after two benefactors. In 1893, the school became a public land grant college, then took its current name in 1939.

eTRIKS
type: Resource
type: NamedIndividual
has db xref: biotools:eTRIKS
has db xref: nlx_158034
synonym: European Translational Information & Knowledge Management Services
synonym: European Translational Information and Knowledge Management Services
IAO_0000115: Research informatics and analytics platform for the IMI OncoTrack consortium.

Predict-TB
type: NamedIndividual
has db xref: nlx_158036
synonym: PreDiCT - TB
abbrev: PreDiCT-TB
IAO_0000115: Consortium to accelerate the search for new, more effective combinations of treatments to tackle Tuberculosis and address pre-clinical research barriers to the discovery and development of new TB drug combinations. To overcome the challenges in Tuberculosis drug development they will create tools to accelerate PK-PD (Pharmacokinetic / Pharmacodynamic) analysis that are connected to clinical outcomes. By addressing the gaps in preclinical information, the consortium aims to provide a framework and tools to facilitate the transition of the best combinations of drugs to late phase development. They aim to develop an integrated set of laboratory-based models that will provide much-needed data to indicate the most appropriate doses and combinations of drugs for patients. In addition, the project will generate a comprehensive database of patient data from previous and on-going clinical trials for use as a reference for evaluating the performance of combination anti-TB drug regimens in these newly developed laboratory models. Ultimately, they aim to enable researchers to be able to use the information generated by the novel models to design better clinical trials involving TB patients. The aims of the consortium: * To systematically evaluate two successive panels of representative anti-tuberculosis drugs (licensed and novel) using a suite of standard, novel and enhanced preclinical model systems, with respect to performance in clinical trials * To refine the set of preclinical systems on the basis of these results in order to identify and define the currently optimal critical path in discovery and pre-clinical development for tuberculosis. * To develop an integrated PK-PD / Disease modelling and simulation framework for tuberculosis which will facilitate prediction of optimal combinations and design of clinical studies.

OncoTrack
type: NamedIndividual
has db xref: nlx_158037
synonym: Onco Track
synonym: OncoTrack - Methods for systematic next generation oncology biomarker development
IAO_0000115: An international consortium to develop and assess novel approaches to identify and characterize biological markers for colon cancer that will deepen the understanding of the variable make-up of tumors and how this affects the way patients respond to treatment. They will use cutting edge laboratory-based genome sequencing techniques coupled to novel computer modelling approaches to study both the biological heterogeneity of colon cancers (i.e. patient to patient variability) as well as tumor variation within the patient for example, by comparing primary tumors with metastases. This five year project brings together top scientists from European academic institutions offering a wide range of expertise, and partners them with pharmaceutical companies. The project is based on the premise that this genetic and epigenetic information, combined with a description of the molecular pathology of the tumor, will allow OncoTrack to generate a more accurate in-silico model of the cancer cell. This will facilitate the identification of predictive markers that can be used to guide the optimal therapy strategy at the level of the individual patient - and will also provide on-going prognostic guidance for the clinician. This project will not only advance understanding of the fundamental biology of colon cancers but will provide the means and approach for the identification of previously undetected biomarkers not only in the cancer under study, but potentially also in other solid cancers and, in doing so, open the door for personalized management of the oncology patient.

Alcohol and Alcohol Problems Science Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-00221
synonym: Alcohol Alcohol Problems Science Database
IAO_0000115: Portal to support researchers and practitioners searching for information related to alcohol research including links to a number of databases, journals, and Web sites focused on alcohol research and related topics. Also included is a link to the archived ETOH database, the premier Alcohol and Alcohol Problems Science Database, which contains over 130,000 records and covers the period from 1972 through 2003. Included in ETOH are abstracts and bibliographic references to journal articles, books, dissertation abstracts, conference papers and proceedings, reports and studies, and chapters in edited works. ETOH's scope reflects the multidisciplinary nature of the alcohol research field. The range of subject areas contained in ETOH includes: medicine, biochemistry, psychology, psychiatry, epidemiology, sociology, anthropology, treatment, prevention, education, accidents and safety, legislation, criminal justice, public policy, and health services research. The ETOH database is indexed with vocabulary from the Alcohol and Other Drug Thesaurus: A Guide to Concepts and Terminology in Substance Abuse and Addiction (AOD Thesaurus), Third Edition. More than 5,000 terms in the AOD Thesaurus are used as ETOH descriptors. The Databases/Resources section includes databases and resources for alcohol researchers and practitioners. It includes an introduction to the National Library of Medicine's PubMed and some sample searches on alcohol to run in the PubMed database; descriptions of and links to the various databases of the National Clearinghouse for Alcohol and Drug Information (NCADI); a selection of alcohol and other drug databases with their descriptions and links; links to peer-reviewed journals most often used by alcohol researchers; and links to a selection of Web sites pertinent to the substance abuse field.

Astellas Pharma Inc.
type: Organization
type: NamedIndividual
has db xref: nlx_158074
synonym: 4503
synonym: Astellas Pharma
abbrev: Astellas
IAO_0000115: Japanese pharmaceutical company formed from the merger of Yamanouchi Pharmaceutical Co., Ltd. and Fujisawa Pharmaceutical Co., Ltd. Astellas' franchise areas are urology, immunology (transplantation), dermatology, cardiology, and infectious disease. Priority areas for R&D are infectious diseases, diabetes, gastrointestinal diseases, oncology, and diseases of the central nervous system. The company's headquarters are in Tokyo, with research centers in Tsukuba and Osaka. Clinical development is centered in Northbrook, Illinois and Leiderdorp, Netherlands. Combined revenues of the two pre-merger companies were $7.9 billion in 2004. Worldwide the company employs about 17,000 people. (Wikipedia)

sciple.org
type: Resource
type: NamedIndividual
has db xref: nlx_143523
synonym: Science People
synonym: Science People: how people do Science - interviews with neuroscientists
synonym: SciPle
abbrev: SciPle.org
IAO_0000115: SciPle.org uses a two-step data-driven approach to foresee future trends in neuroscience. 1. We build profiles of neuroscientists by collecting interviews with them. 2. These profiles are combined with trends in neuroscience literature to gain insight into the evolution of the "next big thing". SciPle.org merges these two approaches to build an objective model of the neuroscience system, which will allow us to better understand and predict evolving topics and the role played by neuroscientists in shaping and following the current and future trends in neuroscience. We build profiles of neuroscientists by collecting interviews with them: neuroscientists are the agents shaping the neuroscience field. Their interests, drives, motivations and dreams drive their research. Neuroscientists exist in an ecosystem of hidden emergent forces which result from their interactions with thousands of other neuroscientists. Our approach consists in sampling a large pool of neuroscientists. Having a large enough sample (across a reasonable time lag) will allow the building of representative profiles of neuroscientists. * Future: We are aggregating interviews from a large pool of neuroscientists asking them what they envisage for the future of neuroscience. SciPle algorithm will parse those interviews and produce a visualization of the most likely future scenario of the neuroscience field. * Connectivity: We are developing algorithms that will allow profiling of neuroscientists (on the basis of their interviews) and track links (common views on the future and present of neuroscience) between scientists. 1. You send us back SciPle's questionnaire 2. We discover who are the fellows who share the same vision as yours on the future of neuroscience 3. Meet your fellows at conferences and find out whether SciPle was right!

EpiTarget
type: Resource
type: NamedIndividual
has db xref: nlx_158041
synonym: EPITARGET - Targets and biomarkers for antiepileptogenesis
abbrev: EPITARGET
IAO_0000115: A multidisciplinary project focused on the process leading to epilepsy, epileptogenesis, in adults. Their main hypothesis is that there are combinations of various causes, acting in parallel and/or in succession, that lead to epileptogenesis and development of seizures. Their central premise and vision is that a combinatorial approach is necessary to identify appropriate biomarkers and develop effective antiepileptogenic therapeutics. The project will focus on: * identifying novel biomarkers and their combinations for epileptogenesis after potentially epileptogenic brain insults in clinically relevant animal models, such as traumatic brain injury (TBI) and status epilepticus (SE); * exploring multiple basic mechanisms of epileptogenesis and their mutual interactions; * and translating these findings towards the clinic by validating biomarkers in human samples accessible to the consortium.

IBMA toolbox
type: Resource
type: NamedIndividual
has db xref: nlx_158042
IAO_0000115: Image-Based Meta-Analysis toolbox for SPM. Implementation of z-based statistics: Fisher's, Stouffer's.

IAESTE
type: Resource
type: NamedIndividual
has db xref: nlx_158047
synonym: International Association for the Exchange of Students for Technical Experience
IAO_0000115: An independent, non-profit and non-political student exchange organization that provides students in technical degrees (primarily Science, Engineering and the applied arts) with paid, course-related, training abroad and employers with highly skilled, highly motivated trainees, for long or short term projects.

Consortium for Reliability and Reproducibility
type: Resource
type: NamedIndividual
has db xref: nlx_158048
synonym: Consortium for Reliability and Reproducibility (CoRR)
abbrev: CoRR
IAO_0000115: Consortium that has aggregated resting state fMRI (R-fMRI) and diffusion imaging data from laboratories around the world, creating an open science resource for the imaging community, that facilitates the assessment of test-retest reliability and reproducibility for functional and structural connectomics. Given that this was a retrospective data collection, they have focused on basic phenotypic measures that are relatively standard in the neuroimaging field, as well as fundamental for analyses and sample characterization. Their phenotypic key is organized to reflect three classifications of variables: 1) core (i.e., minimal variables required to characterize any dataset), 2) preferred (i.e., variables that were strongly suggested for inclusion due to their relative import and/or likelihood of being collected by most sites), and 3) optional (variables that are data-set specific or only shared by a few sites). CoRR includes 33 datasets consisting of: * 1629 Subjects * 3357 Anatomical Scans * 5093 Resting Functional Scans * 1302 Diffusion Scans * 300 CBF and ASL Scans

Lhasa Limited
type: Resource
type: NamedIndividual
has db xref: nlx_158058
synonym: Lhasa Ltd.
abbrev: Lhasa
IAO_0000115: A not-for-profit membership organization and educational charity that facilitates collaborative data sharing projects in the pharmaceutical, cosmetics and chemistry-related industries specializing in the development of expert computer systems for toxicity and metabolism prediction. They provide a number of extensive and continually updated knowledge bases and the software needed to interrogate them. Its charitable aims include the sponsorship of activities that advance scientific knowledge and understanding and they regularly support computational chemistry events and initiatives that are of interest to Lhasa Limited members and the wider scientific community. All applications for sponsorship will be considered on their individual merits.

PEAR
type: Resource
type: NamedIndividual
has db xref: OMICS_00674
synonym: Pair-end read merger
synonym: PEAR: Pair-end read merger
IAO_0000115: Software for an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.

MIAPA
type: Resource
type: NamedIndividual
has db xref: nlx_158100
synonym: Minimal Information for a Phylogenetic Analysis
IAO_0000115: Central hub for resources related to developing and deploying a Minimal Information for a Phylogenetic Analysis (MIAPA) standard.

Neuroflocks - tweets from SfN2010
type: Resource
type: NamedIndividual
has db xref: nlx_143524
synonym: Neuroflocks Sfn10
synonym: Neuroflocks:Sfn10
synonym: NeuroFlocks:SfN2010
abbrev: NeuroFlocks SfN2010
IAO_0000115: Neuroflocks is an unique tool to navigate tweets from the past SfN meeting and find out the hot topics tweeted during the conference (SfN-2010). We have collected all tweets using the hashtag #sfn10 and made them browsable via a simple visual search interface. Type in the word you want to search for and only tweets containing that word will light up! You can click on single tweets, browse the tweet content, click on the Twitter user and find new Neuroscience-enthusiast twitterers! You can also find out what was really HOT during the conference (Re-Tweeted tweets, RT have been color coded). Moreover, the tweets follow a time gradient from the inside out: the spiral's center contains tweets from the beginning of the meeting while tweets on the outside of the spiral were tweeted at the end of the meeting. Enhanced versions of neuroflocks are currently under development !!!

Sciencewise
type: Resource
type: NamedIndividual
has db xref: nlx_143528
synonym: Sciencewise - ERC
synonym: Sciencewise Expert Resource Center
synonym: Sciencewise Expert Resource Centre
synonym: Sciencewise Expert Resource Centre for Public Dialogue In Science and Innovation
synonym: Sciencewise-ERC
IAO_0000115: Sciencewise-ERC is the UK's national center for public dialogue in policy making involving science and technology issues. It provides co-funding and specialist advice and support to Government departments and agencies to develop and commission public dialogue activities in emerging areas of science and technology. It consists of a comprehensive online resource of information, advice and guidance together with a wide range of support services aimed at policy makers and all the different stakeholders involved in science and technology policy making, including the public. Sciencewise-ERC works with central Government and its agencies, and executive, advisory and non-departmental public bodies. Some of the Government departments include the Department for Environment, Food and Rural Affairs (Defra), the Department of Energy and Climate Change (DECC) and most recently HM Treasury.

PatientsLikeMe
type: Resource
type: NamedIndividual
has db xref: nlx_143529
IAO_0000115: A for-profit health data-sharing platform that can transform the way patients manage their conditions, change the way industry conducts research and improve patient care. PatientsLikeMe aligns patient and industry interests through data-sharing partnerships. They work with trusted nonprofit, research and industry Partners who use this health data to improve products, services and care for patients. They take the information patients share about their experience with the disease and sell it to their partners (i.e., companies that are developing or selling products to patients). These products may include drugs, devices, equipment, insurance, and medical services. Except for the restricted personal information entered when registering for the site, participants should expect that every piece of information submitted (even if it is not currently displayed) may be shared with their partners and any member of PatientsLikeMe, including other patients. They do not rent, sell or share personally identifiable information for marketing purposes or without explicit consent. Because they believe in transparency, they tell members exactly what they do and do not do with their data. Patients have the opportunity to share both personal stories and health data about their conditions to help uncover great ideas and new knowledge. By sharing information on the site, they can put their disease experiences in context and find answers to the questions they have. Every partnership we develop must bring them closer to aligning patient and industry interests. Their end goal is improved patient care and quality of life.

Onyx Pharmaceuticals
type: Organization
type: NamedIndividual
has db xref: nlx_158070
synonym: Onyx Pharmaceuticals Inc.
abbrev: ONXX
abbrev: Onyx
IAO_0000115: November 2020, Onyx merged with Legacy Acquisition Corp. to form PARTS iD, Inc. Our data intelligence, integrated platforms, product cataloging, digital marketing expertise, and virtual warehousing have ensured our continued leadership in the competitive marketplace.

Amorfix
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100007611
has db xref: grid.422608.a
has db xref: nlx_158072
synonym: Amorfix Life Science
synonym: Amorfix Life Sciences
synonym: Amorfix Life Sciences Ltd.
synonym: ProMIS Neurosciences
abbrev: AMF
IAO_0000115: Product development company focused on therapeutic products and diagnostic devices targeting misfolded protein diseases. On July, 2015 the company name was changed to ProMIS Neurosciences, Inc.

Associates in Process Improvement
type: Resource
type: NamedIndividual
has db xref: nlx_158073
abbrev: API
IAO_0000115: Organization that develops methods, works with leaders and teams, and provides education and training to help organizations improve their products and services and to build their capability for on-going improvement.

Minimal Standard Terminology of Digestive Endoscopy
type: Resource
type: NamedIndividual
has db xref: nlx_157483
abbrev: MSTDE
IAO_0000115: Metathesaurus Version of Minimal Standard Terminology Digestive Endoscopy. Bethesda, MD: National Library of Medicine, 2001.

Avid Radiopharmaceuticals
type: Organization
type: NamedIndividual
has db xref: nlx_158076
synonym: Avid Radiopharmaceuticals Inc.
IAO_0000115: Subsidiary of Eli Lilly and Company who develops new molecular imaging agents capable of changing the medical management of significant, chronic human diseases by identifying the first stages of pathological change, potentially assisting in earlier diagnosis, and better management and development of new therapies. The company has developed a radioactive tracer called florbetapir (18F). Florbetapir can be used to detect beta amyloid plaques in patients with memory problems using positron emission tomography (PET) scans, making the company the first to bring to market an FDA-approved method that can directly detect this hallmark pathology of Alzheimer's disease.

BASF Corporation
type: Organization
type: NamedIndividual
has db xref: nlx_158078
synonym: BASF Corporation - The Chemical Company
synonym: BASF Corporation North America
synonym: BASF SE
abbrev: BASF Corp
IAO_0000115: German multinational chemical company and largest chemical producer in the world. BASF Group comprises subsidiaries and joint ventures in more than 80 countries and operates six integrated production sites and 390 other production sites in Europe, Asia, Australia, the Americas and Africa.

Foldit
type: Resource
type: NamedIndividual
has db xref: nlx_143530
synonym: Fold It
synonym: Foldit: Solve Puzzles for Science
IAO_0000115: Foldit is a revolutionary new multiplayer online computer game that engages non-scientists in solving hard prediction problems, enabling you to contribute to important scientific research. Foldit players interact with protein structures using direct manipulation tools and user-friendly versions of algorithms from the Rosetta structure prediction methodology, while they compete and collaborate to optimize the computed energy. Here are the basic principles to keep in mind when folding proteins. Your score on each protein is based on how well you do with these three things: # Pack the protein: The smaller the protein, the better. More precisely, you want to avoid empty spaces (voids) in the structure of the protein where water molecules can get inside. So you want the atoms in the protein to be as close together as possible. Certain structures, such as sheets, will even connect together with hydrogen bonds if you line them up right and get them close together. This is also good. Key word: Compact. # Hide the hydrophobics: Hydrophobics are the sidechains that don't want to be touching water, just like oil or wax. Since most proteins float around in water, you want to keep the hydrophobics (orange sidechains) surrounded by as many atoms as possible so the water won't get to them. The other side of this rule is that hydrophilics (blue sidechains) do want to be touching water, so they should be exposed as much as possible. Key word: Buried. # Clear the clashes: Two atoms can't occupy the same space at the same time. If you've folded a protein so two sidechains are too close together, your score will go down a lot. This is represented by a red spiky ball (clash) where the two sidechains are intersecting. If there are clashes, you know something is wrong with your protein. So make sure everything is far enough apart. Key word: Apart. The current series of Science Puzzles, the Grand Challenges, are meant to generate the evidence needed to prove that human protein folders can …

BioClinica
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100007742
has db xref: grid.430790.9
has db xref: ISNI: 0000 0004 0602 1531
has db xref: nlx_158082
has db xref: Wikidata: Q4914605
synonym: BioClinica Inc.
IAO_0000115: Pennsylvania-based company supporting pharmaceutical and medical device innovation with imaging core lab, EDC, IVR / IWR, CTMS, and supply chain forecasting and optimization. Its initial service was medical imaging for clinical trials. It is used to capture, collect, control quality, provide blinded reading services to the final delivery to the sponsor company and to the FDA or EMEA if required for medical images in a wide range of imaging modalities. (Wikipedia)

Biogen Idec
type: Organization
type: NamedIndividual
has db xref: nlx_158083
synonym: Biogen Idec Inc.
abbrev: BIIB
IAO_0000115: Global biotechnology company based in Cambridge, Massachusetts, specializing in discovering, developing, and delivering important therapies for the treatment of neurodegenerative, hematologic and autoimmune diseases to patients worldwide.

BioReliance
type: Organization
type: NamedIndividual
has db xref: nlx_158085
synonym: BioReliance Corp.
synonym: BioReliance Corporation
abbrev: BREL
IAO_0000115: Company that provides testing and manufacturing services to pharmaceutical and biopharmaceutical companies that span the product cycle from early pre-clinical development to licensed production.

Charles River Laboratories
type: Resource
type: NamedIndividual
has db xref: grid.452317.6
has db xref: nif-0000-00462
has db xref: nlx_158088
has db xref: SCR_013551
has db xref: Wikidata: Q28974283
synonym: Charles River
synonym: Charles River Laboratories Inc.
synonym: Charles River Laboratories International Inc.
abbrev: CRL
IAO_0000115: Commercial organism provider selling mice, rats and other model animals. American corporation specializing in a variety of pre-clinical and clinical laboratory services for the pharmaceutical, medical device and biotechnology industries. It also supplies assorted biomedical products and research and development outsourcing services for use in the pharmaceutical industry. (Wikipedia)

Chemotargets
type: Organization
type: NamedIndividual
has db xref: nlx_158089
synonym: Chemotargets SL
IAO_0000115: A computationally-oriented biotech company located in Barcelona that is focused on the drug discovery and development areas. Chemotargets' goal is to help the biopharma industry fast-forward the process of bringing new medicines to market, speeding up drug discovery and development programs and making them more cost-efficient. To this end, they have designed, and continue to develop, an integrated technology platform involving a broad spectrum of cutting-edge computational methodologies.

Chevron Corporation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100004366
has db xref: grid.450626.3
has db xref: ISNI: 0000 0004 0599 8199
has db xref: nlx_158090
has db xref: Wikidata: Q319642
synonym: Chevron Corp
synonym: Chevron Corp.
abbrev: Chevron
abbrev: CVX
IAO_0000115: An American multinational energy corporation headquartered in San Ramon, California, and active in more than 180 countries, that is engaged in every aspect of the oil, gas, and geothermal energy industries, including exploration and production; refining, marketing and transport; chemicals manufacturing and sales; and power generation. Chevron is one of the world's largest oil companies; as of 2013, it ranked third in the Fortune Global 500-2014 list of the world's largest companies. (Adapted from Wikipedia)

University of Geneva; Geneva; Switzerland
type: NamedIndividual
has db xref: nlx_38255
synonym: Universite de Geneve
synonym: University of Geneva
synonym: Université de Genève
abbrev: UNIGE

Jmol
type: Resource
type: NamedIndividual
has db xref: nlx_158093
synonym: Jmol: an open-source Java viewer for chemical structures in 3D
IAO_0000115: An open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems and features an applet, application, and systems integration component.

Glyco3D
type: Resource
type: NamedIndividual
has db xref: nlx_158094
IAO_0000115: A family of databases covering the 3D features of monos, di, oligo, polysaccharides, glycosyltransferases, lectins, monoclonal antibodies and glycosaminoglycan-binding proteins. Other databases are also made available that completes the picture of glycan 3D structure decoding. that are made freely available to the scientific community. A search engine has been developed that scans the full content of all the data bases for queries related to sequential information of the carbohydrates or other related descriptors. This database ensemble offers a unique opportunity to characterize the 3D features that a given oligosaccharide can assume in different environments.

Paleobiology Database
type: Resource
type: NamedIndividual
has db xref: nlx_158095
has db xref: r3d100012690
synonym: PaleoBioDB
synonym: PaleoDB
abbrev: PBDB
IAO_0000115: A non-governmental, non-profit public database for paleontological data providing researchers and the public with information about the entire fossil record. It has been organized and operated by a multi-disciplinary, multi-institutional, international group of paleobiological researchers. Its purpose is to provide global, collection-based occurrence and taxonomic data for organisms of all geological ages, as well data services to allow easy access to data for independent development of analytical tools, visualization software, and applications of all types. The Database's broader goal is to encourage and enable data-driven collaborative efforts that address large-scale paleobiological questions. Paleontological data files are accepted for upload. However, PaleoBioDB needs some basic data types to be included in order to perform an upload. The Application Programming Interface (API) gives scientists, students, and developers programmatic access to taxonomic, spatial, and temporal data contained within the database.

Phenoscape
type: Resource
type: NamedIndividual
has db xref: biotools:Phenoscape
has db xref: nlx_158096
IAO_0000115: Project to create a scalable infrastructure that enables linking phenotypes across different fields of biology by the semantic similarity of their descriptions.

Minimum Information About a Simulation Experiment
type: Resource
type: NamedIndividual
has db xref: nlx_158097
synonym: MIASE Guidelines
abbrev: MIASE
IAO_0000115: A set of guidelines (community effort) suitable for use with any structured format for simulation experiments to identify the Minimal Information About a Simulation Experiment necessary to enable the reproducible simulation experiments. The Guidelines list the information that a modeller needs to provide to enable the execution and reproduction of a numerical simulation experiment, derived from a given set of quantitative models. MIASE is designed to help modelers and software tools to exchange their simulation settings and to foster collaboration. In 2011, he MIASE guidelines were accepted by researchers from 19 different institutes.

Tree of Life: Phylogeny of Spiders
type: Resource
type: NamedIndividual
has db xref: nlx_158099
synonym: Assembling the Tree of Life: Phylogeny of Spiders
synonym: ATOL: Phylogeny of Spiders
abbrev: Phylogeny of Spiders
IAO_0000115: Project whose aim is to produce a robust phylogeny of all the deepest branches within a mega-diverse group, the spiders, by combining a massive amount of newly generated comparative genomic data with a substantial set of new and re-assessed data on morphology and behavior. They propose to collect a huge amount of genomic information in order to test and improve the results achieved by over 50 detailed morphological cladistic analyses conducted by more than 30 investigators during the past 15 years. The insignificant amount of genomic work to date on spiders has been uncoordinated and of little utility for broad-scale phylogenetic investigation. The advent of high-throughput DNA sequencing, however, makes it feasible to examine substantial parts of the genome across a dense sampling of spider taxa. They propose to sequence at least 50 loci (genome samples of 500-1,000 or more base pairs that can be sequenced as single pieces in both directions simultaneously) for representatives of at least 500 genera of spiders and their closest relatives (the whipscorpion orders Amblypygi, Uropygi, and Schizomida). These genera will be carefully selected by a sampling strategy designed to maximize the resolution of deep branches within spider phylogeny, and will purposefully include all the previously most-favored study organisms of ethologists, ecologists, physiologists, and developmental and molecular biologists, thus integrating and contextualizing their research. Data matrices will be produced that combine the new genomic data with a new, comprehensive survey of morphological and behavioral homologies, offering a unique index to all comparative data on one large group. New computer software, designed in large part by members of their group and using massively parallel processing to achieve supercomputing capability, makes such analyses feasible.

Alzheimer Europe
type: Organization
type: NamedIndividual
has db xref: grid.424021.1
has db xref: ISNI: 0000 0001 0739 010X
has db xref: nlx_158313
has db xref: Wikidata: Q16827712
abbrev: AE
IAO_0000115: A non-governmental organization aimed at raising awareness of all forms of dementia by creating a common European platform through co-ordination and co-operation between Alzheimer organizations throughout Europe. Alzheimer Europe is also a source of information on all aspects of dementia.

Telethon Foundation
type: Resource
type: NamedIndividual
has db xref: nlx_143533
synonym: TeleThon.it
abbrev: Telethon
IAO_0000115: Since 1990 Telethon, along with millions of Italians, has stepped up to the challenge of beating muscular dystrophy and the other genetic diseases. It is a marathon against time, because there are many people who live with these rare disorders, and the resources to deal with them have to be carefully measured out because there is not much public or private funding invested in this field of research, and the path to finding cures is often long and tortuous. The foundation In order to guarantee as much research funding as possible into muscular dystrophy and other genetic diseases, the Telethon team works throughout the year and has adopted a management system for the donated funds that is strict and efficient. For every euro raised by Telethon, about eighty euro cents reach the cutting edge laboratories and excellent research centers. Scientific area The selection of the best research projects, the funding of dedicated researchers and the foundation and maintenance of its research institutes make Telethon a point of Italian excellence in the world. Along with recognition from the international scientific community, Telethon's world of research is the biggest ally of all the people who live with muscular dystrophy or other genetic disorders every day. The online database provides complete information about the projects funded by Telethon from 1991 to the present. The archive contains information about all the Foundation's efforts in the field of biomedical research. In addition to a search by disease, it is possible, using the advanced search function, to interrogate the database by groups of disorders, by the name of a researcher or research institute, or by the town, province, or region where projects are based. The use of another search filter makes it possible to check which research projects are ongoing and which have come to an end.

WebCite
type: Resource
type: NamedIndividual
has db xref: nlx_158104
IAO_0000115: An on-demand archiving system for webreferences (cited webpages and websites, or other kinds of Internet-accessible digital objects), which can be used by authors, editors, and publishers of scholarly papers and books, to ensure that cited webmaterial will remain available to readers in the future. Users make a local copy of the cited webpage / webmaterial and archive the cited URL to enable readers permanent access to the cited material. If cited webreferences in journal articles, books etc. are not archived, future readers may encounter a 404 File Not Found error when clicking on a cited URL. It's free and takes only 30 seconds. A WebCite-enhanced reference is a reference which contains - in addition to the original live URL (which can and probably will disappear in the future, or its content may change) - a link to an archived copy of the material, exactly as the citing author saw it when he accessed the cited material.

NeuroStars
type: Resource
type: NamedIndividual
has db xref: nlx_158105
synonym: Neuro stars
IAO_0000115: A question answering web site and forum that focuses on neuroinformatics and neuroscience. Initially conceived by Istvan Albert's highly successful BioStar website within the Bioinformatics community, NeuroStars is born as an experiment to engage the Neuroinformatics community after some unfruitful attempts in StackExchange's Area51. Posts that are detailed and specific, written clearly and simply are welcome.

NeuroVault
type: Resource
type: NamedIndividual
has db xref: nlx_158106
has db xref: r3d100012842
synonym: NeuroVault - A public repository of unthresholded brain activation maps
IAO_0000115: Data repository where researchers can publicly store and share unthresholded statistical brain activation maps produced by MRI and PET studies.

ChannelPedia
type: Resource
type: NamedIndividual
has db xref: nlx_158108
synonym: Channel pedia
abbrev: Channelpedia
IAO_0000115: An information management framework for comprehensive ion channel information. It is a knowledge base system centered on genetically expressed ion channel models and it encourages researchers of the field to contribute, build and refine the information through an interactive wiki-like interface. It is web-based, freely accessible and currently contains 187 annotated ion channels with 50 Hodgkin-Huxley models (September 2014). Channelepdia provides an ideal platform to collectively build ion channel knowledge base by accommodating both structured and unstructured data. The current version of Channelpedia contains the following sections : Introduction, Genes, Ontologies, Interactions, Structure, Expression, Distribution, Function, Kinetics and Models. Newly published literature related to ion channels is automatically queried every week from PubMed and added to respective categories. Currently, Channelpedia contains ~180,000 abstracts related to ion channels from Pubmed.

Inserm Transfert
type: Organization
type: NamedIndividual
has db xref: grid.14498.30
has db xref: nlx_158128
synonym: Inserm Transfert SA
synonym: Inserm-Transfert SA
IAO_0000115: A private subsidiary of the French National Institute of the Health and Medical Research (Inserm), dedicated to technology transfer (from invention disclosure to industrial partnership). It manages European and International research projects, supports large scale projects in epidemiology and public health. It has run a proof of concept fund. The company is also committed to seed financing in the biotech sector, through its dedicated seed fund company Inserm Transfert Initiative. www.inserm-transfert.fr

Primm Biotech
type: Organization
type: NamedIndividual
has db xref: grid.425563.3
has db xref: nlx_152431
has db xref: Wikidata: Q30285010
synonym: Primm Biotech inc.
IAO_0000115: An Antibody supplier

BioResource Impact Factor
type: Resource
type: NamedIndividual
has db xref: nlx_158109
synonym: Bio Resource Impact Factor
abbrev: BRIF
IAO_0000115: A collective international initiative to construct a framework intended to implement tools to recognize and measure the use of bioresources for research. A BRIF would make it possible to trace the quantitative use of a bioresource, the kind of research using it and the efforts of the people and institutions that construct it and make it available. It targets 4 main objectives that are currently ongoing: # the assignment of a unique and persistent identifier to the bioresource by an independent international institution or body, # the construction of the BRIF algorithm on the basis of a number of agreed parameters for the follow-up of the use of bioresources, # the modification of editorial guidelines in order to integrate coherently the citation and acknowledgement of the bioresources used in scientific articles and # the assessment of incentives for bioresources access and sharing policies.

BioSHaRE
type: NamedIndividual
has db xref: nlx_158110
synonym: Biobank Standardisation and Harmonisation for Research Excellence
synonym: Biobank Standardisation and Harmonisation for Research Excellence in the European Union
abbrev: BIOSHARE-EU
IAO_0000115: A consortium of leading biobanks and international researchers from all domains of biobanking science to ensure the development of harmonized measures and standardized computing infrastructures enabling the effective pooling of data and key measures of life-style, social circumstances and environment, as well as critical sub-components of the phenotypes associated with common complex diseases. The overall aim is to build upon tools and methods available to achieve solutions for researchers to use pooled data from different cohort and biobank studies. This, in order to obtain the very large sample sizes needed to investigate current questions in multifactorial diseases, notably on gene-environment interactions. This aim will be achieved through the development of harmonization and standardization tools, implementation of these tools and demonstration of their applicability. BioSHaRE researchers are collaborating with P3G, the Global Alliance for Genomics and Health, IRDiRC (International Rare Diseases Research Consortium), H3Africa and other organizations on the development of an International Code of Conduct for Genomic and Health-Related Data Sharing. A draft version is available for external review. Generic documents have been prepared covering areas of biobanking that are of major importance. SOPs have been finalized for blood withdrawal (SOPWP5001blood withdrawal), manual blood processing (SOPWP5002blood processing), shipping of biosamples (SOPWP5003shipping) and withdrawal, processing and storage of urine samples (SOPWP5004urine).

PeerLibrary
type: Resource
type: NamedIndividual
has db xref: nlx_158113
synonym: Peer Library
IAO_0000115: Open source project providing a collaborative layer of knowledge over academic publications by allowing users to share real-time highlights and annotations. Participate in open discussion that drives ideas and academia forward. It provides a supportive space to learn about research and ask questions of peers and experts. Follow authors and other users to understand their perspectives, make connections, and discover new ideas.

Nephromine
type: NamedIndividual
has db xref: nlx_158114
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE; REPLACED BY NEPHROSEQ; A growing database of publicly available renal gene expression profiles, a sophisticated analysis engine, and a powerful web application designed for data mining and visualization of gene expression. It provides unique access to datasets from the Personalized Molecular Nephrology Research Laboratory incorporating clinical data which is often difficult to collect from public sources and mouse data. Please note, Nepromie has become Nephroseq in 2016.. http://dx.doi.org/10.1016/j.kint.2016.01.015.

EURORDIS
type: Organization
type: NamedIndividual
has db xref: grid.433753.5
has db xref: nlx_143535
has db xref: Wikidata: Q5412882
synonym: EURORDIS - Rare Diseases Europe
IAO_0000115: EURORDIS is a non-governmental patient-driven alliance of patient organizations and individuals active in the field of rare diseases, dedicated to improving the quality of life of all people living with rare diseases in Europe. It is a not-for-profit organization and represents more than 479 rare disease organizations in 45 different countries (of which 25 are EU Member States), covering more than 4,000 rare diseases. It is therefore the voice of the 30 million patients affected by rare diseases throughout Europe. EURORDIS aims at improving the quality of life of people living with rare diseases in Europe through advocacy at the European level, support for research and drug development, networking patient groups, raising awareness and other actions designed to fight against the impact of rare diseases on the lives of patients and family. EURORDIS' training programs and resources are designed to strengthen the capacity of rare disease patients' representatives. Training empowers patients' representatives to advocate effectively for rare diseases at both the local and EU level. Key issues affecting patients of Rare Diseases on which we actively work: * Sustaining rare diseases as an EU public health priority * Making Rare Diseases A Public Health Priority In All Member States * Rare Diseases: An International Public Health Priority * Improving Access To Orphan Drugs * Improving Access To Quality Care * Promoting cross-border healthcare and patient mobility * Bridging Patients And Research * Genetic testing and newborn screening

Asthma UK
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100000362
has db xref: grid.453156.0
has db xref: ISNI: 0000 0000 9981 854X
has db xref: nlx_158172
IAO_0000115: Charity that aims to significantly reduce the number of asthma deaths, hospitalizations and living lives compromised by asthma helping over five million people with asthma in the UK through research, campaigning, health promotion and engagement with the asthma community. Asthma UK is a significant investor in asthma research within the UK and to date has invested over 50 million pounds into research for better treatments and ultimately a cure for asthma.

MDL
type: Resource
type: NamedIndividual
has db xref: nlx_158170
synonym: Modelling Description Language
IAO_0000115: A human writeable and human readable language to express the information required to describe pharmacometric models and tasks using these models. The specification of the MDL offers a standard for coding models and associated objects and defining how to execute tasks. The standards for defining MDL objects are independent of any specific target modelling software. This allows the user to specify the model in a consistent manner and facilitates understanding of the model and associated tasks, regardless of the software used to build the model. New modelling applications may take advantage of the standard without having to re-invent how to describe common modelling processes.

LIPID MAPS Structure Database
type: Resource
type: NamedIndividual
has db xref: nlx_158117
synonym: LIPID MAPS Structure Database (LMSD)
abbrev: LMSD
IAO_0000115: Collection of structures and annotations of biologically relevant lipids that contains unique lipid structures. Structures of lipids from : LIPID MAPS Consortium's core laboratories and partners; lipids identified by LIPID MAPS experiments; biologically relevant lipids manually curated from LIPID BANK, LIPIDAT, Lipid Library, Cyberlipids, ChEBI and other public sources; novel lipids submitted to peer-reviewed journals; and computationally generated structures for appropriate classes. All the lipid structures adhere to the structure drawing rules proposed by the LIPID MAPS consortium. A number of structure viewing options are offered: gif image (default), Chemdraw (requires Chemdraw ActiveX/Plugin), MarvinView (Java applet) and JMol (Java applet). All lipids have been classified using the LIPID MAPS Lipid Classification System. Each lipid structure has been assigned a LIPID MAPS ID (LM_ID) which reflects its position in the classification hierarchy. In addition to a classification-based retrieval of lipids, users can search using either text-based or structure-based search options.

MRC Cognition and Brain Sciences Unit
type: Organization
type: NamedIndividual
has db xref: grid.415036.5
has db xref: ISNI: 0000 0001 2177 2032
has db xref: nlx_158118
has db xref: Wikidata: Q5141152
synonym: Cognition and Brain Sciences Unit
abbrev: CBU
IAO_0000115: Unit studying human cognition and the brain with about 90 researchers and postgraduate students investigating topics such as attention, emotion, language and memory. They are developing new treatments for depression, improving hearing through cochlear implants, and helping children to overcome memory problems. With a large collection of scientists engaged in both basic and translational research on the mind and brain, the Unit provides an exceptional training and academic environment that benefits postgraduate students and researchers at all levels. A significant part of their research makes use of brain imaging and they have excellent on-site facilities for magnetic resonance imaging (MRI) magnetoencephalography (MEG) and electroencephalography (EEG). They also have clinical facilities at Addenbrooke's Hospital. The Unit has close links both with the hospital and with Cambridge University.

AddNeuroMed
type: NamedIndividual
has db xref: nlx_158122
synonym: The AddNeuroMed Study
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9,2023. Project portal for a cross European study designed to find biomarkers, or tests, for Alzheimer's disease. Its objectives are to produce and improve experimental models of Alzheimer's for biomarker discovery and to identify a biomarker for Alzheimer's disease suitable for diagnosis, prediction, and monitoring disease progression for use in clinical trials and in clinical practice. The baseline dataset database was scheduled to be completed and locked in 2008 and become available to researchers by 2009. Requests to access the data will be reviewed by the scientific projects committee.

European Federation of Pharmaceutical Industries and Associations
type: Organization
type: NamedIndividual
has db xref: grid.484123.8
has db xref: ISNI: 0000 0000 9246 8110
has db xref: nlx_158124
has db xref: Wikidata: Q1376562
abbrev: EFPIA
IAO_0000115: Federation representing the pharmaceutical industry operating in Europe. Through its direct membership of 33 national associations and 40 leading pharmaceutical companies, it is the voice on the EU scene of 1,900 companies committed to researching, developing and manufacturing new medical treatments. In addition, it is active in partnering in EU Research programmes, such as the IMI (Innovative Medicines Initiative), Europe's largest public-private partnerships. They also work on corporate social responsibility initiatives with others healthcare stakeholders, such as patient groups and healthcare professionals. EFPIA has specialized committees and task forces focused on key areas of activity. EFPIA also includes two specialized groups focusing on vaccines and biotechnology, respectively: * Vaccines Europe (formerly European Vaccine Manufacturers, EVM) produces approximately 80% of vaccines used worldwide * European Biopharmaceutical Enterprises (EBE) harness biotechnology to develop approximately one-fifth of new medicines

University of Rochester; New York; USA
type: Organization
type: NamedIndividual
has db xref: nlx_81263
synonym: University of Rochester
IAO_0000115: Private research university in Rochester, New York. University grants undergraduate and graduate degrees, including doctoral and professional degrees.

Hybrigenics
type: Organization
type: NamedIndividual
has db xref: nlx_158127
IAO_0000115: A bio-pharmaceutical company with a focus on research and development of new targets & therapies against proliferative diseases. Its current development program is based on inecalcitol, a vitamin D receptor agonist being studied in three potential indications: * alone in chronic lymphocytic leukaemia * in combination with imatinib in chronic myeloid leukaemia * in prostate cancer, for use with current standards of care Hybrigenics'' research program investigates the action of enzymes called Deubiquitinating Enzymes (DUBs) in the recycling of onco-proteins and the utility of proprietary patented DUB inhibitors against various cancer indications. Hybrigenics Services, a Hybrigenics subsidiary, markets very specialized scientific services to researchers in all areas of life sciences who want to identify, validate and inhibit protein interactions in animal, plant or microbiological cells.

Selleck Chemicals LLC
type: Organization
type: NamedIndividual
has db xref: nlx_152457
synonym: Selleck Chemicals
IAO_0000115: An Antibody supplier

reMYND
type: Organization
type: NamedIndividual
has db xref: nlx_158130
synonym: reMYND NV
IAO_0000115: Organization that drives the development of disease-modifying treatments against Alzheimer's, Parkinson's, Diabetes and other protein misfolding disorders through two independently managed business units: * Contract Research: The in-vivo Contract Research Organization (CRO) helps its clients to assess the pharmacokinetics and -dynamics of their experimental treatments against Alzheimer's disease. The main focus is on efficacy testing of candidate drugs in reMYND's proprietary Alzheimer mouse models expressing the clinical APP-London allele as single transgene or in combination with clinical alleles of human PS1 and TAU. * Drug Discovery: The Drug Discovery and Development Unit (DDD) focuses on disease-modifying treatments against protein-misfolding disorders, such as Alzheimer's disease (tau), Parkinson's disease (-synuclein), and Diabetes. In addition, reMYND grants licenses and markets commercial kits of RadarScreen, a technology for rapid and cost-effective identification of genotoxic liabilities in early stage drug discovery. reMYND has been substantially supported by grants from IWT and from The Michael J Fox Foundation.

AgedBrainSYSBIO
type: NamedIndividual
has db xref: nlx_158132
IAO_0000115: Consortium focused on identifying the foundational pathways responsible for the aging of the brain, with a focus on Late Onset Alzheimer's disease. They aim to identify the interactions through which the aging phenotype develops in normal and in disease conditions; modeling novel pathways and their evolutionary properties to design experiments that identify druggable targets. As early steps of neurodegenerative disorders are expected to impact synapse function the project will focus in particular on pre- or postsynaptic protein networks. The concept is to identify subsets of pathways with two unique druggable hallmarks, the validation of interactions occurring locally in subregions of neurons and a human and/or primate accelerated evolutionary signature. The consortium will do this through six approaches: * identification of interacting protein networks from recent Late-Onset Alzheimer Disease-Genome Wide Association Studies (LOAD-GWAS) data, * experimental validation of interconnected networks working in subregion of a neuron (such as dendrites and dendritic spines), * inclusion of these experimentally validated networks in larger networks obtained from available databases to extend possible protein interactions, * identification of human and/or primate positive selection either in coding or in regulatory gene sequences, * manipulation of these human and/or primate accelerated evolutionary interacting proteins in human neurons derived from induced Pluripotent Stem Cells (iPSCs) * modeling predictions in drosophila and novel mouse transgenic models * validation of new druggable targets and markers as a proof-of-concept towards the prevention and cure of aging cognitive defects. The scientists will share results and know-how on Late-Onset Alzheimer Disease-Genome Wide Association Studies (LOAD-GWAS) gene discovery, comparative functional genomics in mouse and drosophila models, in mouse transgenic approaches, research on human induced pluripotent stem cells (hiPSC) a…

Quretec
type: Organization
type: NamedIndividual
has db xref: grid.436973.c
has db xref: nlx_158133
has db xref: Wikidata: Q30291134
synonym: Quretec Ltd
synonym: Quretec Ltd.
IAO_0000115: Commercial organization that builds software for collection, management, and analysis of complex data, most typical in biomedical domain. The solutions are generic and can be used for multitude of uses and application domains.

AirPROM
type: NamedIndividual
has db xref: nlx_158142
synonym: Airway Disease Predicting Outcomes through Patient Specific Computational Modelling
IAO_0000115: Consortium focused on developing computer and physical models of the airway system for patients with asthma and chronic obstructive pulmonary disease (COPD). Developing accurate models will better predict how asthma and COPD develop, since current methods can only assess the severity of disease. They aim to bridge the gaps in clinical management of airways-based disease by providing reliable models that predict disease progression and the response to treatment for each person with asthma or COPD. A data management platform provides a secure and sustainable infrastructure that semantically integrates the clinical, physiological, genetic, and experimental data produced with existing biomedical knowledge from allied consortia and public databases. This resource will be available for analysis and modeling, and will facilitate sharing, collaboration and publication within AirPROM and with the broader community. Currently the AirPROM knowledge portal is only accessible by AirPROM partners.

Medical University of South Carolina; South Carolina; USA
type: Organization
type: NamedIndividual
has db xref: nlx_34109
synonym: Medical University of South Carolina
abbrev: MUSC
IAO_0000115: Public medical school in Charleston, South Carolina. Opened in 1824 as small private college aimed at training physicians. One of the oldest continually operating schools of medicine in the United States and the oldest in the Deep South.

Antilope Project
type: NamedIndividual
has db xref: nlx_158143
abbrev: Antilope
IAO_0000115: Consortium focused on making electronic health data more interoperable, both within and outside of Europe, with the intention to create, validate, and disseminate standard methods to test and certify electronic health solutions and services. In particular it will: Drive the adoption of recognized sets of profiles and underlying standards for eHealth interoperability, and improve the impact of the EU and International eHealth standards development process; Define and validate testing guidelines and common approaches on Interoperability Labelling and Certification processes at European and at National / Regional level. Four work packages were created to provide guidelines, recommendations and frameworks based on a set of use cases, related profiles and standards, Interoperability Quality Management System, testing guidelines and Certification process. All the deliverables will be presented for validation and promotion by organizing workshops across Europe.

Minimal Standard Terminology of Digestive Endoscopy - French
type: Resource
type: NamedIndividual
has db xref: nlx_157484
synonym: Minimal Standard Terminology of Digestive Endoscopy French
abbrev: MSTDE-FRE
IAO_0000115: Metathesaurus Version of Minimal Standard Terminology Digestive Endoscopy, French Translation, 2001

AtheroRemo
type: NamedIndividual
has db xref: nlx_158144
synonym: AtheroRemo Consortium
synonym: European Collaborative Project on Inflamation and Vascular Wall Remodelling in Atherosclerosis - AtheroRemo
IAO_0000115: Project targeting vulnerable plaques causing unexpected acute myocardial infarcts and sudden cardiac deaths by identifying and validating novel drug targets as well as devising and validating diagnostic tests. It has been designed to advance the present knowledge on the role of inflammatory remodeling in the different stages of atherosclerosis. It will also provide important knowledge for the development of strategies for prevention and clinical management of vascular diseases.

Breast Cancer Somatic Genetics Study
type: NamedIndividual
has db xref: nlx_158147
abbrev: BASIS
IAO_0000115: Consortium to generate complete catalogs of somatic mutations in 500 breast cancers, of the ER+ve HER2- subclass, under the International Cancer Genome Consortium model by high coverage, shotgun genome sequencing of both tumor and normal DNA. The strategy is to collect, store, review, quality control and extract DNA and RNA from breast cancer and normal tissues from 500 ER+, HER2- breast cancer cases which will be subjected to a coordinated series of genomic analyses including whole genome shotgun sequencing, genome-wide copy number analysis, mRNA expression analysis, miRNA expression analysis and genome-wide methylation analysis. A comprehensive catalogue of somatic mutations will be generated from each cancer. Somatic mutation catalogues from the 500 cancers will be analysed and integrated with expression and methylation data to identify novel cancer genes, characterize subverted biological pathways that are operative, describe patterns of somatic mutation and explore early translational applications of personalized somatic genomic data for patients with ER+, HER2- breast cancer. The results will impact the understanding of the causes and biology of breast cancer and will lead to major advances in detection, prevention and treatment in one of the most common diseases and causes of death in the developed world. The Consortium has completed a number of investigative exercises into the experimental protocols and technological practices relating to whole genome sequencing, epigenetics and transcriptomics including: * Completion of extensive testing of current RNA-seq protocol. * Designed and implemented a new, improved RNA-seq protocol which utilizes RNA samples regardless of their RNA Integrity Number. * Completed pilot testing of the Infinium 450k array and associated bi-sulfite sequencing. * Refined the whole genome sequencing library production protocols to produce more robust libraries. * Improved the primary variant-calling algorithms (for substitutions, inserti…

Elephant
type: Resource
type: NamedIndividual
has db xref: nlx_158148

BetaBat
type: NamedIndividual
has db xref: nlx_158149
synonym: BetaBat - Development of novel treatment strategies based on knowledge of cellular dysfunction in diabetes
synonym: Development of novel treatment strategies based on knowledge of cellular dysfunction in diabetes
synonym: Development of novel treatment strategies based on knowledge of cellular dysfunction in diabetes (BetaBat)
IAO_0000115: Project that aims to develop new treatment strategies based on knowledge of cellular dysfunction in diabetes. They will perform a detailed organelle diagnosis based on both focused and systems biology approaches, which will provide the scientific rationale for the design of specific interventions to boost the capacity of beta cells and brown adipocytes to regain homeostatic control. They propose that only by understanding the complex molecular mechanisms triggering cellular dysfunction in diabetes, and by integrating this knowledge at the systems level, will it be possible to develop interventional therapies that protect and restore beta cell and (Brown adipose tissue) BAT function. The ultimate goal is to offer individual therapeutic choices based on both genetic information and organelle diagnosis.

Swiss Institute of Allergy and Asthma Research
type: Resource
type: NamedIndividual
has db xref: nlx_158175
abbrev: SIAF
IAO_0000115: Originally established as a research institute for tuberculosis, it now performs applied, basic research in the field of allergies and asthma. Research activities are focused on immune-pathological mechanisms of allergic, asthmatic and cutaneous inflammations and the structural basis and peculiarities of allergens, as well as development of novel tools for the diagnosis and treatment of allergic disease.

Ontology of Physical Exercises
type: Resource
type: NamedIndividual
has db xref: nlx_157535
abbrev: OPE
IAO_0000115: Ontology that provides a reference for describing an exercise in terms of functional movements, engaged musculoskeletal system parts, related equipment or monitoring devices, intended health outcomes, as well as target ailments for which the exercise might be employed as a treatment or preventative measure.

Big Data Public Private Forum
type: NamedIndividual
has db xref: nlx_158150
synonym: BIG consortium
synonym: Big Data Public Private Forum (BIG)
synonym: Big Data Public-Private Forum
synonym: BIG Project
synonym: BIG Project - Big Data Public-Private Forum
abbrev: BIG
IAO_0000115: A consortium working towards the definition and implementation of a clear strategy that tackles the necessary efforts of Big Data (in terms of research and innovation) while also providing supporting actions for the successful implementation of the Big Data economy. Building an industrial community around Big Data in Europe is the priority of this project, together with setting up the necessary collaboration and dissemination infrastructure to link technology suppliers, integrators and leading user organizations.

BIOHYBRID
type: NamedIndividual
has db xref: nlx_158152
synonym: Biohybrid templates for peripheral nerve regeneration
IAO_0000115: Consortium with the goal of repairing damaged nerve trunks that will engage in the preclinical development of an artificial biohybrid nerve device for the regenerative treatment of traumatic injuries of peripheral nerves. Based on the extensive basic and clinical experience within this consortium the artificial nerve device will be developed together with standardized application and evaluation parameters. A key objective of this study is to generate a protocol that serves as a template for future clinical trials in the regenerative therapy of damaged peripheral nerves. The results of the multidisciplinary research will feed into the establishment of artificial biohybrid devices as stand alone alternatives to accepted standard procedures and tools. Furthermore, standardized application guidelines and evaluation parameters will be set up to enable continuous progress and evaluation of the outcome of clinical application.

Mosquito Gross Anatomy Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157485
abbrev: TGMA
IAO_0000115: A structured controlled vocabulary of the anatomy of mosquitoes.

BIOIMAGE-NMD
type: NamedIndividual
has db xref: nlx_158153
synonym: Developing imaging technologies for therapeutic interventions in rare diseases
synonym: Developing imaging technologies for therapeutic interventions in rare diseases (BIOIMAGE-NMD)
IAO_0000115: Project whose objective is to deliver combined structural and molecular imaging biomarkers with proven utility for the detection of therapeutic effects in patients with rare neuromuscular diseases (NMD). The project has three specific objectives: # To develop a new generation of muscle diffusion Magnetic Resonance Imaging (MRI). This diffusion imaging technology will be used to augment a state of the art simultaneous MRI / Magnetic Resonance Spectroscopic Imaging (MRSI) protocol for quantitative muscle imaging. # To provide a proof of principle in Duchenne Muscular Dystrophy (DMD) that simultaneous MRI/MRSI can be used as a biomarker to monitor therapeutic efficacy in clinical trials in neuromuscular diseases. # To develop a novel simultaneous Positron Emission Tomography (PET)/MRI technology to advance innovative drug development programs for personalized medicines based on Antisense Oligonucleotide technology

BiomarCaRE
type: Resource
type: NamedIndividual
has db xref: nlx_158154
synonym: BiomarCaRE.EU
synonym: Biomarker for Cardiovascular Risk Assessment in Europe
synonym: Biomarker for Cardiovascular Risk Assessment in Europe (BIOMARCARE)
abbrev: BIOMARCARE
IAO_0000115: EU funded consortium including over 30 partner from academia and industry. BiomarCaRE aims to determine the value of established and emerging biomarkers to improve risk estimation of cardiovascular disease in Europe. BiomarCaRE relies on an exceptional resource of large scale epidemiological cohorts with long term follow-up and available bio specimens based on the population of the MORGAM Project as well as several cardiovascular disease cohorts and clinical trials.

European Lung Foundation
type: Resource
type: NamedIndividual
has db xref: nlx_158176
synonym: Euro Lung Foundation
abbrev: ELF
IAO_0000115: Foundation with aim of bringing together patients, the public and respiratory professionals to positively influence lung health and respiratory medicine. ELF aims to communicate respiratory science to those outside of the respiratory field, to ensure that people with lung diseases and the general public have a chance to influence respiratory research and guidelines at a European level.

PEDPLOT
type: Resource
type: NamedIndividual
has db xref: nlx_154526
IAO_0000115: Pedigree Plotting Program for the Pedfile Format (entry from Genetic Analysis Software)

Blueprint Epigenome
type: Resource
type: NamedIndividual
has db xref: nlx_158155
synonym: BLUEPRINT - A BLUEPRINT of Haematopoietic Epigenomes
abbrev: BLUEPRINT
IAO_0000115: Consortium to further the understanding of how genes are activated or repressed in both healthy and diseased human cells with a focus on distinct types of haematopoietic cells from healthy individuals and on their malignant leukemic counterparts. They will generate at least 100 reference epigenomes and study them to advance and exploit knowledge of the underlying biological processes and mechanisms in health and disease. Reference epigenomes will be generated by state-of-the-art technologies from highly purified cells for a comprehensive set of epigenetic marks in accordance with quality standards set by International Human Epigenome Consortium (IHEC). Access to the data is provided as well as the protocols used to collect the different blood cell types, to perform the different types of epigenomic analyses, etc.). This resource-generating activity will be complemented by hypothesis-driven research into blood-based diseases, including common leukemias and autoimmune disease (Type 1 Diabetes), by discovery and validation of epigenetic markers for diagnostic use and by epigenetic target identification. Since epigenetic changes are reversible, they can be targets for the development of novel and more individualized medical treatments. The involvement of companies will energize epigenomic research in the private sector by the development of smart technologies for better diagnostic tests and by identifying new targets for compounds. Thus the results of the project may lead to targeted diagnostics, new treatments and preventive measures for specific diseases in individual patients, an approach known as "personalized medicine". The Blueprint Data Access Committee will consider applications for access to data sets stored in the European Genome-phenome Archive (EGA) when authorized to do so by the Blueprint consortium and the holders of the original consent documents. Access is conditional upon availability of samples and/or data and signed agreement by the researcher(s) and…

CALLIOPE Network
type: NamedIndividual
has db xref: nlx_158158
synonym: CALLIOPE - Creating a European coordination network for eHealth interoperability implementation
synonym: Creating a European coordination network for eHealth interoperability implementation
synonym: Creating a European Coordination Network for eHealth Interoperability Implementation (CALLIOPE)
abbrev: CALLIOPE
IAO_0000115: Consortium to act as a forum for the diversity of stakeholders in the implementation of electronic health systems. It comprises a dedicated forum where decision makers, implementers, professionals, patients and other stakeholders can share visions, experiences and good practices on how to establish interoperable eHealth services. The process of consensus-building has reached six main achievements. # Offering support to European decision-makers with regard to EU level actions on eHealth. # Enlarging active representation of EU and European Free Trade Association (EFTA) activities. CALLIOPE established a roster of 22 national members in 2010 # Enlarging active involvement of European eHealth stakeholder organizations. # Developing and validating an open working method among stakeholders # Creating a working collaboration method between the appropriate eHealth large-scale pilot(s) and a wider range of Member States & and sta-keholders CALLepSO collaboration # Building an eHealth Interoperability roadmapping process. A full iterative cycle of the Roadmapping process has been now completed and the second issue of the EU eHealth Interoperability Roadmap has been delivered.

Canadian Consortium on Neurodegeneration in Aging
type: NamedIndividual
has db xref: nlx_158160
synonym: Canadian Consortium on Neurodegeneration in Aging (CCNA)
abbrev: CCNA
IAO_0000115: Consortium that will be the premier research hub for all aspects of research involving neurodegenerative diseases that affect cognition in aging - including Alzheimer's disease. They will promote high impact, inter-institutional and interdisciplinary collaboration through a pan-Canadian approach, and will position Canadian researchers to lead and participate in a new wave of national and international initiatives with congruent goals. The consortium focuses research into the basic mechanisms of neurodegenerative diseases, accelerating the development of tools that can be used to assist in the diagnosis and treatment of the diseases. The intended outcome of these tools is to improve the quality of life and services patients with neurodegenerative diseases. As part of the Canadian contribution to the International Collaborative Research Strategy for Alzheimer's disease, the consortium brings together Canadian government agencies (federal and provincial), foundations, pharmaceutical companies, philanthropists and international stakeholders to identify if there are common causes and risk factors to neurodegenerative diseases. The consortium is focused on three themes: * Primary Prevention aimed at preventing the disease from developing * Secondary Prevention focused on delaying the clinical manifestations of the already developing disease * Quality of Life designed for helping individuals, caregivers and the health system in the context of a clinically developed disease.

Alzheimer's Research UK
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100002283
has db xref: grid.453466.6
has db xref: ISNI: 0000 0000 9689 1581
has db xref: nlx_158161
has db xref: Wikidata: Q2840694
synonym: Alzheimers Research UK
abbrev: ARUK
IAO_0000115: The UK's leading dementia research charity that funds world-class, pioneering scientists at leading universities to find preventions, treatments and a cure for dementia.

CHEM21
type: NamedIndividual
has db xref: nlx_158163
synonym: CHEM21.eu
synonym: Chemical Manufacturing Methods for the 21st Century Pharmaceutical Industries
synonym: Chemical Manufacturing Methods for the 21st Century Pharmaceutical Industries (Chem21)
IAO_0000115: A European public-private consortium examining ways to make chemical research and the pharmaceutical industry more sustainable and environmentally friendly with the aim of developing sustainable biological and chemical alternatives to finite materials, such as precious metals, which are currently used as catalysts in the manufacture of medicines. The project has looked at the industry and identified needs and barriers, and is now working to develop methods to navigate around them to reduce costs for companies and thus reduce prices for patients. Chem21 also involves an educational training component that will help instill the project's results in the next wave of scientists. The project has four focus areas that are driving it toward the desired impact on the 21st century pharmaceuticals industry: * New, more efficient catalyst classes made available for greening processes and the generation of novel molecules * Alternative methodologies clearly described to allow broader use * New modified microorganisms for preparing pharma building blocks disclosed * Training materials developed for driving longer-term innovation

Systematized Nomenclature of Medicine - International Version
type: Resource
type: NamedIndividual
has db xref: nlx_157604
synonym: Systematized Nomenclature of Medicine International Version
abbrev: SNMI
IAO_0000115: Ontology of systematized nomenclature of human and veterinary medicine: SNOMED International. Cote, Roger A., editor. Northfield (IL): College of American Pathologists; Schaumburg (IL): American Veterinary Medical Association, Version 3.5, 1998.

COMPACT
type: NamedIndividual
has db xref: nlx_158164
synonym: Collaboration on the optimisation of macromolecular pharmaceutical access to cellular targets
synonym: Collaboration on the Optimization of Macromolecular Pharmaceutical Access to Cellular Targets
IAO_0000115: Consortium to reduce delivery and targeting bottlenecks for developing novel innovative biopharmaceutical based medicines. The project aims to shed new light on the obstacles biopharmaceuticals (medicines based on biological molecules such as proteins, peptides or nucleic acids) need to overcome to get to where they are needed in the body. The team will then use this information to develop and validate biopharmaceutical formulations to deliver these novel drugs to their targets. By finding more effective ways of administering these biopharmaceutical drugs, and improving their ability to travel through the body to where they are needed, COMPACT will allow more patients to benefit from biopharmaceuticals. Furthermore, designing less invasive administration routes and reducing the dose (and therefore the side effects) and frequency of administration will help to improve patient compliance with treatments.

DDMoRe
type: NamedIndividual
has db xref: nlx_158165
synonym: Drug Disease Model Resources
synonym: Drug Disease Model Resources (DDMoRe)
IAO_0000115: DDMoRe project to develop common standards and tools to allow scientists to share their models. Developed model repository which enables access to curated and shared knowledge for benefit of model informed drug discovery.

MDL-IDE
type: Resource
type: NamedIndividual
has db xref: nlx_158168
synonym: Modelling Description Language - Integrated Development Environment
synonym: Modelling Description Language Integrated Development Environment
abbrev: MDL IDE
IAO_0000115: Software framework within which files containing Modelling Description Language (MDL) code can be created and edited offering a user-friendly, customizable modelling experience including syntax highlighting and on-demand model formatting. MDL model development is enhanced by productivity features such as the support for templates (re-usable blocks of MDL code that can be parameterised for ease of inclusion in multiple models) and content assist (the automatic display of possible alternatives based on the current editing location in the model). Common operations are supported by wizards which provide a step-by-step guide through the necessary functionality, while an advanced validation engine immediately highlights any inconsistencies or errors detected in the model and offers a list of suggested options to correct the problem. The MDL-IDE includes in-built functionality to convert an MDL model into the equivalent NM-TRAN control stream (.ctl file). Organizationally, it can support multiple distinct projects within a workspace, offering a natural separation between disparate models but retaining the ability to switch between the models quickly and easily. Additionally a large main window with a tabbed layout allows multiple models to be open for editing or viewing simultaneously.

PHOTONIS
type: Organization
type: NamedIndividual
has db xref: nlx_158234
synonym: PHOTONIS USA Pennsylvania
synonym: PHOTONIS USA PENNSYLVANIA INC.
IAO_0000115: Commercial organization that manufactures Vacuum Electron Devices and Associated RF Circuits for Communications, Science, Radar, Industry & Directed Energy Applications. Other products include photo-detectors for scientific and medical applications and specialized material processing and plating services.

EARIP
type: NamedIndividual
has db xref: nlx_158171
synonym: European Asthma Research and Innovation Partnership
synonym: European Asthma Research and Innovation Partnership (EARIP)
IAO_0000115: Consortium that convenes asthma experts from across Europe to define research gaps to reduce the impact of asthma. The project activities range from basic cell science research, to assessing and improving European healthcare systems. Their activities include workshops, prioritization exercises, consensus strategies, and the development and publication of a set of recommendations about what's needed to reduce asthma deaths and hospitalizations. The eventual goal is to have a comprehensive R&D roadmap for asthma. EARIP will target a number of asthma research areas to ensure a comprehensive overview of all current research strategies from across Europe is included in the project road map. These include: * Research into biological targets, aiming to discover new targets and better define the role of existing biological targets * Identify new systems, models and tools for phenotypic stratification * Develop better and more efficient healthcare systems across Europe * Define and develop new diagnostic tools * Assess and improve patient self-management systems and provide suggestions for how these can be developed * Identify how to establish a European Innovation Partnership (EIP) for the management of asthma * Establish a European research network of clinical asthma research facilities

European Federation of Allergy and Airways Diseases Patients Associations
type: Organization
type: NamedIndividual
has db xref: grid.434606.3
has db xref: nlx_158177
synonym: European Federation of Allergy & Airways Diseases Patients Associations
synonym: European Federation of Allergy and Airways Diseases Patients' Associations
abbrev: EFA
IAO_0000115: A non-profit network of allergy, asthma and Chronic Obstructive Pulmonary Disease (COPD) patients' organisations, representing 35 national associations in 22 countries and over 400,000 patients. They're dedicated to making Europe a place where people with allergies, asthma and COPD have the best quality care and a safe environment, live uncompromised lives and are actively involved in all decisions influencing their health. They work on behalf of patients to: * Promote awareness of allergies and airways diseases among policymakers and the general public. * Broaden our understanding of these conditions by increased collaboration between national patient associations. * Share knowledge and experience to beneficially educate both the public and EFA members. * Promote patient concerns and opinions within the European institutions and enable national patient associations to gain representation at EU level. * Improve their health and quality of life.

EBiSC
type: Resource
type: NamedIndividual
has db xref: nlx_158178
synonym: EBiSC - European Bank for induced pluripotent Stem Cells
synonym: EBiSC Project
synonym: European Bank for induced pluripotent Stem Cells
IAO_0000115: Consortium to address the increasing demand by researchers for quality-controlled, disease-relevant research grade induced Pluripotent Stem Cell (iPSC) lines, data and cell services by demonstrating an operational banking and distribution service of iPSC lines after 3 years and establishing subsequently for Europe a centralized, not-for-profit bank providing all qualified users with access to scalable, cost-efficient and customized products. The main facility will be at the Babraham Research Campus (Cambridge, UK) and will undertake cell expansion, QC and characterization. The European Cell Culture Collection (ECACC) of Public Health England (Department of Health, UK) will coordinate cell line distribution. The Fraunhofer IBMT (Saarbr��cken, Germany) will provide comprehensive operational back up. In a phased business strategy EBiSC will hot-start distribution of lines contributed by iPSC Centres in 2014, lines collected based on specified user demand, will reach full scale operations in 2016, and with extended funding will become self-sustaining as a not for profit banking operation by 2019. EBiSC will spearhead Europe in the international standardization of iPSC banking by forging collaborative links with similar endeavors in the USA and Asia. It will also provide training to encourage adoption and use of the bank. The project has up to one year after completion to disseminate intellectual property or data created by the project.

Roslin Cells
type: Organization
type: NamedIndividual
has db xref: nlx_158181
synonym: Roslin Cells Ltd
IAO_0000115: Organization that supplies undifferentiated, clinical grade, human pluripotent stem cell lines to the life science community, and works with academic, clinical and commercial colleagues to enable and facilitate the use of these high grade cells in the development of new reagents, drugs and cellular therapeutics. They also seek to drive the economic development of the stem cell sector in Scotland. Their products can act as a valuable tool in supporting clients' drug discovery, development and clinical research programmes.

European Lead Factory
type: Organization
type: NamedIndividual
has db xref: grid.498269.8
has db xref: nlx_158182
synonym: EU Lead Factory
abbrev: ELF
IAO_0000115: Consortium that promotes the discovery of novel small molecule candidates suitable for subsequent optimization either to drug candidates or to high-quality pharmacological tools for the experimental validation of targets using open innovation and crowd sourcing. It is designed to provide best-in-class resources and funding-in-kind, to academics or small and medium enterprises (SMEs) who are working on promising biology targets or chemistry scaffolds. Screening of compounds to assess their activity is also funded and performed by the EU Lead Factory, with collaboration to help develop an Improved Hit List from the Qualified Hit List. They will provide collaborative screening of previously safeguarded, high quality corporate compounds. Around 300,000 compounds in the EFPIA Compound Collection, contributed by EFPIA members, will be screened against both commercially contributed biology targets and targets from public sources. The second phase of the consortium is to build a substantial new Public Compound Collection of around 200,000 compounds. Together, the EFPIA and Public compound collections will form a 500,000-strong Joint European Compound Collection. Target program owners and compound contributors will receive a Qualified Hit List (QHL) of up to 50 compounds complete with relevant information to help in the development of an Improved Hit List (IHL). Target program owners, will have exclusive access to threshold active compounds in their QHL. After the three-year exclusivity period, QHL/IHL information will be made public. Milestone payments are due if direct exploitation proceeds, not for research use. And owners and contributors will give EFPIA participants the right to submit a first bid (which they do not have to accept).

European Gram Negative AntiBacterial Engine
type: NamedIndividual
has db xref: nlx_158183
synonym: European Gram Negative Antibacterial Engine (ENABLE)
synonym: European Gram-negative Antibacterial Engine
abbrev: ENABLE
IAO_0000115: Consortium working to advance the development of potential antibiotics against Gram-negative bacteria, such as Escherichia coli. The project creates and manages a drug discovery engine for testing and optimizing molecules that are still in the earlier stages of drug discovery but have the potential to become future drug candidates capable of treating resistant Gram-negative infections. The project will focus on the discovery and pre-clinical stages of drug development, as well as (potentially) phase 1 clinical trials. ENABLE will run several drug discovery programs in parallel and the consortium seeks external hit and lead programs to join, through a series of open calls during the project. Researchers who have interesting molecules will have the opportunity to collaborate with a diverse range of experts in microbiology, pharmacology and chemistry to help advance their molecule through the drug development process until it is an attractive candidate for clinical testing. Specifically, the project is working towards: # identifying three antibacterial lead molecules which, following extensive testing, have been identified as having promising antimicrobial activity; # identifying two antibacterial clinical candidate molecules # advancing at least one compound into preclinical and phase 1 clinical studies, i.e. early clinical safety testing in humans.

University of Cincinnati Research and Training in Cardiovascular Biology
type: Resource
type: NamedIndividual
has db xref: nif-0000-02100
synonym: University of Cincinnati Research Training in Cardiovascular Biology
abbrev: UC Research and Training in Cardiovascular Biology
IAO_0000115: Our 24 faculty members approach the Research and Training in Cardiovascular Biology program from different subspecialties that include genetics, metabolism, development, cellular biology, systems biology, structural biology, biophysics, pharmacology, molecular biology, bioinformatics and biochemistry. While these subspecialties are clearly diverse, our faculty collaboratively leverages these areas toward the common goal of understanding cardiovascular disease from the gene all the way up to integrated organism function (systems biology). This diverse array of subspecialties provides a truly unique training environment that few centers can match. Another critical aspect of our training program is our steadfast commitment to a superior and nurturing training environment for our predoctoral trainees, postdoctoral trainees and clinician-scientists. Our training faculty are uniformly committed to monitoring our personnel for success in every way possible, to not only ensure their future placement in the academic ranks but to also build a stronger cardiovascular community around the country. The current National Institutes of Health-sponsored Research and Training in Cardiovascular Biology was instituted in 1978 by Arnold Schwartz, MD, PhD. This program has trained more than 120 scientists, who have pursued independent research careers and are holding prominent scientific positions worldwide. Our trainees have been distinguished as chairs of basic science departments, directors of centers or pharmaceutical companies, clinical directors and tenured faculty members in academic research. The overall emphasis continues to focus on integrative training and well-rounded knowledge of the fundamentals in biochemical, molecular, physiological and pharmacological underpinnings of cardiovascular disease. Dr. Schwartz has been a constant guiding force since the program was established. The University of Cincinnati, with Cincinnati Children's, has also developed a reputation as a lead…

EU-AIMS
type: NamedIndividual
has db xref: nlx_158184
synonym: European Autism Interventions
synonym: European Autism Interventions - A Multicentre Study for Developing New Medications
IAO_0000115: Consortium aiming to generate tools that will enhance understanding of autism spectrum disorders (ASD) and pave the way for the development of new, safe and effective treatments for use in both children and adults. For example, the team will gather samples from people bearing certain mutations associated with ASD; this will pave the way for the generation of cell lines that can be used to test treatments. Elsewhere, the researchers will advance the use of brain scans as a tool to boost ASD drug discovery and also identify which people with ASD might respond best to a given drug. The project will also create a pan-European network of clinical sites. As well as making it easier to run clinical trials, this network will create an interactive platform for those with ASD and professionals. By the end of the 5 year project they expect to provide novel validated cellular assays, animal models, new fMRI methods with dedicated analysis techniques, new PET radioligands, as well as new genetic and proteomic biomarkers for patient-segmentation or individual response prediction. They will provide a research network that can rapidly test new treatments in man. These tools should provide their EFPIA partners with an added competitive advantage in developing new drugs for ASD.

GetReal
type: NamedIndividual
has db xref: nlx_158185
IAO_0000115: Consortium that aims to improve the efficiency of the medicine development process by better incorporating estimates of relative effectiveness into drug development and to enrich decision-making by regulatory authorities and health technology assessment (HTA) bodies through: * Bringing together regulators, HTA bodies, academics, companies, patients and other societal stakeholders; * Assessing existing processes, methodologies, and key research issues; * Proposing innovative (and more pragmatic) trial designs and assessing the value of information; * Proposing and testing innovative analytical and predictive modelling approaches; * Assessing operational, ethical, regulatory issues and proposing and testing solutions; * Creating new decision making frameworks, and building open tools to allow for the evaluation of development programs and use in the assessment of the value of new medicines; * Sharing and discussing deliverables with, among others, Pharmaceutical companies, regulatory authorities, HTA / reimbursement agencies, clinicians and patient organizations; * Developing training activities for researchers, decision makers and societal stakeholders in the public and private sector in order to increase knowledge about various aspects of relative effectiveness. The expected impact is that it will contribute to the knowledge base, particularly to inform clinical decision making and improve the efficiency of the R&D process. GETREAL will help to generate a consensus on best practice in the timing, performance and use of real life clinical studies in regulatory and reimbursement decision-making. It will also help to create a strong platform for the communication of results and for future discussions in this important area.

Vitiligo Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_158187
synonym: VitiligoBioBank.org
abbrev: VBB
IAO_0000115: A non-profit collection of biological samples and detailed associated clinical data, designed to facilitate medical research into vitiligo, a devastating skin disease that is much neglected. They collect, store and analyze biological samples throughout the network of collaborators in 11 countries, using standard collection protocols and unified patient record, which are then made available to the scientific community and research organizations investigating pathogeneses, diagnostics, new treatments, and ultimately a cure for vitiligo. The core asset is a large collection of well-organized hair, blood, serum and DNA samples, integrated with comprehensive and anonymized patient records.

Mosquito Insecticide Resistance Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157486
abbrev: MIRO
IAO_0000115: Application ontology for entities related to insecticide resistance in mosquitos

IMIDIA
type: NamedIndividual
has db xref: nlx_158189
synonym: IMIDIA - Innovative Medicines Initiative for Diabetes: Improving beta-cell function and identification of diagnostic biomarkers for treatment monitoring in Diabetes
synonym: Innovative Medicines Initiative for Diabetes
IAO_0000115: Consortium aiming to improve pancreatic beta-cell function and identification of diagnostic biomarkers for treatment monitoring in diabetes. It brings together academic teams, pharmaceutical companies, and a Small to Medium Enterprises (SMEs), which provides a unique blend of expertise and forms a strong basis for a successful enterprise to ultimately improve industrial competitiveness and Public Health in Europe. The program aims at delivering: * Novel tools for the study of human beta-cell development, function and survival; their modulation by potential therapeutic compounds; and for in vivo beta-cell imaging. * Biomarkers for the diagnosis and prognosis of beta-cell failure and for monitoring diabetes progression and treatment. * Knowledge on novel molecular pathways and sites that control beta-cell life & death as well as mass and function.

Investigator Databank
type: NamedIndividual
has db xref: nlx_158192
synonym: Cross-Pharmaceutical Investigator Databank
abbrev: CPID
IAO_0000115: Consortium between several pharmaceutical companies to develop a database that shares clinical trial investigator information that each company has on file to reduce administrative burden for investigators and to increase visibility of qualified investigators to research sponsors. Hosted by a 3rd party, DrugDev, it is the one place where pharmaceutical companies can share investigator and site information and investigators can view, edit, and comment on their own information. Industry members will be able share information from their clinical trial management systems including investigator / site contact details, GCP training records, past trial participation, and recruitment history. Upon investigator opt-in, this information is used by each participating company to identify sites for upcoming studies; to help set recruitment targets and timelines; and to share start-up documents such as CV, GCP, and site profile forms. The Databank has grown to include nearly 180,000 investigators (May 2014) and is already bringing benefits to its member companies in identifying qualified investigators for their studies. It also reported the inclusion of 7,335 protocols and 50K sites, representing a patient population around 1.9M.

University of Manitoba; Manitoba; Canada
type: NamedIndividual
has db xref: nlx_67930

Kinetics for Drug Discovery
type: NamedIndividual
has db xref: nlx_158193
abbrev: K4DD
IAO_0000115: Project whose goal is to improve understanding of how potential drugs bind with their target, and develop methods and tools to allow researchers to study drug-target interactions with greater ease. These tools would help researchers to determine whether a drug candidate is likely to be safe and effective much earlier in the drug development process. The first goal of the team is to enhance understanding of binding kinetics; exactly how do small molecules interact with their targets? Ultimately, the project aims to develop a range of robust techniques, methods and models that could be easily incorporated into the drug development pathway and enable scientists and drug designers worldwide to reliably predict a molecule's kinetic properties (its "kinotype"). This information will allow drug developers to more easily determine the safety and efficacy of a molecule and will weed out ineffective or unsafe molecules earlier in the drug development process. Eventually, the project also hopes to raise awareness of the importance of considering the kinetic aspects of drug-target interactions throughout drug development.

Kidney Health Initiative
type: NamedIndividual
has db xref: nlx_158194
synonym: Kidney Health Initiative (KHI)
abbrev: KHI
IAO_0000115: Consortium that brings together the kidney community (patient advocacy groups, industry, government agencies, and professional organizations) to overcome existing challenges, including regulatory and nonregulatory barriers, and optimize the development and safety of products that impact kidney health including drugs, devices, biologics, and food products. The goals of the consortium are to: * Facilitate dialogue and research that informs regulatory processes with regard to the kidney health of patients being treated for kidney-related as well as other diseases. * Assess current medical therapies and diagnostics to identify areas in need of greater innovation and/or better defined regulatory pathways. * Develop innovative and efficient trial designs appropriate to answer the most important questions related to kidney health. * Establish expert consensus around common terminology and key definitions related to kidney health. * Develop approaches to the systematic collection of retrospective or prospective data, such as registries and/or global databases, and establishment of data standards. * Coordinate think tanks, public forums, educational exchanges, and other events to promote discussion and updates on topics in kidney health pertaining to drug, device, biologics, and food product development and evaluation. * Create transparent infrastructure and processes that facilitate collaboration and communication among the greater nephrology community and the FDA, including: * Seek input from all stakeholders (including nephrologists and other health professionals, patient groups, industry, the National Institutes of Health, the Centers for Medicare and Medicaid Services, the Health Resources and Services Administration, and other federal agencies). * Leverage previously conducted and ongoing clinical studies, research infrastructure, and databases. * Create an open and efficient mechanism for encouraging and objectively evaluating potential projects submitted to KHI. * In…

MIP-DILI
type: NamedIndividual
has db xref: nlx_158195
synonym: Mechanism based Integrated systems for the Prediction of Drug Induced Liver Injury
synonym: Mechanism-Based Integrated Systems for the Prediction of Drug-Induced Liver Injury
synonym: Mechanism-Based Integrated Systems for the Prediction of Drug-Induced Liver Injury (MIP-DILI)
IAO_0000115: Consortium that brings together Europe's top industrial and academic experts to develop new tests that will help researchers detect potential liver toxicity issues much earlier in drug development, saving many patients from the trauma of liver failure. The team aims to deepen the understanding of the science behind drug-induced liver injury, and use that knowledge to overcome the many drawbacks of the tests currently used. A major focus will be on a systematic and evidence-based evaluation of both currently available and new laboratory test systems, including cultures of liver cells in one-dimensional and three dimensional configurations. The project will also develop models that take into account the natural differences between patients. This is important because factors such as certain genes, the liver's immune response, and viral infections have all been associated with an increased risk of DILI. The project will seek to address the current lack of human liver cells available to researchers by using induced pluripotent stem cells (iPSCs) generated from patients who are particularly sensitive to DILI. Another strand of the project will develop computer models to unravel the complex, often inter-related mechanisms behind DILI. Finally, the team will assess how accurate the results of laboratory tests are at predicting actual outcomes in patients.

Philips Research
type: Organization
type: NamedIndividual
has db xref: nlx_158235
IAO_0000115: A global organization that helps Philips introduce innovations that improve people's lives by providing technology options for innovations in the area of health and well-being, targeted at both developed and emerging markets. Positioned at the front-end of the innovation process, they work on everything from spotting trends and ideation to proof of concept and - where needed - first-of-a-kind product development.

NEWMEDS
type: NamedIndividual
has db xref: nlx_158196
synonym: NEWMEDS - Novel Methods leading to New Medications in Depression and Schizophrenia
synonym: Novel Methods leading to New Medications in Depression and Schizophrenia
IAO_0000115: Consortium that will develop new models and methods to enable novel treatments for schizophrenia and depression including three important missing tools that will facilitate the translation of scientific findings into benefits for patients. The project will focus on developing new animal models which use brain recording and behavioral tests to identify innovative and effective drugs for schizophrenia. The project will develop standardized paradigms, acquisition and analysis techniques to apply brain imaging, especially fMRI and PET imaging to drug development. It will examine how new genetic findings (duplication and deletion or changes in genes) influence the response to various drugs and whether this information can be used to choose the right drug for the right patient. And finally, it will try and develop new approaches for shorter and more efficient trials of new medication - trials that may require fewer patients and give faster results.

DepressionTools.org Clinical Significance Calculator
type: Resource
type: NamedIndividual
has db xref: nlx_158198
synonym: Clinical Significance Calculator
abbrev: DepressionTools.org
IAO_0000115: Online instrument that estimates whether a biomarker predicting outcome of depression treatment is likely to be clinically significant.

Pharmacological Imaging and Pattern Recognition toolbox
type: Resource
type: NamedIndividual
has db xref: nlx_158199
synonym: Pharmacological Imaging and Pattern Recognition
abbrev: PIPR
IAO_0000115: Software toolbox designed to provide machine learning methods for pre-processed imaging data allowing for two (or more) class classification in the context of drug development. The Toolbox includes implementations of Gaussian Process Classification, Support Vector Machines, Ordinal Regression and Sparse Multinomial Logistic Regression for fMRI, Structural and ASL imaging data.

DUPCheck
type: Resource
type: NamedIndividual
has db xref: nlx_158200
abbrev: DUPCHECK
IAO_0000115: A web-based tool to screen for duplicate patients in clinical trials within and across studies, sponsors and therapeutic areas.

ORBITO
type: NamedIndividual
has db xref: nlx_158204
synonym: Oral biopharmaceutics tools (ORBITO)
synonym: orbito - Innovative Tools for Oral Biopharmaceutics
IAO_0000115: Project that aims to increase understanding of how orally-administered drugs are taken up from the gastrointestinal tract into the body, and apply this knowledge to create new laboratory tests and computer models that will better predict the performance of these drugs in patients over a range of clinically relevant conditions. The integration of in vitro and in silico approaches will provide a biopharmaceutics toolkit, validated using clinical data, to accelerate drug development. Ultimately, the project will help to facilitate and speed up the formulation development process and significantly reduce the need for animal experiments in this area as well as for human clinical studies in the future. For patients, the main benefit will be in the form of high quality medicines where the dose required is well calculated and is released in a way that consistently provides an optimal clinical effect.

Patients to Trials Consortium
type: NamedIndividual
has db xref: nlx_158205
synonym: p2t consortium
abbrev: Patients2Trials Consortium
IAO_0000115: A three-member pharmaceutical industry consortium that aims to provide a new platform to improve access to information about clinical trials for patients and providers. The platform aims to enhance the existing clinicaltrials.gov by providing more detailed and patient-friendly information about available trials and embedding a machine-readable target health profile to improve the ability of healthcare software to match individual health profiles with applicable clinical trials. Using clinicaltrials.gov as its foundation and Eli Lilly' '''s Application Programming Interface (API), the consortium is focused on creating an open platform to make this data more amenable to patients and providers, as well as creating an opportunity to integrate a patient' '''s electronic health record into the clinical trial matching service. This feature will allow patients to search for trials using their own Blue Button data. The following features are planned add-ons to clinicaltrials.gov: * Target Profile is a machine readable query, that can be executed against an electronic file (or record) with patient health data such as an Electronic Health Record (EHR), an Electronic Medical Record (EMR) or Personally Controlled Health Record (PCHR) * Augmented Content is public, IRB approved information about the study that has not been published on clinicaltrials.gov, and that is shared with / targeted for patients with a matching Target Profile. The following are the incremental goals of the consortium: * Advancement of the Lilly API platform to support read/write interaction and additional data objects and information. * The initial 3 sponsor organizations - Lilly, Pfizer and Novartis - will upload Target Profiles for a select set of clinical trials. A Target Profile is a machine interpretable description of the characteristics of patients who may qualify for that trial i.e. a query that can be executed against a patient' '''s electronic health record or personal health record. Additionally…

PharmaCog
type: NamedIndividual
has db xref: nlx_158206
synonym: Pharma-Cog
synonym: Prediction of cognitive properties of new drug candidates for neurodegenerative diseases in early clinical development
IAO_0000115: Project aiming to tackle bottlenecks in Alzheimer' '''s disease research and drug discovery by developing and validating new tools to test candidate drugs for the treatment of symptoms and disease in a faster and more sensitive way. They will provide the tools needed to define more precisely the potential of a drug candidate, reduce the development time of new medicines and thus accelerate the approvals of promising new medicines. By bringing together databases of previously conducted clinical trials and combining the results from blood tests, brain scans and behavioral tests, the scientists will develop a ' '''signature' ''' that gives more accurate information on the progression of the disease and the effect of candidate drugs than current methods do. The scientists will conduct parallel studies in laboratory models, healthy volunteers and patients in order to better predict good new drugs as early as possible. This will enable them, for instance, to find out how memory loss in Alzheimer' '''s disease can be simulated in healthy volunteers, for example with sleep deprivation or drugs that temporarily affect the memory, in order to test the effect of candidate-medicines early in the drug development process.

Mouse Experimental Design Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157487
abbrev: MEDO
IAO_0000115: Ontology of experimental design for high-throughput mouse analysis pipelines.

Pharma-Planta Consortium
type: NamedIndividual
has db xref: nlx_158208
abbrev: Pharma-Planta
IAO_0000115: Consortium to develop efficient and safe strategies for the production of clinical-grade protein pharmaceuticals in plants, and to define the procedures needed for the production of these proteins in compliance with the strict regulatory standards that govern the manufacture of all pharmaceuticals. Ultimately the consortium aimed to take a candidate product all the way through the development pipeline culminating in a phase I human clinical trial. The consortium has a wide range of expertise spanning the areas of molecular biology, plant biology, immunology, recombinant protein expression technology, vaccinology, and plant biotechnology. The objectives listed at the beginning of the Pharma-Planta project are as follows: # To produce a recombinant pharmaceutical molecule in transgenic plants, which will be developed through all regulatory requirements, GMP (good manufacturing practice) standards and pre-clinical toxicity testing. This will then be evaluated in Phase I human clinical trials. # To develop robust risk assessment practices for recombinant pharmaceutical molecules produced in plants, based on health and environmental impact, working with regulatory authorities within the EU as well as public groups to ensure that the production systems are as safe and as acceptable as possible, and that they comply with all biosafety regulations. # To define and carry out a coordinated program for securing and managing intellectual property that will facilitate the availability of high priority plant-derived recombinant pharmaceuticals to the poor in developing countries while simultaneously allowing the products to be developed commercially in Europe and North America. # To develop and refine new strategies for the expression of recombinant pharmaceuticals in plants, which can be used on a generic basis for molecules that are normally expressed poorly. # To develop and generate transgenic plants expressing a second generation of recombinant molecules that will be used in…

InBase
type: Resource
type: NamedIndividual
has db xref: nif-0000-03020
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. InBase is a curated database devoted to inteins. It developed by a commercial laboratory, New England BioLabs, that also provides products related to enzyme digests on the same website. Users can access the Intein Registry, to discover properties of individual inteins. They can also submit intein data, browse intein motfis, and view mechanisms and introductions to protein splicing.

PRECISESADS
type: NamedIndividual
has db xref: nlx_158209
synonym: PRECISESADS - Molecular reclassification to find clinically useful biomarkers for systemic autoimmune diseases
IAO_0000115: A project that will study 2,500 people with various systemic autoimmune diseases (SADs), gathering data on the molecular causes of their disease as well as their clinical symptoms, enabling them to pave the way for a new classification of these diseases. The goal is to use OMICs and bioinformatics to identify new classifications for diseases known to share common pathophysiological mechanisms. Results will be shared to deliver a new molecular taxonomy of systemic autoimmune diseases. In order to achieve this, PRECISEADS is informing on a regular basis on the project implementation and results, and involving stakeholders from Europe in its activities in order to broaden the project impact and increase opportunities for cooperation.

PREDECT
type: NamedIndividual
has db xref: nlx_158212
synonym: Preclinical evaluation of drug efficacy in common solid tumours
synonym: Predect New models for preclinical evaluation of drug efficacy in common solid tumours
IAO_0000115: Project that aims to create more appropriate in vitro platforms for target validation and drug discovery for breast, prostate and lung cancers. Laboratory platforms to validate whether target modulation would provide a clinical benefit are usually highly reductionist, often using long-established cell lines growing in 2 dimensions in vitro. These models do not reflect the complexity and heterogeneity of a tumor in situ, where biochemical pathways are wired with connections to the complex tumor environment provided by the stroma. PREDECT has the goal of comparing the pathological and molecular profiles of novel in vitro platforms with those of human tumors. Because obtention of clinical material presents both logistics and quality problems for ongoing and intense studies of target validation, PREDECT aims to use material from genetically engineered mouse models, and some advanced xenografts, whose pathology and molecular profiles closely match cohorts of human tumors. PREDECT hopes to provide more appropriate in vitro platforms both for target validation and subsequent preclinical studies which will replace a current cascade of tests which are poorly predictive of clinical activity. The project is expected to shift paradigms in cell biology as well as in preclinical target validation where it should permit greater predictivity of drug efficacy in patient cohorts.

READNA
type: NamedIndividual
has db xref: nlx_158213
synonym: READNA - REvolutionary Approaches and Devices for Nucleic Acid analysis
synonym: REvolutionary Approaches and Devices for Nucleic Acid analysis
IAO_0000115: Consortium to accelerate new breakthrough DNA sequencing technologies and methods to enhance existing analysis methods. The ultimate aim is to advance DNA sequencing technologies to a level where a human genome can be analyzed at high resolution for less than 1000 euros in less than one day. The goals of the consortium are to revolutionize nucleic acid analysis methods by improving elements necessary to use the currently emerging generation of nucleic acid sequencers in a meaningful and accessible way, providing methods that allow in situ nucleic acid analysis and methods capable of selectively characterizing mutant DNA in a high background of wildtype DNA, combining RNA and DNA analysis in a single analytical device, providing technology to efficiently analyze DNA methylation (genome-wide, with high resolution and in its long-range context), implementing novel concepts for high-throughput HLA-screening, developing fully integrated solutions for mutational screening of small target regions (such as for screening newborns for cystic fibrosis mutations), developing a device for screening multiple target regions with high accuracy and implementing strategies for effective and high-resolution genotyping of copy number variations. READNA was awarded the Stars of Europe prize in December 2013.

TRANSFoRm Clinical Data Integration Model
type: Resource
type: NamedIndividual
has db xref: nlx_158222
synonym: CDIM ontology
synonym: Clinical Data Integration Model
abbrev: CDIM
IAO_0000115: A global mediation model expressed as an ontology for use in the primary care domain. It uses a realist approach employing Basic Formal Ontology (BFO v1.1) as an upper ontology. Other ontologies were imported or specialized to give deeper definition to the concepts in the domain. These included OGMS, IAO and VSO. The CDIM ontology includes concepts that are especially important to primary care (e.g. episode of care or reason for encounter), but also others to handle temporality in queries (e.g. the start and beginning of processes). The owl file provided for download is the merged file created directly in Prot��g�� through the Refactor/Merge ontologies tool in order to facilitate the load of CDIM in LexEVS for use in the unified interoperability framework.

ONE Study
type: NamedIndividual
has db xref: nlx_158215
synonym: A Unified Approach to Evaluating Cellular Immunotherapy in Solid Organ Transplantation
synonym: The ONE Study
synonym: The ONE Study - A Unified Approach to Evaluating Cellular Immunotherapy in Solid Organ Transplantation
IAO_0000115: Consortium aiming to produce regulatory T cells that are compatible with a kidney transplant patient' '''s immune system, as a measure to suppress the body' '''s natural immune response against a transplanted organ. If successful, this approach will reduce a transplantation patient' '''s life-long dependency on immune suppressing drugs, many of which are often associated with undesirable side effects and can limit the patient' '''s daily routine. The consortium goals are to develop and conduct clinical trials of various immunoregulatory T-cell-based products in organ transplantation recipients, allowing a direct comparison of the safety, clinical practicality and therapeutic efficacy of each cell type. The central focus of the project is to: # Production and manufacture of distinct populations of hematopoietic immunoregulatory T cells # Comparatively study the tolerogenic characteristics of these regulatory cell types # Test these cell therapy products side by side in a clinical trial living donor renal transplant recipients The first workstream will work with different T regulatory cell, tolerogenic DC and suppressive macrophage cell products that are currently in development. In addition to these therapeutics, another goal of this workstream is to develop a cell tracking technology that assesses pharmacodynamics and pharmacokinetics of these cell-based therapies. The second workstream is focused on designing and conducting a cell therapy based clinical trial in renal transplantation, taking into consideration ethics, concurrent immunosuppressive drug use, state-of-the-art immune monitoring, innovative all-in-one data capturing systems, and pharmacovigilance. The goal is to have a comparative evaluation of hematopoietic cell therapy safety in renal transplantation. The third workstream aims to learn more about the specific comparative characteristics of suppressive cell types and to use this knowledge to improve later trial designs and foster novel ideas for new or…

University of Sherbrooke; Quebec; Canada
type: NamedIndividual
has db xref: nlx_153966
synonym: Universite de Sherbrooke
synonym: University of Sherbrooke
synonym: Université de Sherbrooke

TRANSFoRm
type: Resource
type: NamedIndividual
has db xref: nlx_158218
synonym: Translational Research and Patient Safety In Europe
IAO_0000115: Project to develop a ''rapid learning healthcare system'' driven by advanced computational infrastructure that can improve both patient safety and the conduct and volume of clinical research in Europe. Three carefully chosen clinical ''use cases'' will drive, evaluate and validate the approach to the ICT (information and communications technology) challenges. The project will build on existing work at international level in clinical trial information models (BRIDG and PCROM), service-based approaches to semantic interoperability and data standards (ISO11179 and controlled vocabulary), data discovery, machine learning and electronic health records based on open standards (openEHR). TRANSFoRm will extend this work to interact with individual eHR systems as well as operate within the consultation itself providing both diagnostic support and support for the identification and follow up of subjects for research. The approach to system design will be modular and standards-based, providing services via a distributed architecture, and will be tightly linked with the user community. Four years of development and testing will end with a fifth year that will be dedicated to summative validation of the project deliverables in the Primary Care setting. In order to support patient safety in both clinical and research settings, significant ICT challenges need to be overcome in the areas of interoperability, common standards for data integration, data presentation, recording, scalability, and security., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

TRANSFoRm Clinical Research Information Model
type: Resource
type: NamedIndividual
has db xref: nlx_158219
synonym: Clinical Research Information Model
abbrev: CRIM
IAO_0000115: A clinical research information model for the integration of clinical research covering randomized clinical trials (RCT), case-control studies and database searches into the TRANSFoRm application development. TRANSFoRm clinical research is based on primary care data, clinical data and genetic data stored in databases and electronic health records and employs the principle of reusing primary care data, adapting data collection by patient reported outcomes (PRO) and eSource based Case Report Forms. CRIM was developed using the TRANSFoRm clinical use cases of GORD and Diabetes. Their use case driven approach consisted of three levels of modelling drawing heavily on the clinical research workflow of the use cases. Different available information models were evaluated for their usefulness to represent TRANSFoRm clinical research, including for example CTOM of caBIG, Primary Care Research Object Model (PRCOM) of ePCRN and BRIDG of CDISC. The PCROM model turned out to be the most suitable and it was possible to extend and modify this model with only 12 new information objects, 3 episode of care related objects and 2 areas to satisfy all requirements of the TRANSFoRm research use cases. Now the information model covers Good Clinical Practice (GCP) compliant research, as well as case control studies and database search studies, including the interaction between patient and GP (family doctor) during patient consultation, appointment, screening, patient recruitment and adverse event reporting.

Structural Genomics Consortium
type: Resource
type: NamedIndividual
has db xref: nlx_158220
abbrev: SGC
IAO_0000115: Charity registered in United Kingdom whose mission is to accelerate research in new areas of human biology and drug discovery.Not for profit, public-private partnership that carries out basic science of relevance to drug discovery whose core mandate is to determine 3D structures on large scale and cost effectively targeting human proteins of biomedical importance and proteins from human parasites that represent potential drug targets.

Mouse Gross Anatomy and Development Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157488
abbrev: EMAP
IAO_0000115: A structured controlled vocabulary of stage-specific anatomical structures of the mouse (Mus).

TRANSFoRm Data Integration Models
type: Resource
type: NamedIndividual
has db xref: nlx_158223
synonym: Data Integration Model
IAO_0000115: A set of three models, which in conjunction with the semantic mediator enables the execution of queries formulated through the eligibility representation of the Clinical research information model (WT6.4). An ontology-driven mechanism was developed to enable linkage and integration of phenotypic and genotypic data from multiple distributed data sources. It makes use of the Clinical Data Integration Model (CDIM, WT6.5), the Data Source Model (DSM, WT6.6) and the CDIM-DSM mapping model (WT6.6). Queries formulated through the CDIM and vocabulary service (WT7.2) are translated to local queries by the mediator using the individual source instances of the DSM and CDIM-DSM models.

NAF Ataxia Tissue Donation
type: Resource
type: NamedIndividual
has db xref: nlx_144396
synonym: National Ataxia Foundation Ataxia Tissue Donation
synonym: National Ataxia Foundation Tissue Donation Program
synonym: National Ataxia Foundation: Ataxia Tissue Donation
IAO_0000115: A website where users can find information on donating tissue for ataxia research.

Fondazione Centro San Raffaele; Milan; Italy
type: Resource
type: NamedIndividual
has db xref: nlx_158224
synonym: Fondazione Centro San Raffaele
abbrev: FCSR
IAO_0000115: A non-profit organization to support the research of the IRCCS San Raffaele Hospital with the aim of helping the development of science in the service of medicine. To make progress and achieve new successes, which may also be of benefit to future generations, the Fondazione Centro San Raffaele Hospital supports through participation in invitations to national and international research and fundraising activities to individuals and businesses. The lines of research in 2013 which focuses on the activities of the Foundation, in synergy with the San Raffaele hospital: # Molecular and functional approaches to the study of neurological and psychiatric disorders # Molecular and cellular therapies for regenerative medicine # Study and modulation of innate and adaptive immune response # Cellular and molecular approaches to the study of solid tumors and blood # Molecular and cellular approaches to the study and treatment of cardiovascular and metabolic diseases # Genetic mechanisms, molecular and cellular disease and aging # Genomics and post-genomics for the study of the mechanisms of disease and response to drugs # Molecular and cellular imaging for the study of oncological diseases and molecular imaging of cardiovascular disease

Electro Scientific Industries
type: Organization
type: NamedIndividual
has db xref: nlx_158228
synonym: Electro Scientific Industries Inc.
abbrev: ESI
IAO_0000115: A high technology company that is a developer and supplier of photonic and laser systems for microelectronics manufacturers. They manufacture a variety of products for testing and repairing equipment, and particularly products designed for use by manufacturers of other high-tech products. These include laser trimming systems. (Adapted from Wikipedia)

KOEHLER eClinical
type: Organization
type: NamedIndividual
has db xref: nlx_158229
synonym: KOEHLER eClinical GmbH
IAO_0000115: An independent owner-operated contract research organization providing clinical research services to the biopharmaceutical industry and life science organizations. If you are looking for data management, biostatistics and EDC solutions or plan to conduct a high quality phase I-IV or non-interventional study in and outside of Germany KOEHLER eClinical is your partner in study planning, conduct, evaluation and publication.

Pharmatching
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_158230
synonym: Pharmatching GmbH
synonym: Pharmatching.com
IAO_0000115: A matchmaker portal for the pharmaceutical industry worldwide offering a directory and contact platform. This includes a database of ten thousands of profiles of companies offering pharma services as well as a selection of companies including niche providers delivering the service of interest. The platform is used to search for human medicinal products, veterinary medicinal products, cosmeceuticals, nutriceuticals, medical devices, and diagnostics. The company''s platform also enables users to post their service requests, service offers, and APIs/intermediates; and interact with other users. In addition, it offers advice and operational support services for outsourcing and inlicensing processes, such as strategic, scientific, and regulatory advice related to due diligence and decision making of research and development, sourcing, and M and A processes; conduct of third party GMP and pharmacovigilance audits; customized interim solutions; and qualified person functions for GMP and pharmacovigilance. The company also serves various sectors of the life science industry, such as contract manufacture, laboratory investigations and contractual testing, clinical research organizations and pre-clinical research organizations, consulting and legal counseling, logistics and distribution, education, marketing, IT, and investment and financing sectors; and small and medium enterprises/pharma, academic, public institutions, and freelancers. (Bloomberg Businessweek)

ALTA
type: Organization
type: NamedIndividual
has db xref: grid.424010.3
has db xref: nlx_158231
synonym: ALTA s.r.l.u.
synonym: ALTA Srlu
IAO_0000115: A service-provider company specialized in developing and managing scientific research projects. Its mission is to support research activities from the idea to the realization of project. ALTA assists in finding the proper strategy, building European Consortia and putting science in the most appropriate administrative and management framework.

Olink Bioscience
type: Organization
type: NamedIndividual
has db xref: nlx_158232
abbrev: Olink
IAO_0000115: Commercial organization that produces products for biomarker research and development. Their goal is to help customers and collaborators to improve clinical decisions through the use of molecular biomarkers. Their tools bring new insights into disease processes, improve disease detection, and contribute to a better understanding of biology.

Enzo Life Sciences
type: Organization
type: NamedIndividual
has db xref: grid.482398.c
has db xref: ISNI: 0000 0004 0375 3702
has db xref: nlx_152356
synonym: Alexis
synonym: Assay Designs
synonym: BIOMOL
synonym: Enzo Life Sciences inc.
synonym: Stressgen Bioreagents
IAO_0000115: An Antibody supplier

Comprehensive Biomarker Center
type: Organization
type: NamedIndividual
has db xref: nlx_158236
synonym: Comprehensive Biomarker Center Gmbh
synonym: febit
synonym: febit GmbH
abbrev: CBC
IAO_0000115: Commercial organization that discovers, validates & analyzes genomic biomarkers with a focus on body fluid samples. Take advantage of their proven expertise in biomarker signature development and speed up your biomarker studies.

FlexGen
type: Organization
type: NamedIndividual
has db xref: nlx_158237
synonym: FlexGen B.V.
IAO_0000115: A biotechnology company that has developed technology for synthesizing custom microarrays, the FlexArrayer. Its is a desk-top sized instrument which allows the researcher to generate, in their own laboratory, either a custom oligonucleotide array in a single day or oligonucleotide pool in a few days. Recent developments in synthesis chemistry allows many modifications to be incorporated or for alternative chemistries to be considered., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Genewave
type: Organization
type: NamedIndividual
has db xref: grid.434679.b
has db xref: ISNI: 0000 0004 0373 8166
has db xref: nlx_158238
has db xref: Wikidata: Q30256844
IAO_0000115: A development-stage diagnostics company whose mission is to curb the spread of hospital-acquired infections and anti-microbial resistance by developing a small-footprint, inexpensive, and automated diagnostic instrument that will quickly deliver patient-specific information on 50+ genetic markers. With their on-chip, high-multiplex approach, they expect to offer a higher-performing, lower-cost, and more versatile solution versus bacterial culture and competing approaches in development.

Janssen Research and Development
type: Organization
type: NamedIndividual
has db xref: nlx_158241
synonym: Janssen Research & Development
synonym: Janssen Research & Development LLC
abbrev: Janssen R&D
IAO_0000115: Pharmaceutical company with a mission to discover and develop innovative medicines that ease patients'' suffering, and solve the most important unmet medical needs of our time. As one of the Janssen Pharmaceutical Companies, their strategy is to identify the biggest unmet medical needs and match them with the best science, internal or external, to find solutions for patients worldwide. They leverage their world-class discovery and development expertise, and operational excellence, to bring innovative, effective treatments in five therapeutic areas: cardiovascular and metabolism, immunology, infectious diseases and vaccines, neuroscience, and oncology.

Public Health England; London; United Kingdom
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100002141
has db xref: grid.271308.f
has db xref: ISNI: 0000 0004 5909 016X
has db xref: nlx_158245
has db xref: Wikidata: Q7257402
synonym: Health Protection Agency
synonym: Health Protection Agency; England; United Kingdom
synonym: HPA
synonym: Public Health England
abbrev: PHE
IAO_0000115: An executive agency of the Department of Health in the United Kingdom to protect and improve the nation''s health and well-being, and reduce health inequalities. It employs 5,500 staff, who are mostly scientists, researchers and public health professionals. They have 15 local centers and 4 regions (north of England, south of England, Midlands and east of England, and London). They work closely with public health professionals in Wales, Scotland and Northern Ireland, and internationally. Its formation came as a result of reorganization of the National Health Service (NHS) in England. It took on the role of the Health Protection Agency, the National Treatment Agency for Substance Misuse and a number of other health bodies. They are responsible for: * making the public healthier by encouraging discussions, advising government and supporting action by local government, the NHS and other people and organisations * supporting the public so they can protect and improve their own health * protecting the nation''s health through the national health protection service, and preparing for public health emergencies * sharing information and expertise with local authorities, industry and the NHS, to help them make improvements in the public''s health * researching, collecting and analyzing data to improve our understanding of health and come up with answers to public health problems * reporting on improvements in the public''s health so everyone can understand the challenge and the next steps * helping local authorities and the NHS to develop the public health system and its specialist workforce

Microsens
type: Organization
type: NamedIndividual
has db xref: nlx_158251
synonym: Microsens Diagnostics Ltd.
synonym: Microsens Medtech
synonym: Microsens Medtech Ltd
synonym: Microsens Medtech Ltd.
IAO_0000115: Commercial organization specializing in bacterial detection including tuberculosis, therapeutic protein and protein aggregation diseases. * Tools for rapid and simple bacteria and virus extraction including tuberculosis * Seprion technology for the detection and study of protein aggregates and protein aggregation diseases * LiMA technology for the ultra sensitive detection of bacteria and bacterial contamination

Biomedicum Genomics
type: Organization
type: NamedIndividual
has db xref: nlx_158263
synonym: Biomedicum Genomics Ltd
synonym: Biomedicum Genomics Oy
abbrev: BMGen
IAO_0000115: Organization that provides academic and industrial clients access to functional genomics technologies, services and partnering solutions including genome-wide expression, copy number profiling, miRNA expression, DNA-protein interaction (ChIP-on-chip), Illumina high-throughput sequencing including nucleic acid quality and quantity assessment. For gene silencing and ectopic expression purposes, they offer high-titer shRNA and ORF lentiviruses targeting genes of interest. They also offer customized services e.g. preparation of gain or loss-of-function cell lines and protein interactomics-based services (yeast two-hybrid). In addition, they provide access to wide array of computational data analyses. BMGen also offers partnering deals for clients interested in customized integration of several technologies.

European Biotechnology Network
type: Resource
type: NamedIndividual
has db xref: nlx_158528
synonym: European Biotechnology Network AISBL
abbrev: EBN
IAO_0000115: Non-profit organization that facilitates co-operation between professionals in biotechnology and the life sciences all over Europe bringing research groups, universities, SMEs, large companies and indeed all actors in biotechnology together to build and deliver partnerships.

HipSci
type: Resource
type: NamedIndividual
has db xref: nlx_158252
synonym: Human Induced Pluripotent Stem Cells Initiative
IAO_0000115: A UK national induced pluripotent stem (iPS) cell resource that will create and characterize more than 1000 human iPSCs from healthy and diseased tissue for use in cellular genetic studies. Between 2013 and 2016 they aim to generate iPS cells from over 500 healthy individuals and 500 individuals with genetic disease. They will then use these cells to discover how genomic variation impacts on cellular phenotype and identify new disease mechanisms. Strong links with NHS investigators will ensure that studies on the disease-associated cell lines will be linked to extensive clinical information. Further key features of the project are an open access model of data sharing; engagement of the wider clinical genetics community in selecting patient samples; and provision of dedicated laboratory space for collaborative cell phenotyping and differentiation.

ZF-screens
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_158253
synonym: ZF Screens
synonym: ZF-screens B.V.
synonym: ZF-screens BV
IAO_0000115: A commercial organization with expertise and multiple departments that focus on both fish physiology and molecular cell biology. ZF-pharma has developed patented technology for the automated in vivo high-throughput screening of pharmaceutical drug candidates against diseases. They seek industrial partners that are interested in obtaining a license for this technology or, alternatively, would prefer to outsource screening of TB drugs to ZF-pharma. NewCatch BV has developed a tool for use in sustainable aquaculture. The tool will first be used for reproduction of the highly valued fish species eel, pikeperch and sole. They seek industrial / aquaculture partners interested in obtaining a license for ZF-implants in other fish species. NewCatch BV carries out fish reproductive research, for instance European eel (Anguilla anguilla), exploring maturation and reproduction. ZF-Genomics offers multiple sequencing services, including mRNAseq and microRNA analysis and de novo and reference genome assemblies. In addition they also offer the bioinformatics services that are needed to make sense of the sequence data. In addition, they perform Next generation sequencing tasks for (inter)national research project partners and for external customers.

Orion
type: Organization
type: NamedIndividual
has db xref: nlx_158257
synonym: Orion Corporation
synonym: Orion Pharma
IAO_0000115: A globally operating Finnish developer, manufacturer and marketer of human and veterinary pharmaceuticals, active pharmaceutical ingredients and diagnostic tests. They are continuously developing new drugs and treatment methods. Pharmaceutical RD focuses on central nervous system drugs, oncology and critical care drugs, and Easyhaler pulmonary drugs.

Institute of Cancer Research
type: Organization
type: NamedIndividual
has db xref: grid.18886.3f
has db xref: ISNI: 0000 0001 1271 4623
has db xref: nlx_158259
has db xref: Wikidata: Q6039999
synonym: The Institute of Cancer Research
abbrev: ICR
IAO_0000115: Academic cancer research center, a postgrad college, and a charity in the United Kingdom that is making discoveries that defeat cancer. With their partners The Royal Marsden NHS Foundation Trust they form the largest comprehensive cancer center in Europe and perform high quality and original basic research and translational studies, with the aim of developing better treatments for the benefit of cancer patients worldwide. The ICR offers comprehensive, modern facilities for research and studentships supported by the Wellcome Trust, MRC, CRUK and EPSRC and the ICR''s own resources which are awarded on a competitive basis. The ICR offers postgraduate research degrees (MPhil, PhD and MD (Res)) and a modular postgraduate taught degree in oncology aimed at clinicians undertaking specialist training in the field of Clinical or Medical Oncology leading to a Postgraduate Certificate, Postgraduate Diploma or MSc in Oncology.

Royal College of Psychiatrists Podcasts
type: Resource
type: NamedIndividual
has db xref: nlx_15826
synonym: Let Wisdom Guide
synonym: LetWisdomGuide
abbrev: RC PSYCH Podcasts
IAO_0000115: Each month our podcast team will be broadcasting the very latest breakthroughs and discoveries in neurosciences, psychiatry and psychology.

VTT Technical Research Centre of Finland
type: Resource
type: NamedIndividual
has db xref: nlx_158261
synonym: Teknologian Tutkimuskeskus VTT
synonym: Valtion Teknillinen Tutkimuskeskus
abbrev: VTT
IAO_0000115: A multitechnological applied non-profit research organisation in Northern Europe that provides high-end technology solutions and innovation services. They enhance their customers'' competitiveness, thereby creating prerequisites for society''s sustainable development, employment, and well-being. VTT has ISO9001:2008 certificate and ISO14001:2004 certificate.

Systematized Nomenclature of Medicine - Clinical Terms
type: Resource
type: NamedIndividual
has db xref: nlx_157603
abbrev: SNOMEDCT
IAO_0000115: Ontology of SNOMED (Systematized Nomenclature of Medicine) clinical terms.

ConnectedDiscovery
type: Organization
type: NamedIndividual
has db xref: nlx_158347
synonym: Connected Discovery
IAO_0000115: Commercial organization that develops pre-competitive solutions to the knowledge challenges facing drug discovery by connecting companies, leading academics and biotech specialists. It provides the bandwidth, knowledge and experience to successfully deliver pre-competitive projects through leadership, technical consulting, workflow expertise and software production. They possess over 30 years collective experience of large pharma drug discovery, computational science and knowledge management experience.

Bellvitge Biomedical Research Institute
type: Resource
type: NamedIndividual
has db xref: nlx_158270
synonym: Fundaci�� Institut d''Investigaci�� Biom��dica de Bellvitge
synonym: Institut d''Investigacio Biomedica de Bellvitge
synonym: Institut d''Investigacio Biomedica de Bellvitge (IDIBELL)
synonym: Institut d''Investigaci�� Biom��dica de Bellvitge
synonym: Institut d''Investigaci�� Biom��dica de Bellvitge (IDIBELL)
abbrev: IDIBELL
IAO_0000115: A research center focused on cellular medicine, where the basic research focuses and works on relevant clinical matters and fosters economic development. The center manages the research of the Bellvitge University Hospital, the Institut Catal�� d''Oncologia (Catalan Institute of Oncology) and the University of Barcelona. It is one of the first five Spanish research centers accredited as health research institute by the Instituto de Salud Carlos III (Health Institute Carlos III).

Althia
type: Organization
type: NamedIndividual
has db xref: nlx_158279
synonym: Advanced Laboratories of Translational Health
synonym: Althia Health
synonym: Althia Health Ltd.
synonym: S.L.
synonym: SL
IAO_0000115: A biomedical company in Spain focused on the development of new tools for diagnosis and personalized treatment of oncological diseases and precancerous. It has three areas of activity in permanent innovation: Assistance in Diagnosis / Prognosis in solid and hematological tumors, Translational Research covering the gap between basic and clinical research and advanced radiotherapy treatments based image-guided single dose (SD-IGRT). Their objectives are: * Provide an integrated tissue and tumor molecular phenotype analysis using the most advanced technologies in diagnosis, to guide the most appropriate treatment for each patient. * Discover and validate molecular patterns by molecular systems and platforms including pathology, to generate predictive algorithms through computational biology, evolution and determining the response of patients with a particular tumor profile. Althia has laboratories equipped with the most advanced equipment and technologies in Barcelona and Granada Genyo Center, with offices in Madrid.

Quartz Bio
type: Organization
type: NamedIndividual
has db xref: nlx_158280
synonym: Quartz Bio S.A.
abbrev: QBIO
IAO_0000115: A Swiss service and consulting company specialized in the computational analysis of biomarker data from clinical trials. Their technical expertise spans across multiple biomaker technological platforms such as genetics, transcriptomics, protein assays and cellular assays. Quartz Bio is a spin-off of Merck Serono with the capital of the company entirely owned by its employees.

Centre for Genomics and Oncological Research
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100007321
has db xref: grid.470860.d
has db xref: ISNI: 0000 0004 4677 7069
has db xref: nlx_158281
synonym: Pfizer-University of Granada-Junta de Andaluc??a Centre for Genomics and Oncological Research
synonym: Pfizer-University of Granada-Junta de Andaluc??a Centre for Genomics and Oncological Research (GENYO)
abbrev: GENYO
IAO_0000115: Center for excellence research in genomic medicine, focusing on the comprehensive study and understanding of the genetic basis of human diseases in general, placing special emphasis on cancer and its genetic disorders related to inheritance. GENYO was created as a multidisciplinary research space, where different professionals from the healthcare, university and business areas interact, making it possible to generate new systems to diagnose, prevent and treat diseases based on the joint and coordinated application of first-rate knowledge in the different areas of genetics. The center is the benchmark center of the Andalusian Program for Research in Clinical Genetics and Genomic Medicine, a program which, together with those of Cell Therapy and Regenerative Medicine, and Nanomedicine have the main objective of supporting and fostering translational research in Advanced Therapies. The activities performed within these three research programs are developed in coordination with the Andalusian Initiative for Advanced Therapies (IATA), an initiative of the Andalusian Government promoted by the Regional Ministries of Health and Innovation, Science and Enterprise.

NeuroTrends
type: Resource
type: NamedIndividual
has db xref: nlx_158295
synonym: NeuroTrends - Uncovering methodological trends in Functional MRI research
IAO_0000115: Service that extracts and analyzes methodological information from thousands of published studies across the functional neuroimaging literature. It currently offers searching articles by methodological choices, visualization of methods trends over time, and extraction of methods information from text. It currently includes 282,476 methodological details about 21,562 articles, published between 1992 and 2014. (2014) * Search for articles by title, authors, and methods. * Interactive visualizations of methodological parameters over time, by author, and more. * All data are programmatically accessible through a simple application programming interface. It''s simple to re-analyze the data or integrate with your own application.

WU-Minn HCP 500 Subjects MR and MEG Release
type: Resource
type: NamedIndividual
has db xref: nlx_158287
synonym: HCP 500 Subjects
synonym: HCP 500 Subjects MR + MEG Release
synonym: HCP 500 Subjects MR and MEG Release
synonym: HCP 500 Subjects Release
synonym: WU-Minn HCP 500 Subjects
synonym: WU-Minn HCP 500 Subjects MR + MEG Release
synonym: WU-Minn HCP 500 Subjects Release
abbrev: HCP S500
abbrev: WU-Minn S500
IAO_0000115: Behavioral and 3T MR imaging data from over 500 healthy adult participants with 14 subjects also scanned in resting-state MEG (rMEG) and task MEG (tMEG). Highlights: * Behavioral and demographic data on 550 subjects. * MR imaging data preprocessed using updated pipelines (structural pipeline v3.1, functional pipeline v3.1, diffusion pipeline v3.1, task analysis pipeline v3.3). * Updates to pipelines include a new intersubject registration method called MSMSulc. All MR data from Q1-Q3 releases have been reprocessed. HCP strongly advises against mixing data from this release with previously-released data. * Individual task fMRI grayordinate-based analysis results (available at 2mm, 4mm, 8mm, and 12mm smoothing levels) and volume-based analysis results (4mm smoothing) are available for all complete 500 Subjects tfMRI data, using an updated task analysis pipeline v3.3. * New extensively processed 100- and 400+-subject group-average functional MR data. * Updates to MEG data and access in ConnectomeDB. Structural MRI-based MEG anatomical models and MR data for the 14 MEG1 Release subjects. * Improvements to behavioral data organization and data dictionary, including the addition of previously unreleased restricted behavioral and demographic data. * All imaging data soon to be available on the cloud through Amazon S3. (More information to come!)

GENSAT at NCBI - Gene Expression Nervous System Atlas
type: Resource
type: NamedIndividual
has db xref: nif-0000-02905
abbrev: NCBI GENSAT Database
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 19, 2012. Due to budgetary constraints, the National Center for Biotechnology Information (NCBI) has discontinued support for the NCBI GENSAT database, and it has been removed from the Entrez System. The Gene Expression Nervous System Atlas (GENSAT) project involves the large-scale creation of transgenic mouse lines expressing green fluorescent protein (GFP) reporter or Cre recombinase under control of the BAC promoter in specific neural and glial cell populations. BAC expression data for all the lines generated (over 1300 lines) are available in online, searchable databases (www.gensat.org and the Database of GENSAT BAC-Cre driver lines). If you have any specific questions, please feel free to contact us at info_at_ncbi.nlm.nih.gov The GENSAT project aims to map the expression of genes in the central nervous system of the mouse, using both in situ hybridization and transgenic mouse techniques. Search criteria include gene names, gene symbols, gene aliases and synonyms, mouse ages, and imaging protocols. Mouse ages are restricted to E10.5 (embryonic day 10.5), E15.5 (embryonic day 15.5), P7 (postnatal day 7), and Adult (adult). The project focuses on two techniques * Evaluation of unmodified mice lines for expression of a given gene using radiolabelled riboprobes and in-situ hybridization. * Creation of transgenic mice lines containing a BAC construct that expresses a marker gene in the same environment as the native gene

TIDE BC
type: Resource
type: NamedIndividual
has db xref: nlx_158289
synonym: TIDE-BC
synonym: Treatable Intellectual Disability Endeavor in B.C.
abbrev: TIDE
IAO_0000115: A collaborative care and research initiative with a focus on prevention and treatment of Intellectual disability (ID) that is due to inborn errors of metabolism (IEM), which can be treated with diet or drugs. Health care policy and institutional culture is still operating under the old premise that all ID is incurable and thus, many children born with treatable ID are at risk of not being treated. To acknowledge the multidisciplinary scope and the ways in which health care professionals and researchers will collaborate, the goals of the TIDE BC project are demonstrated within a framework of 7 Work Packages: * Implementation of a new Protocol for diagnostic evaluation of ID, focusing of treatable conditions; * Development of infrastructure to facilitate implementation, evaluation and sustainability of the Protocol; * Investments into next generation genomic technologies; * Improving evidence of and access to treatments; * Evaluation and health economy; * Knowledge dissemination; * Education and Mentoring. The objectives addressed in all Work Packages reflect a highly integrated cluster combining clinical care, research, evaluation, and knowledge dissemination.

BC Childrens Hospital Foundation
type: Organization
type: NamedIndividual
has db xref: grid.498685.e
has db xref: ISNI: 0000 0001 1432 0695
has db xref: nlx_158291
has db xref: Wikidata: Q4835281
synonym: BC Children's Hospital Foundation
abbrev: BCCHF
IAO_0000115: Funding resource that raises funds to support BC Children's Hospital, Sunny Hill Health Centre for Children and the Child and Family Research Institute. The Foundation also works with Sunny Hill's Board of Directors to manage the Sunny Hill Foundation for Children. In 2013, BC Children's Hospital Foundation received donations from more than 150,000 people and had revenues of over $83 million.

POLYMUN Scientific
type: Organization
type: NamedIndividual
has db xref: nlx_158293
synonym: Polymun Scientific Immunbiologische Forschung GmbH
abbrev: POLYMUN
IAO_0000115: A private commercial company generating revenues by contract development and manufacturing biopharmaceuticals as well as creating liposomal formats of drugs for contract partners. These revenues are invested in the proprietary product pipeline and the further development of technology platforms. The R&D projects and technologies are open for co-development and licensing. Polymun operates in accordance with current GMP guidelines and holds an Austrian production license for pharmaceuticals (??63 Austrian Pharmaceutical Law) thus meeting the EU requirements for drug manufacturing. Its core competence is the development and manufacture of biopharmaceuticals, using both mammalian and microbial cell technology. A fine example are Polymun''s broadly neutralizing HIV-1 antibodies produced in CHO cells. Other examples are recombinant human and porcine trypsin produced in yeast. Cell culture was also the basis for the development of a live attenuated influenza vaccine produced in Vero cells which led to the further investigation in genetically modified influenza viruses used as carrier for foreign epitopes (HIV, TB). Also the innovative liposome technology was initiated in order to optimize the formulation of the pharmacologically potent enzyme SOD, produced by Polymun in E. coli. Today, Polymun can apply this drug delivery platform to all kinds of pharmaceutically active ingredients. The industrial applicability in scale and price is a common focus throughout all projects and technologies.

Data.gov Science and Research Data Catalog
type: Resource
type: NamedIndividual
has db xref: nlx_158294
synonym: Science & Research - Data Catalog
synonym: Science and Research - Data Catalog
synonym: Science.Data.gov
abbrev: Science & Research Data Catalog
IAO_0000115: A catalog of high-value public science and research data sets from across the Federal Government.

Systems Chemical Biology and Chemogenomics Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157605
abbrev: CHEMBIO
IAO_0000115: Ontology for Systems Chemical Biology and Chemogenomics

ENEA
type: Resource
type: NamedIndividual
has db xref: nlx_158297
synonym: Ente per le Nuove Technologie
synonym: Italian National Agency for New Technologies Energy and Sustainable Economic Development
synonym: l''Agenzia nazionale per le nuove tecnologie l''energia e lo sviluppo economico sostenibile
synonym: l''Energia e l''Ambriente
IAO_0000115: Italian national agency for new technologies, energy and sustainable economic development with the following main research issues: * Energy Efficiency * Renewable Energy Sources * Nuclear Energy * Climate and the Environment * Safety and Health * New Technologies * Electric System Research The Agency''s activities are devoted to: * basic, mission-oriented, and industrial research exploiting wide-ranging expertise as well as experimental facilities, specialized laboratories, advanced equipment; * new technologies and advanced applications; * dissemination and transfer of research results, thus promoting their exploitation for production purposes; * provide public and private bodies with high-tech services, studies, measurements, tests and assessments; * training and information activities aimed at broadening sector expertise and public knowledge and awareness. The Agency''s multidisciplinary competences and great expertise in managing complex research projects are put at the disposal of the Country system.

Diamyd Medical
type: Organization
type: NamedIndividual
has db xref: nlx_158298
synonym: Diamyd Medical AB
abbrev: DMYD B
IAO_0000115: A diabetes company active in the field of pharmaceutical development. The Company develops the diabetes vaccine Diamyd with the active ingredient GAD, which has the potential to become a key piece of the puzzle of a future solution to prevent, treat or cure type 1 diabetes and other forms of diabetes. Diamyd Medical has independently pursued the development of the diabetes vaccine Diamyd to global Phase III trials, leading to one of Sweden''s largest biotech agreements ever. The company has secured an exclusive license for a patent application for the specific combination therapy GAD plus the endogenous substance GABA, which has demonstrated favorable results in preclinical trials. The license also encompasses rights for the therapeutic use of GABA to treat diabetes and other inflammation-related disorders.

DataLad
type: Resource
type: NamedIndividual
has db xref: nlx_158300
synonym: Data Lad
synonym: DataGit

Git
type: Resource
type: NamedIndividual
has db xref: biotools:Git
has db xref: nlx_158301
IAO_0000115: A free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. Git is easy to learn and has a tiny footprint with lightning fast performance. It outclasses SCM tools like Subversion, CVS, Perforce, and ClearCase with features like cheap local branching, convenient staging areas, and multiple workflows.

bioRxiv
type: Resource
type: NamedIndividual
has db xref: biotools:bioRxiv
has db xref: nlx_158302
synonym: bioRxiv - the preprint server for biology
IAO_0000115: A free archive and distribution service for unpublished preprints in the life sciences allowing authors to make their findings immediately available to the scientific community and receive feedback on draft manuscripts before they are submitted to journals. An article may be posted prior to, or concurrently with, submission to a journal but should not be posted if it has already been published. Once an article is published in a journal, bioRxiv will update the preprint with a link to the published version.

Mosaic Systems
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_158306
synonym: Mosaic Systems BV
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on October 21, 2014. Commercial organization that provides technology, tools, and services for the development and production of biologics from therapeutics and drugs, food ingredients, and agriculture products. The company specializes in biologics separation and purification. Its products are used for industrial process chromatography applications. (Businessweek)

Sartorius
type: Organization
type: NamedIndividual
has db xref: nlx_158308
synonym: Sartorius AG
synonym: Sartorius Stedim Biotech
synonym: Sartorius Stedim Biotech S.A.
synonym: Sartorius-Stedim Biotech
abbrev: SSB
IAO_0000115: Commercial organization that provides laboratory and process technologies and equipment. Their products and services help customers around the globe implement complex and quality-critical processes in biopharmaceutical production and laboratory environments in a time- and cost-efficient way. Sartorius operates its own production facilities in Europe, Asia and America, and also has sales offices and local representatives in more than 110 countries.

Eisai
type: Organization
type: NamedIndividual
has db xref: grid.418767.b
has db xref: ISNI: 0000 0004 0599 8842
has db xref: nlx_158312
has db xref: Wikidata: Q29123933
synonym: Eisai Co. Ltd.
synonym: EISAI Ltd
IAO_0000115: A global pharmaceutical company.

LINCS Information Framework
type: Resource
type: NamedIndividual
has db xref: nlx_158348
synonym: LIFE LINCS Information Framework
synonym: lifekb
IAO_0000115: LIFE search engine contains data generated from LINCS Pilot Phase, to integrate LINCS content leveraging semantic knowledge model and common LINCS metadata standards. LIFE makes LINCS content discoverable and includes aggregate results linked to Harvard Medical School and Broad Institute and other LINCS centers, who provide more information including experimental conditions and raw data. Please visit LINCS Data Portal.

Greek Association of Alzheimers Disease and Related Disorders
type: Organization
type: NamedIndividual
has db xref: grid.428867.7
has db xref: nlx_158314
synonym: Alzheimer Hellas
synonym: Greek Association of Alzheimer Disease and Related Disorders
synonym: Greek Association of Alzheimer Disease and Relative Disorders
synonym: Greek Association of Alzheimer's Disease and Related Disorders
abbrev: GAADRD
IAO_0000115: A non-profit organization whose aim is to offer advice concerning the care of Alzheimer' '''s disease patients, information and services for the people affected and their families. Also, to offer mutual help to the family members of the patients in order to reduce the social, economic and emotional cost deriving from the long care of people suffering from dementia. Lastly, the association attempts to publicize the social needs of the population affected and to inform the public in order to be acquainted with the problem. The mission of the Greek Association of Alzheimer' '''s Disease is * the early diagnosis of dementia by scientists * the promotion of research * education and training for all the stakeholders * the development of Care Units for patients with Alzheimer' '''s Disease * the provision of useful information and advise (24 hour help-line) on dementia problems (caring, legal or financial issues) * the presentation of lectures by health professionals and informal carers, covering all aspects of Alzheimer Disease * and the development of professional seminars during the whole year.

GOlr
type: Resource
type: NamedIndividual
has db xref: nlx_158322
synonym: Gene Ontology Solr index
IAO_0000115: A public Solr index for the Gene Ontology. This index will replace some of the query functionality for GOOSE as well as become the new backend for AmiGO 2 and other services.

Innovative Concepts in Drug Development
type: Organization
type: NamedIndividual
has db xref: nlx_158326
synonym: ICDD-sas
abbrev: ICDD
IAO_0000115: A contract research organization (CRO) that are mitochondrial experts, operating mitochondrial function screening platforms by using accepted pharmaceutical innovative technologies. The dynamic analysis of several typical markers of central and mitochondrial metabolism, redox status, or mitochondrial biogenesis are included in the determination of bioenergetic balance in living cells of human origin. These platforms are used to validate the activity of pharmaceuticals, cosmetics and environmental assets xenobiotics on mitochondrial targets associated with the activity or toxicity of these products under the selected models. They specialize in the selection of drugs affecting the progression of neurodegenerative diseases and offer proven models of Huntington's disease, Parkinson's and Alzheimer's, using primary cells of human origin. They have developed and use technology cellulomique and proteomics to identify early response profiles and clinical safety of pharmaceutical products for diseases of the CNS.

Qualissima
type: Organization
type: NamedIndividual
has db xref: grid.492092.4
has db xref: nlx_158328
synonym: Qualissima GmbH
IAO_0000115: A Research as a Service (RaaS) Company founded by a Clinical Pharmacologist and Neuropsychiatrist that offers to its partners (health products industries and public research), 3 platforms: * Clinical research (CRO and SMO) * Scientific & regulatory consulting * Online surveys (Web portal) Their Research & Development profile allows them to propose innovative concepts such as : * Patient-Leader studies * Translational research studies (fMRI, innovative biomarkers, modeling, ...) * Behavioral parameters as biomarkers studies Qualissima also proposes proof of concept studies, proof of activities studies, medical devices studies and observational studies.

Corengi
type: Resource
type: NamedIndividual
has db xref: nlx_158330
synonym: Clinical Options Research Engine
synonym: Corengi Inc.
IAO_0000115: A comprehensive, free, and interactive platform to help individuals discover more about clinical trials that may be appropriate for them for a variety of diseases. The platform allows stakeholders within the clinical trials community (investigators, site personnel, sponsors, and disease advocates) to engage with potential enrollees and educate them about specific clinical trials. They have identified some of the most commonly used criteria for the clinical trials in each disease. Using these criteria, they developed a questionnaire for a single disease. Then, looking at just those questions, they can start to get a sense of which clinical trials might be appropriate for a particular person which is a helpful to start to narrow down the list of potentially appropriate trials. All clinical trials that are posted on www.clinicaltrials.gov for the diseases that Corengi covers will be on the website.

Network Data Exchange (NDEx)
type: Resource
type: NamedIndividual
has db xref: nlx_158334
has db xref: r3d100000028
synonym: NDEx
synonym: ndex bio
synonym: ndex biology
synonym: Network Data Exchange
synonym: the Network Data Exchange
synonym: UCSD NDEx
IAO_0000115: Repository where scientists and organizations can share, store, manipulate, and publish biological network data. Users can also run their own copies of NDEx Server software in cases where stored networks must be kept in highly secure environment (such as for HIPAA compliance) or where high application load is incompatible with shared public resource. Open source software system that is part of Cytoscape family. Project of Cytoscape Consortium in conjunction with Ideker lab at UCSD School of Medicine. Public forum where biologists can exchange and publish computable network models in many types and formats. NDEx is based on REST web API which can be accessed by any application, including NDEx website and NDEx Cytoscape App. NDEx networks are assigned stable, globally unique URIs and so can be referenced by publications, by other networks, and by analytic applications.

Simcyp
type: Organization
type: NamedIndividual
has db xref: nlx_158337
synonym: Simcyp Limited
synonym: Simcyp Ltd
IAO_0000115: Research based company providing predictive pharmacokinetic and pharmacodynamic tools, workshops and consultancy services. Their user-friendly simulator and databases predict drug absorption, clearance, distribution and metabolic drug-drug interactions from in vitro data. Simcyp's clients include major global pharmaceutical and bioscience companies, leading academic institutes and regulatory authorities. These clients form the Simcyp Consortium, which together with independent International Scientific Advisory Board, guide scientific development at Simcyp.Simcyp was acquired by Certara in 2012.

Sirius Analytical
type: Organization
type: NamedIndividual
has db xref: nlx_158338
synonym: Sirius - The Science of Measurement
synonym: Sirius Analytical Instruments Ltd.
synonym: Sirius Analytical Ltd
abbrev: Sirius
IAO_0000115: Organization that designs and manufactures analytical instrumentation to measure physicochemical parameters for the pharmaceutical and biotech industry, as well as offers physicochemical data and consultancy services. Their instruments provide accurate and reliable values for pKa, log P, log D, solubility and dissolution, particle size and shape analysis. These critical physicochemical parameters are important in drug formulation, and also influence the ability of New Chemical Entities to cross biological membranes such as the gastro-intestinal tract, blood-brain barrier, skin and cell walls. Sirius also offers an analytical service for high quality PhysChem outsourcing, used by hundreds of clients worldwide.

Simulations Plus
type: Organization
type: NamedIndividual
has db xref: grid.418738.1
has db xref: ISNI: 0000 0004 0506 5380
has db xref: nlx_158339
has db xref: Wikidata: Q7521341
synonym: Simulations Plus Inc.
IAO_0000115: Commercial developer of Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) and Physiologically-Based Pharmacokinetic (PBPK) modeling and simulation software for the pharmaceutical and biotechnology, industrial chemical, cosmetic, herbicide, and food ingredient industries. Their software allows pharmaceutical scientists to predict certain key potential endpoints and dynamics, in silico, thereby reducing research & development costs and helping clients make better projects decisions sooner. Consulting services: Their team of highly-skilled scientists is available to assist with your discovery and development activities on a project-by-project basis. They now offer expanded pharmacodynamic modeling services, NONMEM analysis, and regulatory report writing assistance. Their ultimate goal is to develop tools and systems which bridge PBPK modeling with clinical trial data analysis. Training workshops & User Groups: they offer hands-on introductory and advanced training workshops in the United States, Europe, and Asia throughout the year.

Almirall
type: Organization
type: NamedIndividual
has db xref: nlx_158340
synonym: Laboratories Almirall S.A.
synonym: S.A.
IAO_0000115: A pharmaceutical company committed to provide valuable medicines through their own R&D efforts, licenses and collaborations. Through seeking innovative medicines they aim to become a relevant player in respiratory and dermatology diseases with also a strong interest in gastroenterology and pain. The company is headquartered in Barcelona, Spain, and has 14 affiliates in Europe and North America and trading capacity in 22 countries.

ESTEVE
type: Organization
type: NamedIndividual
has db xref: nlx_158341
synonym: Laboratorios del Dr. Esteve S.A.
IAO_0000115: A pharmaceutical chemical group in Spain with a presence worldwide. It operates in the pharmaceutical sector by researching and developing new drugs, marketing a wide range of ethical and OTC products, generics, vaccines and also products for hospital and veterinary use. Through its subsidiary Esteve Qu??mica is also present in the Active Pharmaceutical Ingredients sector.

BioSolveIT
type: Organization
type: NamedIndividual
has db xref: nlx_158346
synonym: BioSolveIT GmbH
IAO_0000115: Commercial provider of software solutions for drug discovery applications offering tools, services, and research collaborations. The software portfolio ranges from design, over screening, to the visualization of ligand libraries, for hit identification, optimization, and scaffold hopping. With a stellar scientific advisory board and founders from academia who intensely collaborate with pharma, BioSolveIT catalyzes products off of university research successes with proven pharmaceutical industry application. They provide software products within the areas of ligand and structure-based drug design and is the pioneer of computational fragment-based ligand design. BioSolveIT innovate break-throughs in drug discovery by supplying smooth, user-centered designed tools bringing different researchers together for efficient multidisciplinary drug design.

Mouse Pathology Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157489
abbrev: MPATH
IAO_0000115: A structured controlled vocabulary of mutant and transgenic mouse pathology phenotypes

EnCor Biotechnology Inc.
type: Organization
type: NamedIndividual
has db xref: nlx_152355
IAO_0000115: Company committed to development, characterization and manufacture of antibody and ELISA type assays for academic, biopharmaceutical and clinical research.

SciBite
type: Organization
type: NamedIndividual
has db xref: nlx_158349
synonym: SciBite Limited
IAO_0000115: An informatics service focusing on competitor intelligence and text-mining within the life sciences. It mines a diverse array of scientific content to look for mentions of targets, indications, companies, drugs and technologies of interest to those involved in human health and drug discovery. A free newsletter service is provided to allow everyone to explore the therapeutic landscape and stay informed and a range of professional products and services are offered for those who need more in-depth analysis of the therapeutic landscape. Its text-mining engine can be configured to a variety of different use cases and performs with very high throughput. SciBite has a number of big-pharma and scientific publishers as current customers. SciBITES is free on the website but for extended functionality, including a data mining API and access to internal or commercial documents, you may wish to consider an installation of the SciBITES server software within your organization.

Alacris Theranostics
type: Organization
type: NamedIndividual
has db xref: grid.473915.d
has db xref: nlx_158354
synonym: Alacris Theranostics GmbH
abbrev: Alacris
IAO_0000115: Commercial organization that uses next generation sequencing technologies coupled with computational modeling of tumor and somatic tissues in order to identify individualized therapies for cancer patients. The company also uses these technologies to help pharmaceutical partners stratify patients for their clinical trials. Alacris has an exclusive worldwide commercial license for the computational modeling of tumors and somatic tissues using proprietary computational systems modeling technologies ModCell developed at the Max Planck Institute for Molecular Genetics (MPI-MG) in Berlin coupled with next generation sequencing and genotyping technology developed at Harvard Medical School in Boston. The company also is building up the first next generation sequencing center in Europe for clinical operations.

Experimental Pharmacology and Oncology Berlin-Buch
type: Organization
type: NamedIndividual
has db xref: nlx_158355
synonym: EPO - Experimental Pharmacology & Oncology GmbH
synonym: EPO Berlin-Buch GmbH
synonym: EPO-GmbH
synonym: Experimental Pharmacology & Oncology Berlin-Buch
synonym: Experimental Pharmacology & Oncology Berlin-Buch GmbH
synonym: Experimental Pharmacology & Oncology GmbH
abbrev: EPO
IAO_0000115: A small and medium-sized enterprise (SME) that has expertise in preclinical pharmacology, pharmacokinetics, and toxicology for the characterization of novel anticancer therapeutics and predictive biomarkers like: cytostatics, biologicals (peptides, antibodies), (anti)-hormones, immunomodulators (cytokines), and gene therapeutics. EPO has modern laboratories licensed for animal experiments and gene technology (S2) and a broad panel of murine and human tumor models growing in immunocompetent (SPF-quality, syngeneic strains) or immunodeficient mice (nude, SCID, NOD/SCID). EPO has established imaging technologies to monitor in vivo tumor growth.

Interface Europe
type: Organization
type: NamedIndividual
has db xref: nlx_158364
abbrev: IE
IAO_0000115: THIS RESOURCE IS OUT OF SERVICE, documented on July 23, 2021.Commercial organization with expertise in European research and innovation that provide both science providers (researchers) and technology users (Industry including SMEs, public authorities, Universities, clusters, etc.) tailor-made services to give the highest possible European added value to their project.

GABO:mi
type: Organization
type: NamedIndividual
has db xref: grid.10404.31
has db xref: ISNI: 0000 0004 0377 0748
has db xref: nlx_158356
synonym: GABO MI Society for workflow management
synonym: GABO:mi Gesellschaft f??r Ablauforganisation :milliarium mbH & Co. KG
synonym: GABO:mi Gesellschaft f??r Ablauforganisation:milliarium mbH & Co KG
synonym: GABO:mi Gesellschaft f??r Ablauforganisation:milliarium mbH & Co. KG
synonym: GABO:mi Gesellschaft fur Ablauforganisation :milliarium mbH & Co. KG
synonym: GABO:mi Gesellschaft fur Ablauforganisation:milliarium mbH & Co. KG
synonym: GABO:mi Society for workflow management
synonym: GABO:milliarium
IAO_0000115: THIS RESOURCE IS OUT OF SERVICE, documented on July 23, 2021. Small and medium-sized enterprise (SME) that is expert in management of research projects. Initially, they provide support with help and advice when applying for European research grants - free of charge. From project start, they take over contract negotiations, financial management, reporting to the EC, meeting organization, public relations and much more. ARTTIC Innovation GmbH took over GAVBO:mi.

American College of Clinical Pharmacy
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100005321
has db xref: grid.417936.e
has db xref: ISNI: 0000 0001 2097 285X
has db xref: nlx_158370
has db xref: Wikidata: Q23894214
abbrev: ACCP
IAO_0000115: A professional and scientific society that provides leadership, education, advocacy, and resources enabling clinical pharmacists to achieve excellence in practice and research. Their membership is composed of practitioners, scientists, educators, administrators, students, residents, fellows, and others committed to excellence in clinical pharmacy and patient pharmacotherapy. The Practice and Research Networks (PRNs) represent focused interest groups of ACCP members, providing a means for clinical pharmacists with common practice and research interests to gather for professional interaction, networking, and continuing education. Activities within individual PRNs may vary depending on the interests and perceived needs of their members. All PRNs conduct educational programs within their interest areas at the ACCP Annual Meeting and the Spring Practice and Research Forum.

Coordinating center for infectious diseases
type: Government granting agency
type: NamedIndividual
has db xref: nlx_inv_1005039
abbrev: CCID
abbrev: CH
IAO_0000115: funding.html

Psynova Neurotech
type: Organization
type: NamedIndividual
has db xref: nlx_158360
synonym: Psynova Neurotech Ltd
abbrev: Psynova
IAO_0000115: Commercial organization focused on the development and exploitation of novel biomarkers for psychiatric illnesses. They provide industrial and academic partners with comprehensive biomarker discovery services in commercial and collaborative projects. They operate in the field of psychiatric disorders and their products and services are designed to excel biomarker research. In 2010, Psynova Neurotech and its partner company Rules-Based-Medicine Inc (now MyriadRBM) conducted a beta launch of a blood test aiding in the diagnosis of schizophrenia (http://www.veripsych.com/). They are now refining the test and have shifted their focus to the development of new blood-based biomarker tests that aid in the diagnosis, prognosis and differential diagnosis of schizophrenia, bipolar disorder and major depression. They offer not only their pre-selceted Multiple Reaction Monitoring (MRM) and Multiplex Immunoassay products, but also custom build panels. If they are provided with a list of analyses to evaluate, they can produce an analytical panel according to individual needs utilizing either MRM or Multiplex Immunoassay technologies., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Cellartis
type: Organization
type: NamedIndividual
has db xref: nlx_158362
synonym: Cellartis AB
synonym: Cellectis AB
synonym: Takara Bio Inc.
IAO_0000115: THIS RESOURCE IS OUT OF SERVICE, documented on July 23, 2021. Company focusing on stem cell derived products and services for drug discovery, toxicity testing and applications within regenerative medicine. The company leverages long-standing experience in stem cell handling and scale up together with leading expertise in differentiation of cells into mature and functional human cells. The laboratories are prepared to meet the EU and US guidelines for current Good Manufacturing Practice (cGMP). Now part of Takara Bio Inc.

CXR Biosciences
type: Organization
type: NamedIndividual
has db xref: nlx_158363
synonym: Concept Life Sciences
synonym: CXR Biosciences Ltd.
IAO_0000115: Commercial organization that provides preclinical services and expertise, specializing in investigative toxicology, exploratory and discovery toxicology, metabolism and pharmacokinetics. CXR Biosciences is now Concept Life Sciences.

Centers for Medicare and Medicaid Services
type: NamedIndividual
has db xref: nlx_157919
synonym: Centers for Medicare & Medicaid Services
synonym: CMS.gov
abbrev: CMS

KaLy-Cell
type: Organization
type: NamedIndividual
has db xref: nlx_158365
IAO_0000115: Commercial organization that offers human and animal hepatocyte products as well as other products derived from liver tissue, kits and media. Services they offer include in vitro metabolism, in vitro toxicology and cell therapy.

SOLVO Biotechnology
type: Organization
type: NamedIndividual
has db xref: nlx_158367
synonym: Solvo Biotechnology ZRT
abbrev: SOLVO
IAO_0000115: Commercial organization that is a worldwide provider of drug transporter technology, assays and reagents. Leveraging their expertise in efflux and uptake transporters, they generate quality reports for submission to FDA / EMA. From small molecules to protein therapeutics, SOLVO can test all transporter needs. Drug transporter Services and Products include: * Over 100 solutions for a wide range of transporters * Uptake transporter assays * Efflux transporter assays in cellular and membrane-based models * Transporter Consultancy Services * FDA- and EMA-ready reports * Ready-to-use Kits * In vitro and in vivo methods for studying transporters in the BBB, intestine, liver and kidney * Custom assay development

American Association of Kidney Patients
type: Resource
type: NamedIndividual
has db xref: nlx_158369
abbrev: AAKP
IAO_0000115: Association of kidney patients focused on patient-centered education, advocacy and community. They share educational pieces covering every level of kidney disease, advocate for improved access to high-quality health care through regulatory and legislative reform at the federal level, and make an effort to bring kidney patients together to promote community, conversations and to seek out services that help maximize patients'' everyday lives.

American Nephrology Nurses Association
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100005526
has db xref: grid.469735.a
has db xref: ISNI: 0000 0000 9310 7210
has db xref: nlx_158371
synonym: American Nephrology Nurses'' Association
abbrev: ANNA
IAO_0000115: Non-profit professional association that represents nurses who work in all areas of nephrology including hemodialysis, chronic kidney disease, peritoneal dialysis, acute care, and transplantation. Most members work in freestanding dialysis units, hospital outpatient units, and hospital inpatient units. ANNA develops and updates standards of clinical practice, educates practitioners, stimulates and supports research, disseminates knowledge and new ideas, promotes interdisciplinary communication and cooperation, and monitors and addresses issues encompassing the breadth of practice of nephrology nursing.

American Society for Apheresis
type: Organization
type: NamedIndividual
has db xref: grid.492367.d
has db xref: ISNI: 0000 0004 0637 8282
has db xref: nlx_158372
abbrev: ASFA
IAO_0000115: An organization of physicians, scientists, and allied health professionals whose mission is to advance apheresis medicine for patients, donors and practitioners through education, evidence-based practice, research and advocacy. ASFA represents a broad range of professionals involved in: donor apheresis, apheresis in transplantation & therapeutic apheresis.

American Society of Diagnostic and Interventional Nephrology
type: Resource
type: NamedIndividual
has db xref: nlx_158373
synonym: American Society of Diagnostic & Interventional Nephrology
abbrev: ASDIN
IAO_0000115: Society that aims to promote the proper application of new and existing procedures to improve the care of patients with kidney disease. They promote education, research, public policy and clinical practice initiatives relating to diagnostic and interventional procedures. ASDIN works closely with other societies and programs to achieve its goals. All professionals involved in the care of patients with kidney disease are welcome to join and become active in the Society. Activities of the Society include: * the establishment of practice standards, * certification of physicians in specific procedures, * accreditation of training programs in specific procedures, * development of training tools and techniques, * sponsoring symposia and training courses, * and the dissemination of information through periodic meetings and through print and other media.

American Society of Pediatric Nephrology
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100009890
has db xref: grid.478432.e
has db xref: nlx_158376
abbrev: ASPN
IAO_0000115: An organization of pediatric nephrologists and affiliated health care professionals to promote optimal care for children with kidney disease through advocacy, education and research; and to disseminate advances in clinical practice and scientific investigation.

American Society of Transplantation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100005160
has db xref: grid.461608.d
has db xref: ISNI: 0000 0001 0409 3433
has db xref: nlx_158377
has db xref: Wikidata: Q4745115
abbrev: AST
IAO_0000115: An organization of transplant professionals dedicated to advancing the field of transplantation and improving patient care by promoting research, education, advocacy, and organ donation.

Anthera Pharmaceuticals
type: Organization
type: NamedIndividual
has db xref: grid.476018.c
has db xref: ISNI: 0000 0004 6016 674X
has db xref: nlx_158378
has db xref: Wikidata: Q4771754
synonym: Anthera Pharmaceuticals Inc.
abbrev: Anthera
IAO_0000115: Biopharmaceutical company focused on developing and commercializing products to treat serious diseases associated with inflammation and autoimmune diseases.

Arbor Research Collaborative for Health
type: Organization
type: NamedIndividual
has db xref: grid.413857.c
has db xref: ISNI: 0000 0004 0628 9837
has db xref: nlx_158379
synonym: University Renal Research and Education Association
synonym: URREA
abbrev: Arbor Research
IAO_0000115: A not-for-profit research organization committed to improve patient care through research that shapes medical policies and practice. In particular, they conduct health outcomes research on chronic disease and end-stage organ failure, with expertise in biostatistical analysis, clinical practice, health economics, public policy, database management and integration, and project coordination. Through research projects that are national and global in scope, their scientific collaborations provide valuable and timely information to the worldwide health care community. They are a leader in interdisciplinary health outcomes and policy research focused on reducing the health and economic burden of chronic diseases and improving the delivery of care.

Association for the Advancement of Medical Instrumentation
type: Organization
type: NamedIndividual
has db xref: grid.489418.8
has db xref: ISNI: 0000 0000 8633 8985
has db xref: nlx_158380
has db xref: Wikidata: Q4809544
abbrev: AAMI
IAO_0000115: A nonprofit organization made up of a diverse community of healthcare technology professionals that support the healthcare community in the development, management, and use of safe and effective medical technology. It is the primary source of consensus and timely information on medical instrumentation and technology. * AAMI is the primary resource for the industry, the professions, and government for national and international standards. * AAMI provides multidisciplinary leadership and programs that enhance the ability of the professions, healthcare institutions, and industry to understand, develop, manage, and use medical instrumentation and related technologies safely and effectively. * AAMI helps members: contain costs, keep informed of new technology and policy developments, add value in healthcare organizations, and improve professional skills and enhance patient care. * AAMI provides a unique and critical forum for members who cover a complete range of interests, from clinical and biomedical engineers and technicians, physicians, nurses, and hospital administrators, to educators and researchers, manufacturers, distributors, government representatives and other healthcare professionals with an interest in medical devices. * AAMI fulfills its mission through: ** continuing education, conferences ** certification of healthcare technical specialists ** the publication of technical documents, periodicals, books, software.

Baxter
type: Organization
type: NamedIndividual
has db xref: grid.487322.8
has db xref: ISNI: 0000 0000 9098 0655
has db xref: nlx_158381
has db xref: Wikidata: Q43895073
synonym: Baxter International
synonym: Baxter International Inc.
abbrev: BAX
IAO_0000115: A global healthcare company with expertise in medical devices, pharmaceuticals and biotechnology. Through its subsidiaries, they develop, manufacture and market products that save and sustain the lives of people with hemophilia, immune disorders, infectious diseases, kidney disease, trauma, and other chronic and acute medical conditions. BioScience Baxter is a manufacturer of recombinant and plasma-based proteins to treat hemophilia and other bleeding disorders; plasma-based therapies to treat immune deficiencies, alpha 1-antitrypsin deficiency, burns and shock, and other chronic and acute blood-related conditions; products for regenerative medicine, such as biosurgery products; and vaccines. Baxter''s Medical Products business manufactures products used in the delivery of fluids and drugs to patients. These include intravenous (IV) solutions and administration sets, premixed drugs and drug-reconstitution systems, IV nutrition products, infusion pumps and inhalation anesthetics. The business also provides products and services related to pharmacy compounding, drug formulation and packaging technologies. In addition, Baxter''s Medical Products business is a leader in Renal home-based therapies, such as peritoneal dialysis, and offers other products and services for people with end-stage kidney disease.

C. R. Bard
type: Organization
type: NamedIndividual
has db xref: nlx_158382
synonym: C. R. Bard Inc
synonym: C. R. Bard Inc.
synonym: C.R. Bard
synonym: C.R. Bard Inc
synonym: C.R. Bard Inc.
synonym: CR Bard
synonym: CR Bard Inc.
abbrev: BARD
abbrev: BCR
IAO_0000115: A multinational developer, manufacturer, and marketer of medical technologies specializing in the manufacture of vascular, urology, oncology and surgical specialty products. BARD pioneered the development of single-patient-use medical products for hospital procedures; today BARD is dedicated to pursuing technological innovations that offer superior clinical benefits while helping to reduce overall costs. Bard is perhaps best known for having introduced the Foley catheter. (Adapted from Wikipedia)

ChemoCentryx
type: Organization
type: NamedIndividual
has db xref: grid.452218.8
has db xref: ISNI: 0000 0004 0408 7502
has db xref: nlx_158383
synonym: ChemoCentryx Inc
synonym: ChemoCentryx Inc.
IAO_0000115: A biopharmaceutical company focused exclusively on discovering, developing and commercializing orally-administered therapeutics to treat autoimmune diseases, inflammatory disorders and cancer. Each drug candidate is a small molecule designed to target a specific chemokine or chemo-attractant receptor, thereby blocking the inflammatory response driven by that particular chemokine while leaving the rest of the immune system unaffected., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

NIF Cell Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157492
synonym: Neuroscience Information Framework (NIF) Cell Ontology
synonym: Neuroscience Information Framework Cell Ontology
abbrev: NIFCELL
IAO_0000115: Ontology for cell types from NIFSTD

JATAC
type: Resource
type: NamedIndividual
has db xref: OMICS_01055
IAO_0000115: Software program for filtering duplicate 454 sequences by comparing flowgram information.

ClinMet
type: Organization
type: NamedIndividual
has db xref: nlx_158384
synonym: Clinical Metabolomics Inc
synonym: Clinical Metabolomics Inc.
IAO_0000115: THIS RESOURCE IS OUT OF SERVICE, documented on July 23, 2021.Organization that uses metabolomics to provide pharmaceutical companies with clinically relevant and practical insight into drug response and safety for renal and cardiovascular diseases, obesity and diabetes. Their combination of skills to achieve exhaustive understanding of a disease along with detailed clinical insights, signature panel of urine-based metabolomic biomarkers, proprietary metabolomics and computational expertise will accelerate the speed and success rate of drug development. ClinMet helps drug developers to efficiently transform promising compounds into safe and effective medicines. Their efficacy and toxicity indices enable pharmaceutical companies to make better clinical trial-related decisions and provide an increased understanding of a drug''s mechanism of action.

DaVita
type: Organization
type: NamedIndividual
has db xref: nlx_158385
synonym: DaVita Healthcare Partners Inc.
synonym: DaVita Inc
synonym: DaVita Inc.
synonym: DaVita Kidney Care
synonym: DaVita.com
IAO_0000115: Healthcare company. Commercial dialysis provider with offerings that include in-center hemodialysis, in-center nocturnal dialysis, peritoneal dialysis, home hemodialysis, vascular access management, chronic kidney disease education, and renal diet assistance. Information on dialysis and chronic kidney disease, including informative articles and animated learning modules, and recipes for the dialysis diet are also available. Take advantage of their discussion forum, Find a Dialysis Center tool, DaVita GFR Calculator and more.

Dialysis Patient Citizens
type: Resource
type: NamedIndividual
has db xref: nlx_158388
abbrev: DPC
IAO_0000115: A nationwide, non-profit, patient-led organization with membership open only to dialysis and pre-dialysis patients and their families working to improve the quality of life for all dialysis patients through education and advocacy. They are dedicated to developing awareness of dialysis issues, advocating for dialysis patients, promoting favorable public policy and improving the partnership between patients and caregivers. Their policies and their mission are guided solely by their membership.

ERA-EDTA
type: Resource
type: NamedIndividual
has db xref: nlx_158389
synonym: European Renal Association - European Dialysis & Transplant Association
synonym: European Renal Association - European Dialysis and Transplant Association
IAO_0000115: An association of European kidney specialists whose objective is advancement of medical science and of clinical work in nephrology, dialysis, renal transplantation, hypertension and related subjects. They aim at providing up-to-date knowledge, exclusively based on scientific data, independent from governments'' policies and from any influence of the industry. It is registered in England and Wales, but its area of activity mainly covers Europe and the Mediterranean area.

FAST BioMedical
type: Organization
type: NamedIndividual
has db xref: grid.505053.6
has db xref: nlx_158390
IAO_0000115: A clinical stage company developing a timely, precise, and convenient method for measuring plasma volume and glomerular filtration rate (GFR). They focus on development and commercialization of a patented technology for quantifying clinically relevant parameters that have been challenging or impossible to measure in the past. The company is currently developing technology for quantifying volume status and kidney function in a clinically actionable timeframe. Their technology could have a significant impact on the treatment of patients with acute kidney injury (AKI) and chronic kidney disease (CKD).

Shire
type: Organization
type: NamedIndividual
has db xref: nlx_158391
synonym: Fibrotech Therapeutics
synonym: Shire plc
synonym: Takeda Pharmaceutical
IAO_0000115: Global specialty biopharmaceutical company that focuses on developing treatments for conditions where the impact of their medicines can make an immediate and tangible difference for patients. They provide treatments in Neuroscience, Rare Diseases, Gastrointestinal, and Internal Medicine. This might be a therapy to treat an extremely rare and life-threatening disease like Hunter syndrome or Fabry disease; or a medicine for a specialist condition like ADHD or ulcerative colitis which if not treated effectively, can dramatically affect the lives of the patient and their whole family.Shire was acquired by Takeda Pharmaceutical company on January 8, 2019.

Hospira
type: Organization
type: NamedIndividual
has db xref: nlx_158395
synonym: Hospira Inc.
IAO_0000115: American global pharmaceutical and medical device company with headquarters in Lake Forest, Illinois.Provider of injectable drugs and infusion technologies and global leader in biosimilars. From September 2015 Hospira is part of Pfizer.

Mallinckrodt Pharmaceuticals
type: Organization
type: NamedIndividual
has db xref: grid.482334.a
has db xref: ISNI: 0000 0004 4652 5312
has db xref: nlx_158397
has db xref: Wikidata: Q30273990
synonym: Mallinckrodt plc
abbrev: Mallinckrodt
IAO_0000115: An independent global pharmaceutical company that produces specialty pharmaceutical products including generic drugs and imaging agents. They manufacture and distribute products used in diagnostic procedures and in the treatment of pain and related conditions. This includes the development, manufacture and distribution of specialty pharmaceuticals, active pharmaceutical ingredients, contrast products and radiopharmaceuticals. They are the largest U.S. supplier, by prescription, of opioid pain medications and the largest U.S. supplier of the medical isotope technetium-99m. The company is among the top 10 generic pharmaceuticals manufacturers in the United States. The company is also the largest producer of bulk acetaminophen. Mallinckrodt also produces cocaine derived from the Coca-Cola coca leaves, extracted by the Stepan Company. (Adapted from Wikipedia, 10/2014)

MediBeacon
type: Organization
type: NamedIndividual
has db xref: nlx_158398
synonym: MediBeacon LLC
IAO_0000115: A commercial optical diagnostic company focused on providing clinicians with critical information to improve patient care. The Optical Renal Function Monitor (ORFM) is their first product platform and is focused on real-time, easy to use, and cost-effective monitoring of kidney function. Their non-invasive monitoring technology works in a similar fashion to pulse oximetry by using a light sensor placed on the skin. After the sensor has been placed, a proprietary biocompatible tracer is administered. The system can then monitor the patient''s real-time point-of-care kidney function. This information will allow for earlier detection of renal issues enabling clinicians to provide earlier, and hence more effective interventions. MediBeacon has created a research grade technique that is clinically applicable for real-time point-of-care Glomerular Filtration Rate measurement (mGFR). MediBeacon has invented a fluorescent tracer agent (MB-102) that is removed from the blood exclusively by the GFR mechanism of the kidneys. Together with their non-invasive detection device, this will deliver a real-time point-of-care measurement of GFR.

Medtronic
type: Organization
type: NamedIndividual
has db xref: grid.481699.b
has db xref: grid.487289.8
has db xref: nlx_17750
has db xref: nlx_158399
has db xref: SCR_010517
has db xref: Wikidata: Q30343856
synonym: Medtronic Inc.
abbrev: MDT
IAO_0000115: Medical technology company that develops and manufactures devices and therapies to treat more than 30 chronic diseases, including heart failure, Parkinson's disease, urinary incontinence, Down syndrome, obesity, chronic pain, spinal disorders, and diabetes. A Commercial healthcare organization for both patients and healthcare professionals. For professionals, it provides products, therapy and procedure solutions, and services.

Centers for Disease Control and Prevention
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100000030
has db xref: grid.416738.f
has db xref: ISNI: 0000 0001 2163 0069
has db xref: nlx_inv_1005036
has db xref: nlx_inv_1005041
has db xref: Wikidata: Q583725
synonym: Centers for Disease Control
abbrev: CDC
IAO_0000115: Government granting agency that works 24/7 to protect America from health, safety and security threats, both foreign and in the U.S. CDC Office of Financial Resources aids in achieving CDC’s mission by quickly and effectively allocating funds to where they are needed.

National Kidney Foundation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100003066
has db xref: grid.419687.5
has db xref: ISNI: 0000 0001 1958 7479
has db xref: nlx_158404
has db xref: Wikidata: Q6973913
abbrev: NKF
IAO_0000115: Organization in the U.S. dedicated to the awareness, prevention and treatment of kidney disease. Initiatives include public and professional education, kidney health screenings, research, and patient services. They publish a number of scientific journals including the American Journal of Kidney Diseases, Advances in Chronic Kidney Disease and the Journal of Renal Nutrition. The NKF also publishes the Kidney Dialysis Outcomes Quality Initiative K/DOQI, a comprehensive set of clinical practice guidelines. (Adapted from Wikipedia)

National Renal Administrators Association
type: Resource
type: NamedIndividual
has db xref: nlx_158405
abbrev: NRAA
IAO_0000115: A nonprofit organization representing dialysis facilities and centers throughout the United States. It supports members from all types of providers including freestanding, hospital-based and national chains through the weekly e-mail newsletter, Renal Watch, the Annual Meeting, periodic workshops and other meetings. NRAA members include dialysis provider companies and management consulting companies and other companies involved in the End Stage Renal Disease (ESRD) industry and supportive of the purposes of NRAA. Individuals not directly employed or otherwise involved in companies that are NRAA members may join as individual Associate Members. The purposes for which the NRAA is organized are as follows: # To provide renal administrators the opportunity for gaining continuing education, obtaining peer recognition and expanding development in the profession. # To promote and encourage education and training for renal administrators. # To recognize individuals who have done or are doing noteworthy service in the field of renal administration. # To educate the public and members of governing bodies of health care organizations to understand the issues surrounding the practice of renal administration. # To represent the professional interests of renal administrators as a national representative spokesperson for the development and implementation of public policy. # To act as a resource on local and national ESRD issues.

GS-EM
type: Resource
type: NamedIndividual
has db xref: nlx_154366
synonym: GenoSpectrum Expectation-Maximuzation
IAO_0000115: Software application (entry from Genetic Analysis Software)

NephCure Kidney International
type: Resource
type: NamedIndividual
has db xref: nlx_158406
synonym: NephCure Foundation
abbrev: NephCure
IAO_0000115: Nonprofit organization committed exclusively to support research seeking the cause of the potentially debilitating kidney disease Focal Segmental Glomerulosclerosis (FSGS) and Nephrotic Syndrome, improve treatment and find a cure. NephCure Kidney International is: * Committed to funding research around the globe that will continue to move us closer to an improved treatment and a cure. * The primary source of information on Nephrotic Syndrome and FSGS. * Leading the charge for legislative action to provide more federal funding for research into Nephrotic Syndrome and FSGS. * Working to attract researchers to this field. * Educating the public and raising awareness about Nephrotic Syndrome and FSGS.

Nephrology Nursing Certification Commission
type: Resource
type: NamedIndividual
has db xref: nlx_158407
synonym: Nephrology Nursing Certification Board
synonym: NNCB
abbrev: NNCC
IAO_0000115: Organization that established credentialing mechanisms to promote patient safety and to improve the quality of care provided to nephrology patients. There is a diversity of examinations providing the opportunity for certification at various levels of education, experience, and areas of practice within nephrology nursing. All of the certification examinations are endorsed by American Nephrology Nurses' ''' Association (ANNA). The Commission recognizes the value of education, administration, research, and clinical practice in fostering personal and professional growth and currently provides six examinations to validate clinical performance: * The Certified Dialysis Nurse examination * The Certified Dialysis LPN/LVN examination * The Certified Nephrology Nurse examination * The Certified Clinical Hemodialysis Technician * The Certified Clinical Hemodialysis Technician - Advanced * The Certified Nephrology Nurse - Nurse Practitioner

Nephropath
type: Organization
type: NamedIndividual
has db xref: nlx_158408
IAO_0000115: Commercial service interpreting renal biopsies using 14 board-certified, fellowship-trained pathologists with decades of experience. They provide doctors with a high quality, clinico-pathologic discussion by the pathologist that read the case. It is their goal to help equip doctors with the results they need to deliver the most effective patient care possible. That is why they deliver same-day biopsy results, including EM, because they know that time often has a critical effect on the outcome of many renal diseases. Nephropath also offers PLA2R serum testing and will soon be offering neuropathology services including muscle and nerve biopsy services.Nephropath is now Arkana Laboratories.

Datahub
type: Resource
type: NamedIndividual
has db xref: nlx_158409
has db xref: r3d100000028
IAO_0000115: Data management platform and data repository based on the CKAN tool for managing and publishing collections of data. It enables the user to search for data, register published datasets, create and manage groups of datasets, and get updates from datasets and groups of interest.

Genentech
type: Organization
type: NamedIndividual
has db xref: nlx_158417
synonym: F. Hoffmann-La Roche Ltd / Genentech
synonym: Genentech Inc
IAO_0000115: A biotechnology corporation that uses human genetic information to discover, develop, manufacture and commercialize medicines to treat patients with serious or life-threatening medical conditions.

Cornell University; New York; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100007231
has db xref: grid.5386.8
has db xref: ISNI:000000041936877X
has db xref: nlx_58666
has db xref: Wikidata:Q49115
synonym: Cornell University
abbrev: Cornell
IAO_0000115: Private and statutory Ivy League research university in Ithaca, New York. Founded in 1865 by Ezra Cornell and Andrew Dickson White, the university was intended to teach and make contributions in all fields of knowledge—from the classics to the sciences, and from the theoretical to the applied.

DataONE
type: Resource
type: NamedIndividual
has db xref: DOI:10.2586
has db xref: DOI:10.17616/R3101G
has db xref: DOI:10.25504/FAIRsharing.yyf78h
has db xref: nlx_158410
has db xref: r3d100010478
synonym: Data Observation Network for Earth
IAO_0000115: A distributed framework and cyberinfrastructure for open, persistent, and secure access to Earth observational data. It ensures the preservation, access, use and reuse of multi-scale, multi-discipline, and multi-national science data via three primary cyberinfrastucture elements and a broad education and outreach program. The DataONE Investigator Toolkit is a collection of software tools for finding, using, and contributing data in DataONE. DataONE currently hosts three Coordinating Nodes that provide network-wide services to enhance interoperability of the Member Nodes and support indexing and replication services. Coordinating Nodes provide a replicated catalog of Member Node holdings and make it easy for scientists to discover data wherever they reside, also enabling data repositories to make their data and services more broadly available to the international community. DataONE Coordinating Nodes are located at the University of New Mexico, the University of California Santa Barbara and at the University of Tennessee (in collaboration with Oak Ridge National Laboratory). DataONE comprises a distributed network of data centers, science networks or organizations. These organizations can expose their data within the DataONE network through the implementation of the DataONE Member Node service interface. In addition to scientific data, Member Nodes can provide computing resources, or services such as data replication, to the DataONE community.

NxStage Medical
type: Organization
type: NamedIndividual
has db xref: nlx_158411
synonym: NxStage Medical Inc
synonym: NxStage Medical Inc.
abbrev: NxStage
abbrev: NXTM
IAO_0000115: A medical device company that develops, manufactures and markets innovative dialysis systems for the treatment of end-stage renal disease, or ESRD, and acute kidney failure.

Asian Cancer Research Group
type: NamedIndividual
has db xref: nlx_158412
abbrev: ACRG
IAO_0000115: An independent, not-for-profit consortium to accelerate research, and improve treatment for patients affected with the most commonly-diagnosed cancers in Asia by generating a genomic data resource for the most prevalent cancers in Asia. ACRG is focusing its initial efforts on Asian liver, gastric and lung cancers. Goals * Generate comprehensive genomics data sets for Asia-prevalent cancers * Conduct all research under good clinical practices and in accordance with local laws * Uncover key mutations and pathways for developing targeted therapies * Discover molecular tumor classifiers for patient stratification * Discover prognostic markers to identify high-risk patients * Freely share resulting raw data with scientific community to empower researchers globally and enable development of new diagnostics and medicines * Publish data analysis results jointly in prominent scientific journals Over the next two years, Lilly, Merck and Pfizer have committed to create an extensive pharmacogenomic cancer database that will be composed of data from approximately 2,000 tissue samples from patients with lung and gastric cancer that will be made publicly available to researchers and, over time, further populated with clinical data from a longitudinal analysis of patients. Comparison of the contrasting genomic signatures of these cancers could inform new approaches to treatment. Lilly has assumed responsibility for ultimately providing the data to the research public through an open-source concept managed by Lilly' '''s Singapore research site. Moreover, Lilly, Merck and Pfizer will each provide technical and intellectual expertise. One dataset can be found at http://gigadb.org/dataset/100034

GigaDB
type: Resource
type: NamedIndividual
has db xref: DOI:10.5524
has db xref: DOI:10.17616/R3TG83
has db xref: DOI:10.25504/FAIRsharing.rcbwsf
has db xref: nlx_158413
has db xref: r3d100010692
synonym: Giga DB
synonym: GigaScience Database
IAO_0000115: Repository to host data and tools associated with articles published by GigaScience & GigaByte journals. GigaDB defines a dataset as a group of files (e.g., sequencing data, analyses, imaging files, software programs) that are related to and support an article or study. Through their association with DataCite, each dataset will be assigned a DOI that can be used as a standard citation for future use of these data in other articles by the authors and other researchers. Datasets in GigaDB all require a title that is specific to the dataset, an author list, and an abstract that provides information specific to the data included within the dataset. Detailed information about the dataset is curated by dedicated biocurators in collaboration with the article authors at the time of publication of the associated manuscript to ensure full transparency and reproducibility of all journal articles published in GigaScience and GigaByte journals.

ACTTION
type: NamedIndividual
has db xref: nlx_158414
synonym: AAACTTiON
synonym: Analgesic Anesthetic and Addiction Clinical Trial Translations Innovations Opportunities and Networks
abbrev: ACTTiON
IAO_0000115: A public-private partnership with the United States Food and Drug Administration (FDA) to identify, prioritize, sponsor, coordinate, and promote innovative activities - with a special interest in optimizing clinical trials - that will expedite the discovery and development of improved analgesic, anesthetic, and addiction medications and to more generally accelerate the development of treatments with improved efficacy and safety. This multi-year, multi-phase initiative is closely aligned with the FDA' '''s Critical Path Initiative. The key objectives of ACTTION involve initiating and supporting strategic collaborations among a broad spectrum of stakeholders - including, but not limited to, academia, the FDA and other government agencies, industry, professional organizations, patient advocacy groups, foundations, and philanthropic organizations - with the goals of sharing data and innovative thinking about the development of novel therapeutics. These strategic collaborations involve a wide range of research projects and other activities, for example, scientific workshops, consensus meetings, and in-depth analyses of clinical trial data to determine the effects of research methods on study assay sensitivity and efficiency. ACTTION launched an initiative to develop training materials for clinical trial subjects (and staff) to be used with pain rating scales and other pain-related patient reported outcomes. Once materials have been developed and evaluated, proof-of-concept trials will be conducted to test the hypothesis that patient and staff training can improve the assay sensitivity of analgesic trials.

Alzheimers Disease Genetics Consortium
type: NamedIndividual
has db xref: nlx_158415
synonym: Alzheimer''''s Disease Genetics Consortium
synonym: Alzheimer''''s Disease Genetics Consortium (ADGC)
abbrev: ADGC
IAO_0000115: Consortium to conduct genome-wide association studies (GWAS) to identify genes associated with an increased risk of developing late-onset Alzheimer' '''s disease (LOAD). The goal of the ADGC is to identify genetic variants associated with risk for AD. It plans to do this through the following collaborative goals: # Identify genes responsible for AD susceptibility # Identify AD sub-phenotype genes rate-of-progression plaque / tangle load / distribution biomarker variability # Generate a genetic data resource for the AD research community Data generated by ADGC is available at the following website: https://www.niagads.org/content/alzheimers-disease-genetics-consortium-adgc-collection

NHS Quality Indicators
type: Resource
type: NamedIndividual
has db xref: nlx_157491
abbrev: NHSQI2009
IAO_0000115: Ontology to organise a 2009 set of over 200 NHS quality indicators from different sources. Relationships between indicators, a basic set of inclusion / exclusion criteria, clinical pathway, clinical code and purpose (per 1992 Institute of Medicine, originally intended to categorise clinical guidelines) are identifies and made searchable.

Towards novel translational safety biomarkers for adverse drug toxicity
type: NamedIndividual
has db xref: nlx_158422
synonym: ADR Safety Biomarkers
synonym: Adverse Drug Reaction Research
abbrev: ADR Research
IAO_0000115: Consortium to develop novel in vitro predictive screening tools and in vivo translational models and biomarkers to improve adverse drug reaction (ADR) hazard identification. This project studies the metabolic effects of eight drugs (among which are paracetamol and diclofenac ) with known side effects in the liver. By looking into the mechanics on a level ranging from the molecule to the patient, the researchers in this project aim to find biomarkers and develop tools for the early prediction of side effects of drugs. One of the breakthroughs in the project is the discovery that a person' '''s genetic profile appears to be one of the mechanics that have an influence on the resistance to adverse drug reactions. The ability to identify adverse effects in an early stage will prevent much discomfort in patients and economic loss. Several PhD theses have been written from this project.

Alzheimers Association Research Roundtable
type: NamedIndividual
has db xref: nlx_158423
synonym: Alzheimer's Association Research Roundtable
abbrev: Research Roundtable
IAO_0000115: A consortium aiming to facilitate the development and implementation of new treatments for Alzheimer's disease by collectively addressing obstacles to research and development, clinical care and public health education. The Roundtable convenes twice each year for a two-day presentation and discussion of specific topics within Alzheimer's research. Topics are selected from a list proposed and voted on by members. Roundtable members explore a broad range of Alzheimer's science topics, including: * New data and technologies that may improve the diagnosis of Alzheimer's disease, especially in its earliest and mildest stages. * Neuropsychological testing, genetic factors, and biochemical and neuroimaging biomarkers that could contribute to an earlier and more accurate Alzheimer's diagnosis. * Lessons learned about clinical trial design that may help shape future clinical trials of drugs aimed at slowing or stopping the progression of Alzheimer's. * The pros and cons of various scales as outcomes measures of clinical trials. The outputs of Roundtable meetings are published as articles in the Alzheimer's Association's journal, Alzheimer's & Dementia. The Research Roundtable also sponsors Alzheimer's Association grants. The chosen project is named Research Roundtable Sponsored Grant and the principal investigator of the project is invited to give a progress report at a Roundtable meeting.

Lions Eye Institute for Transplant and Research
type: Resource
type: NamedIndividual
has db xref: nlx_158427
synonym: Lions Eye Institute
synonym: Lions Eye Institute for Transplant & Research
abbrev: LEITR
IAO_0000115: A nonprofit ocular research center with the largest eye bank in the world that provides eye tissue for research and transplantation to ophthalmic specialists and surgeons nationwide. They empower researchers to conduct real-time studies of healthy and diseased ocular tissue leading to a greater understanding of the events that lead to blindness. Their mission is to improve visual outcomes and quality of life for those who are blind or visually impaired through innovative ocular endeavors.

International AMD Genetics Consortium
type: Resource
type: NamedIndividual
has db xref: nlx_158429
synonym: International Age-related Macular Degeneration Genetics Consortium
abbrev: IAMDGC
IAO_0000115: Consortium aiming to identify the remaining genetic risk variants for Age-related Macular Degeneration (AMD). To increase the statistical power needed to identify genes that have small, yet significant contributions to AMD, the consortium is conducting a meta-analysis on 15 Genome Wide Association Studies (GWAS) pooled from consortium members representing over 8,000 patients with advanced AMD (dry type, neovascular, or both) and 50,000 controls. In addition to verifying known genes, the consortium identified 19 new gene variants. The genes identified in these studies function in the immune system, cholesterol transport and metabolism, and formation and maintenance of connective tissue. This study provides a nearly complete picture of genetic heritability for AMD.

JDRF Artificial Pancreas Project Consortium
type: NamedIndividual
has db xref: nlx_158431
synonym: Artificial Pancreas Project Consortium
synonym: JDRF/NIDDK Artificial Pancreas Project Consortium
abbrev: Artificial Pancreas Consortium
IAO_0000115: Consortium aiming to accelerate the development of systems for automated control of blood glucose in patients with diabetes. Consortium investigators seek to research and develop strategies, which can be commercialized, that will confer the long-term benefits of improved glycemic control by combining novel automated control algorithms and hormone therapies with continuous glucose monitors and pump devices. The field of closed-loop artificial pancreas research requires expert diabetologists partnering with expert mathematicians and engineers. Consortium investigators include endocrinologists and control theorists at research institutions in the US and in Europe. Many of the diabetes device manufacturers have also participated, providing pumps and sensors with enhanced capabilities that allow for closed-loop experiments to be performed. The goals of the consortium include: * Design, optimization, and clinical testing of multiple algorithmic approaches to closed-loop control * An in silico simulation platform, accepted by the FDA, for validating candidate closed-loop control algorithms in place of animal trials * Reusable templates for constructing the Investigational Device Exemption regulatory documents that must be approved by the FDA prior to any in-clinic, computer-assisted, closed-loop control research involving people * A modular software platform-the Artificial Pancreas System-with a protocol-independent user interface and hooks to incorporate an arbitrary control algorithm and control various continuous glucose monitors and pump devices * A secure consortium Web site with a central repository for experimental data and interfaces to submit candidate control algorithms for centralized validation and to upload or download clinical data sets * the first outpatient studies of an overnight controller * the first outpatient studies of a hypoglycemia minimization strategy * the development and testing of a modular treat-to-range closed-loop approach * multiple studies…

EORTC Clinical Trials
type: Resource
type: NamedIndividual
has db xref: nlx_158511
synonym: EORTC protocol database
synonym: European Organisation for Research and Treatment of Cancer Clinical trials
IAO_0000115: A database that contains information about EORTC (European Organisation for Research and Treatment of Cancer) clinical trials but also clinical trials from other organizations, in which EORTC has been/is participating. The protocol database may be browsed by EORTC Research Group, tumor site, treatment, or drug.

NYU Data Catalog
type: Resource
type: NamedIndividual
has db xref: nlx_158439
synonym: NYU Health Sciences Library Data Catalog
IAO_0000115: A searchable data catalog that facilitates researchers'' access to large datasets available either publicly or through institutional or individual licensing. Dataset records include information about the content of the dataset, how to access the dataset, and local experts within NYULMC and NYU to assist in the use of these datasets. The data catalog will expand to include internally generated datasets from NYULMC and NYU in the near future. Use the contact form if you are interested in submitting a dataset to the data catalog.

SeqExpress
type: Resource
type: NamedIndividual
has db xref: OMICS_01289
IAO_0000115: A cross-platform software that estimates gene/isoform expression level via mRNA-Seq data. SeqExpress exams the Sequencing bias in mRNA-Seq and correct it to get more accurate estimation.

Asia Training Consortium
type: NamedIndividual
has db xref: nlx_158433
abbrev: ATC
IAO_0000115: Consortium of pharmaceutical companies and clinical research organizations, plus one regional association, that are pooling their resources to deliver quality training courses for clinical research professionals in the Asia Pacific region. The collaborative training initiatives aim to resolve issues of redundant and duplicate trainings, less than optimal class sizes and lower than ideal training frequencies, all of which are prevalent in the region. ATC also hopes to significantly enhance the number and quality of professionals to meet the resource demands of the globalized industry. The first target audience would be clinical trial investigators and clinical trial management staff - with priorities provided to clinical trial associates, clinical trial project managers, and clinical research managers. As of 2014, 900 days of ATC courses have been taught in classrooms throughout Asia. The ATC''s Foundations of Clinical Project Management is a regularly offered in Shanghai and is available on-line in English and Mandarin.

Biomarkers Across Neurodegenerative Diseases
type: NamedIndividual
has db xref: nlx_158434
abbrev: BAND
IAO_0000115: Consortium that launched a Request for Applications (RFA) to stimulate analyses across the Alzheimer's disease (AD) and Parkinson's disease (PD) research enterprises to engage in further data analysis of existing cohorts, including, but not limited to, biomarker discovery, standardization of assays, genetic profiles, and imaging modalities. The RFA aims to build on existing momentum to leverage similar activities and increase impact across the neurodegenerative disease spectrum. It also builds on recent evidence suggesting substantial overlap between AD, PD, and other neurodegenerative diseases pathologically, but also potentially biologically. The RFA is designed to enable preliminary pilot research or proof-of-principle studies utilizing data and/or samples from two large biomarker studies, the Alzheimer's Disease Neuroimaging Initiative (ADNI) and the Parkinson's Progression Markers Initiative (PPMI), in order to garner further research support from other funding agencies. Application Deadline: March 19, 2014. Efforts under BAND include studies that: * analyze datasets to test hypotheses related to aging and neurodegenerative disorders; * seek to identify panels or pathways that may play a role in disease mechanisms, such as around inflammation; * pursue shared or disparate biochemical markers of disease risk, onset or progression; * assess potential commonalities across the disease spectrum, including around other neurological disorders such as Lewy body dementia. Recent data reported at the 2013 Alzheimer's Association's International Conference stimulated discussion in the research community about the possible cross talk between AD and PD. For example, underlying pathologies / biomarkers, such as cerebrospinal fluid (CSF) alpha-synuclein, have been measured in the sample sets collected for both diseases to help understand similarities and differences in these diseases. Furthermore, similar imaging modalities, such as MRI and PET, are being employed to interrog…

Weston Brain Institute
type: Resource
type: NamedIndividual
has db xref: nlx_158435
IAO_0000115: Canadian granting agency to address the existing translational funding gap in neurodegenerative research of the aging population with a goal of accelerating the development of therapeutics and to encourage innovation in the granting process. To achieve this they address gaps and inefficiencies in the funding market by supporting high-risk, high-reward projects independent of commercial potential, while leveraging world-class business and scientific expertise to build a fast and flexible granting process. The Weston Brain Institute is committing up to $10 million in funding across Canada, each year, through various programs and partnerships. The Weston Brain Institute has ongoing collaborative relationships with the Alzheimer's Drug Discovery Foundation - Canada, Brain Canada, the Michael J. Fox Foundation, as well as a group of scientific advisors chaired by Dr. Andres Lozano.

W. Garfield Weston Foundation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100000243
has db xref: grid.430570.5
has db xref: nlx_158436
synonym: The W. Garfield Weston Foundation
abbrev: Weston Foundation
IAO_0000115: Foundation that gives grants in Canada for the benefit of Canadians and directs its resources to specific organizations in Education, Land Conservation and Science in Canada''s North. In addition, it provides funds to further Canada''s research in neuroscience. These programs are director-initiated and the Foundation therefore does not accept applications for funding. By law, the Foundation is only able to support Canadian charities that are registered with the Canadian Revenue Agency. These charities must have a CRA charitable number and offer programs benefiting Canadians in Canada.

bioCADDIE
type: Resource
type: NamedIndividual
has db xref: nlx_158438
synonym: biomedical and healthCAre Data Discovery and Indexing Ecosystem
synonym: UCSD bioCADDIE
IAO_0000115: Project to facilitate the construction of a Data Discovery Index. The data discovery index (DDI) is to do for data what PubMed (and PubMed Central) did for the literature. Biomedical researchers and healthcare institutions should be enabled to share their data in a way that advances science and protects privacy. They will find ways to facilitate structuring, discovery, and accessing of data without requiring people to understand complex standards that only a few specialized groups can decipher. bioCADDIE will pursue the following aims: # Provide ease in finding accessible data of interest according to disease, data modality (e.g., imaging, molecular measurements), and/or demographics through simple and intuitive computer interfaces that allow quick ranking, visualization, and summarization of data resources - this requires methods for automated indexing (i.e., creation of metadata), tools that allow free text searches, accessibility tools that decode consent requirements, etc. # Assist data producers on how to publish data for maximal discoverability and assessment of impact of disseminated data through data citation networks; and # Train data producers and data users in relevant tools related to biomedical data sharing. This will be done through online resources, workshops, and dissemination of best practices through publication of articles about data discovery in different venues (a) scholarly publications, and (b) lay press news articles.

Biomarkers of Anti-TNF Treatment Efficacy in Rheumatoid Arthritis - Unresponsive Populations
type: NamedIndividual
has db xref: nlx_158440
synonym: Biomarkers of Anti-TNF- Therapy Efficacy in Rheumatoid Arthritis to Define Unresponsive Patients
synonym: Biomarkers of Anti-TNF- Therapy Efficacy in Rheumatoid Arthritis to Define Unresponsive Patients (BATTER-UP)
synonym: Biomarkers of Anti-TNF-alpha Therapy Efficacy in Rheumatoid Arthritis to Define Unresponsive Patients
abbrev: BATTER-UP
IAO_0000115: A consortium evaluating a new biomarker screening test that might help identify patients with rheumatoid arthritis (RA) who are unlikely to benefit from anti-tumor necrosis factor-alpha (TNFalpha) medications. BATTER-UP will enroll around 1,000 patients being treated by one of several marketed anti-TNF RA drugs: Enbrel, Remicade, Humira, Simponi, or Cimzia. Through data analyses and predictive response modeling, the consortium aims to better understand which patients with RA will derive the greatest benefit from TNF inhibitors. The investigators in this observational study will attempt to validate an 8-gene biomarker set based on work by Biogen Idec researchers as likely to predict anti-TNF responsiveness in patients with RA. In preliminary results, the 8-gene biomarker set predicted with 89% accuracy individuals who did not reach European League Against Rheumatism (EULAR) Disease Activity Score (DAS)-28 good response after 14 weeks of treatment. The 8 genes included in the screen are CLTB, MXRA7, CXorf52, COL4A3BP, YIPF6, FAM44A, SFRS2, and PGK1. Biological samples and clinical outcome information will be used to confirm and extend the utility of previously published biomarkers that can predict response to anti-TNF agents. These data may also generate new hypotheses for further testing. The BATTER-UP samples and data will be established as a reference set for investigation of personalized medicine in RA. The study will be a resource of DNA and other biological materials that can be investigated for biomarkers in the future as new technologies arise.

McEwen Centre for Regenerative Medicine
type: Resource
type: NamedIndividual
has db xref: nlx_158445
synonym: McEwen Center
synonym: McEwen Center for Regenerative Medicine
abbrev: McEwen Centre
IAO_0000115: Center aiming to be a catalyst for regenerative medicine by facilitating collaboration, supporting research, and promoting awareness of the field. The center includes 15 scientists at five Toronto hospitals, as well as the University of Toronto, currently working to accelerate the development of more effective treatments for conditions such as heart disease, diabetes, respiratory disease and spinal cord injury. They collaborate with many other research institutions throughout North America, Europe and the Asia / Pacific region. The research is powered by a team of recent doctoral graduates recruited from around the world that are selected through a competitive process. They are a critical tool for supporting the work of McEwen Centre, allowing them to find medical breakthroughs faster.

DanStem
type: Resource
type: NamedIndividual
has db xref: nlx_158446
synonym: Danish Center for Stem Cell Research
synonym: Danish Stem Cell Center
synonym: DanStem - The Center for Stem Cell Research
synonym: The Danish Stem Cell Center
IAO_0000115: Center consisting of 9 research groups who all address basic questions in stem cell and developmental biology with the overall aim of developing new stem cell-based therapeutic approaches for diabetes and cancer. DanStem comprises two sections: * The Novo Nordisk Foundation Section for Basic Stem Cell Biology (BasicStem) * The Section for Strategic Translational Stem Cell Research and Therapy (TransStem) DanStem was established as a result of a series of international recruitments coupled with internationally recognized research groups focused on insulin producing beta cells and cancer research already located at the University of Copenhagen. They all have well-established, international collaborations and actively participate in several international scientific consortia. DanStem is also active in training undergraduates, PhD students and postdocs.

Biomedical Diagnostics Institute
type: NamedIndividual
has db xref: nlx_158448
abbrev: BDI
IAO_0000115: An academic-business-clinical partnership that sponsors research programs focused on the development of next-generation biomedical diagnostic devices. They aim to transform healthcare by pioneering advances in the science and technology of diagnostics and by translating these advances into clinical use. Building on key scientific insights, the BDI will now apply its established capabilities to create integrated Point-of-Care solutions, which will have major impacts on diagnosing disease and sustaining human health.

Asclepia MedChem Solutions
type: Organization
type: NamedIndividual
has db xref: nlx_158536
synonym: Asclepia Outsourcing Solutions
synonym: Asclepia Outsourcing Solutions BVBA
IAO_0000115: Commercial organization that offers medicinal chemistry services and consulting consisting of the combination of structure based drug design and computational chemistry with multi-disciplinary expertise. A proven track record exists in the identification and the delivery of successful drug candidates. They offer solutions within small molecule drug discovery and outsourcing project management.

Beactica
type: Organization
type: NamedIndividual
has db xref: nlx_158537
synonym: Beactica AB
IAO_0000115: A drug discovery company utilizing its methodologies to evaluate the interaction of molecules in order to generate novel therapeutics. They offer expertise and services in the area of surface plasmon resonance (SPR) biosensor-based small molecule interaction analysis and partnerships for fragment-based lead generation using their proprietary Sprint platform.

Big Ten Cancer Research Consortium
type: Resource
type: NamedIndividual
has db xref: nlx_158452
synonym: Big Ten CRC
abbrev: BTCRC
IAO_0000115: A consortium that aims to transform cancer research through collaborative oncology trials that leverage the scientific and clinical expertise of the Big Ten universities. The goal is to align the conduct of cancer research through collaborative, hypothesis-driven, highly translational oncology trials that leverage the scientific and clinical expertise. The clinical trials that will be developed will be linked to molecular diagnostics, enabling researchers to understand what drives the cancers to grow and what might be done to stop them from growing. The consortium also leverages geographical locations and existing relationships among the cancer centers. One of the consortium's goals is to harmonize contracts and scientific review processes to expedite clinical trials. The consortium will only focus on phase 0 to II trials because larger trials - even a randomized phase II trial - are difficult to conduct at a single cancer center.

Hoosier Cancer Research Network
type: Organization
type: NamedIndividual
has db xref: grid.428706.f
has db xref: nlx_158453
has db xref: Wikidata: Q30287333
synonym: Hoosier Oncology Group
abbrev: HCRN
IAO_0000115: An independent nonprofit cancer research organization that provides full-service clinical trial management and support, from conception and study design through project completion and publication. Established to explore and develop leading edge cancer treatments across the United States and internationally, their clinical trials, developed in collaboration with academic and community oncologists, are conducted within a member network of more than 130 clinical research sites. Their vision and mission is to form unparalleled relationships between academic, community, pharmaceutical, and biotech partners with the goal of advancing cancer research, education, and patient advocacy. There are no costs to become a member.

MIT Center for Biomedical Innovation
type: NamedIndividual
has db xref: nlx_158454
synonym: Center for Biomedical Innovation
abbrev: CBI
abbrev: MIT CBI
IAO_0000115: Consortium formed to improve global health by overcoming obstacles to the development and implementation of biomedical innovation. CBI provides a safe and transparent environment for collaborative research among industry, academia, and government, and draws on the expertise of the Massachusetts Institute of Technology' '''s (MIT) Schools of Engineering, Science, and Management, as well as the Harvard-MIT Division of Health Sciences and Technology (HST). The center manages several consortia addressing a variety of challenges in the global biomedical industry by developing, testing, and disseminating new knowledge and tools designed for real world application through the following programs: the Biomanufacturing Program (BioMAN), the Consortium on Adventitious Agents in Biomanufacturing (CAACB), and New Drug Development Paradigms (NEWDIGS). The consortia managed by CBI include: * Biomanufacturing (BioMAN): a collaborative research and educational program in biotherapeutic manufacturing. The objective is to develop new knowledge, science, technologies and strategies that advance the manufacture and global delivery of high quality biopharmaceuticals. BioMAN activities bring together thought leaders from industry, the government/FDA and academia and involve faculty from across the Schools of Science, Engineering and Management at MIT * Consortium on Adventitious Agent Contamination in Biomanufacturing (CAACB): Their mission is to develop a comprehensive understanding of adventitious agents encountered in biomanufacturing, the sources of such agents, and a systematic, risk-based analysis of the most effective strategies and technologies to prevent contamination. * NEW Drug Development ParaDIGmS (NEWDIGS): focuses on transforming the current global pharmaceutical innovation ecosystem to more reliably and sustainably deliver new, better, affordable drugs to the right patients faster. System re-engineering projects are designed and executed with input from industry; regulator…

EU-ADR
type: NamedIndividual
has db xref: nlx_158456
synonym: Exploring and Understanding Adverse Drug Reactions by Integrative Mining of Clinical Records and Biomedical Knowledge
IAO_0000115: Consortium that created the capability to detect Adverse Drug Response (ADR) signals by creating the infrastructure for large-scale monitoring of drug safety using electronic health records (EHR). The platform leverages EHR' '''s comprising demographics, drug use and clinical data of over 30 million patients from several European countries. Special attention was given to patient groups that are not routinely involved in clinical trials, for ethical or practical reasons (e.g. pregnant women, elderly people, people using many drugs simultaneously, and children). This project also studies and compares a number of different techniques that all aim to detect unexpected or disproportional rates of events. The algorithms that they studied originate not only from the field of (pharmaco)epidemiology, but also from fields such as bio-terrorism, machine learning, and classical signal detection. EU-ADR specific objectives are: To detect events, To relate these events to drugs, To develop hypothesis that explain adverse events, To detect adverse events earlier, and To avoid false positives. The web-based platform is available at https://bioinformatics.ua.pt/euadr/ EU-ADR has contributed to the ability to conduct better drug safety studies based on the re-use of healthcare data. By facilitating the early detection of adverse drug reactions, but also providing key information on populations at risk, potential drug interactions, potential underlying mechanisms and intervening pathways in adverse events, etc., the project will allow for improved and more complete information to be available for drug and healthcare delivery, leading to increased patient safety and its associated cost savings. The EU-ADR system can be considered as a complementary tool to already existing pharamcovigilance systems. Should the system be widespread in the long term, it has the potential to contribute to the development of future electronic health record systems, insofar as the expected benefits of these…

International Genomics of Alzheimers Project
type: NamedIndividual
has db xref: nlx_158457
synonym: International Genomics of Alzheimer's Project
abbrev: IGAP
IAO_0000115: Consortium to discover and map the genes that contribute to Alzheimer's disease and completely understand the role inheritance plays. To achieve this goal, they will work to identify all the genes that contribute to the risk of developing this disease. Investigators will have access to combined genetic data from a large number of Alzheimer's disease subjects and compare it to genetic data from an equally large number of elderly people who do not have Alzheimer's. In the initial phase of the work, more than 20,000 people with Alzheimer's and about 20,000 healthy elderly subjects will be compared. As the study progresses, 10,000 additional people with Alzheimer's and the same number of healthy elderly subjects will be added to the study. The subjects for these studies come from different Alzheimer research project locations across Europe, the UK, the US, and Canada. Data is available from their 2014 publication in Translational Psychiatry at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3944635/ (http://www.ncbi.nlm.nih.gov/pubmed/24495969) Currently, there is no public access to the raw individual level genetic data because of privacy considerations. Researchers working with US cohorts deposit data in the database of genotypes and phenotypes (dbGaP), where it is available to all researchers who can show that they are able to guarantee the security of the data. After scanning the DNA of over 74,000 patients and controls from 15 countries, the IGAP consortium reported 11 new regions of the genome involved in late-onset Alzheimer's disease. IGAP published its results in Nature Genetics on October 27, http://www.ncbi.nlm.nih.gov/pubmed/24162737

eEnzyme LLC
type: Organization
type: NamedIndividual
has db xref: nlx_152352
IAO_0000115: An Antibody supplier

Ben-Gurion University of the Negev; Beer-Sheva; Israel
type: University
type: NamedIndividual
has db xref: nlx_156770
synonym: Ben Gurion University
synonym: Ben-Gurion University of the Negev
synonym: Ben-Gurion University of the Negev; Beersheva; Israel
abbrev: BGU
IAO_0000115: Public research university in Beersheba, Israel. Ben-Gurion University of the Negev has five campuses: the Marcus Family Campus, Beer Sheva; the David Bergmann Campus, Beer Sheva; the David Tuviyahu Campus, Beer Sheva; the Sede Boqer Campus, and Eilat Campus.

Alzheimer's Plan Foundation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100007494
has db xref: grid.478982.8
has db xref: nlx_158458
synonym: Alzheimers Plan Foundation
synonym: Fondation Plan Alzheimer
abbrev: National Institute of Health and Medical Research; Rennes; France
IAO_0000115: A non-profit registered French charity that provides a research on Alzheimer's disease and related disorders program with the following goals: * create a dynamic national and international collaborative research of the fundamental absorptions, * densify the network of public and private researchers with an attractive policy * install infrastructure basic, clinical and laboratory performing research * promote interaction with the health industries to reduce development time. At the national level the Foundation has implemented measures Research Plan, through: * animation fabric French medical and scientific research, * coordination of research initiatives * the implementation of actions, * support for specific projects. Internationally, the Foundation is at the origin of an international mobilization of researchers, initiated during the French Presidency of the European Union. Called Joint Programming, this pilot initiative involves 23 countries will coordinate their efforts at European level research on neurodegenerative diseases, especially Alzheimer's disease.

French Muscular Dystrophy Association
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100007393
has db xref: grid.453087.d
has db xref: ISNI: 0000 0000 8578 3614
has db xref: nlx_143536
synonym: A.F.M.
synonym: French Muscular Dystrophy Association (AFM)
abbrev: AFM
IAO_0000115: Disease-related portal with the objective to defeat neuromuscular diseases which are devastating muscle-wasting diseases. It has set itself two missions: curing neuromuscular diseases and reducing the disabilities they cause.

Cohorts for Heart and Aging Research in Genomic Epidemiology
type: Resource
type: NamedIndividual
has db xref: nlx_158460
abbrev: CHARGE
abbrev: CHARGE Consortium
IAO_0000115: Consortium formed to facilitate genome-wide association study meta-analyses and replication opportunities among multiple large and well-phenotyped longitudinal cohort studies. A bibliography of CHARGE publications is available. Its founding member cohorts include: * Age, Gene, Environment, Susceptibility Study -- Reykjavik * Atherosclerosis Risk in Communities Study * Cardiovascular Health Study * Framingham Heart Study * Rotterdam Study Additional core cohorts include: * Coronary Artery Risk Development in Young Adults * Family Heart Study * Health, Aging, and Body Composition Study * Jackson Heart Study * Multi-Ethnic Study of Atherosclerosis

OPKO
type: Organization
type: NamedIndividual
has db xref: grid.497542.9
has db xref: nlx_158461
has db xref: Wikidata: Q55454537
synonym: OPKO Health
synonym: OPKO Health Inc.
abbrev: OPK
IAO_0000115: A multi-national pharmaceutical and diagnostics company that develops, manufactures, and distributes an extensive array of diagnostics and therapeutics for a wide range of indications and conditions. They focus on production of cardiovascular products, vaccines, hormones, antibiotics, gastrointestinal products, and eye care. The company operates in the U.S., Chile, Israel, Mexico, Uruguay, and Spain. (Adapted from Wikipedia)

Otsuka America Pharmaceutical Inc.
type: Organization
type: NamedIndividual
has db xref: nlx_158462
synonym: Otsuka America Pharmaceutical
abbrev: OAPI
IAO_0000115: Healthcare company that oversees all pharmaceutical and medical device commercial activities of Otsuka Group (Otsuka) in North America. Products with emphasis on neuroscience, oncology, cardio-renal, and medical device markets.

Proteon Therapeutics
type: Organization
type: NamedIndividual
has db xref: nlx_158465
synonym: Proteon Therapeutics Inc.
abbrev: Proteon
IAO_0000115: A biopharmaceutical company developing pharmaceuticals for patients with renal and vascular diseases. Their ongoing Phase 3 clinical trial is evaluating whether a single treatment of PRT-201 can reduce vascular access failure, one of the most serious problems experienced by patients with chronic kidney disease (CKD) undergoing hemodialysis. PRT-201 is an investigational drug that may inhibit neointimal hyperplasia, the growth of tissue inside blood vessels that can result in vessel narrowing and reduced blood flow. PRT-201 has received fast track and orphan drug designations for hemodialysis vascular access indications.In September 2019, Proteon Therapeutics merged with ArTara Therapeutics.

Puracath Medical
type: Organization
type: NamedIndividual
has db xref: grid.488077.4
has db xref: nlx_158466
synonym: PuraCath
IAO_0000115: Company developing peritoneal dialysis disinfection system to improve quality of life for dialysis patient by reducing infections related to peritoneal dialysis (PD) and saving time through improved, simplified connection of PD catheters. While decreasing dependence on patient compliance, the goal is to keep patients well protected and healthy throughout the efficient dialysis process.

Quintiles
type: Organization
type: NamedIndividual
has db xref: nlx_158467
synonym: Quintiles Global Clinical Research Organization
synonym: Quintiles Inc.
synonym: Quintiles Transnational
IAO_0000115: Contract research organization, clinical trial services, and pharmaceutical consulting service company. Now IQVIA after merger of Quintiles and IMS Health, Inc.

Reata Pharmaceuticals
type: Organization
type: NamedIndividual
has db xref: nlx_158468
synonym: Reata Pharmaceuticals Inc.
abbrev: Reata
IAO_0000115: Pharmaceutical company focused on investigating experimental oral antioxidative and anti-inflammatory drugs, which dually activate the antioxidative transcription factor Nrf2 (Nuclear factor (erythroid-derived 2)-like 2) and inhibit the pro-inflammatory transcription factor NF-B (nuclear factor kappa-light-chain-enhancer of activated B cells). The antioxidative and anti-inflammatory compounds bardoxolone methyl and RTA 408 are the lead clinical development compounds in their portfolio.

Cancer Research UK
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100000289
has db xref: grid.11485.39
has db xref: ISNI: 0000 0004 0422 0975
has db xref: nlx_143542
has db xref: Wikidata: Q326079
abbrev: CRUK
IAO_0000115: Cancer Research UK is UK's largest charity funding cancer research. Cancer Research UK is a registered charity in England and Wales (1089464) and in Scotland (SC041666). Registered as a company limited by guarantee in England & Wales No. 4325234.

RFMRI.ORG
type: Resource
type: NamedIndividual
has db xref: nlx_158470
synonym: R-fMRI Network
synonym: R-fMRI Network (RFMRI.ORG)
synonym: The R-fMRI Network (RFMRI.ORG): A network for supporting resting-state fMRI related studies!
synonym: The R-fMRI Network - a network for supporting resting-state fMRI related studies
synonym: The R-fMRI Network - RFMRI.ORG
synonym: The R-fMRI Network a network for supporting resting-state fMRI related studies
IAO_0000115: A network for supporting resting-state fMRI (R-fMRI) related studies. It connects R-fMRI researchers (as nodes) by their sharings (as edges). Through the network, ideas, comments, resources, tools, experiences, and data can be shared. Researchers (nodes) with basic neuroscience, methodological, or clinical backgrounds can connect with each other in the network. It also contains a preprint server that allows neuroscientists to share their preprints, comment on each others research and get back valuable information about their experiments from their colleagues. This is based on the arXiv model. Ultimately, the network aims to enhance collaborations among researchers, especially to translate knowledge of basic neuroscience and methodology to clinical applications (bench to bedside).

IADRP
type: Resource
type: NamedIndividual
has db xref: nlx_158471
synonym: International Alzheimer's Disease Research Portfolio
synonym: International Alzheimers Disease Research Portfolio
IAO_0000115: Database that brings together funded Alzheimer's disease (AD) research supported by public and private organizations both in the US and abroad all categorized using the Common Alzheimer's Disease Research Ontology or CADRO. Launched as a joint collaboration between the National Institute on Aging (NIH) and the Alzheimer's Association, IADRP enables users the ability to assess the portfolios of major organizations (currently 30) for areas of overlap as well as areas of opportunities in which to collaborate and coordinate in a collective effort to advance AD research.

QuakeML
type: Resource
type: NamedIndividual
has db xref: nlx_158473
synonym: Quake ML
IAO_0000115: A flexible, extensible and modular XML-based data exchange standard for seismological data which is intended to cover a broad range of fields.

NIMH Educational Resources
type: Resource
type: NamedIndividual
has db xref: nlx_146225
synonym: National Institute of Mental Health Educational Resources
IAO_0000115: A portal to educational resources.

CADRO
type: Resource
type: NamedIndividual
has db xref: nlx_158474
synonym: Common Alzheimer''s Disease Research Ontology
synonym: Common Alzheimer's Disease Research Ontology (CADRO)
IAO_0000115: A classification system developed by the National Institute on Aging and the Alzheimer's Association that can be used to integrate and compare Alzheimer's disease (AD) research portfolios from public and private organizations supporting AD research in the US and abroad. The CADRO was constructed as a three-tier classification system organized around seven major categories: five in research and two resource-related: * Category A. Molecular Pathogenesis and Pathophysiology of Alzheimer's Disease * Category B. Diagnosis, Assessment and Disease Monitoring * Category C. Translational Research and Clinical Interventions * Category D. Epidemiology * Category E. Care, Support and Health Economics of Alzheimer's Diseases * Category F. Research Resources * Category G. Consortia and Public Private Partnerships * Category H. Alzheimer's Disease - Related Dementias Using information from project abstracts and research aims, the above categories were stratified into research topics and these were further divided into research themes. The three levels of classification are meant to enable a fine-grained portfolio analysis that can inform strategic planning and funding decisions. The CADRO was developed as a dynamic portfolio analysis tool that can be used to: (i) capture the changing landscape of AD research funded by different organizations, (ii) identify opportunities for coordination of support for AD research, and (iii) identify funding gaps as well as areas of overlap within and across organizations.

Relypsa
type: Organization
type: NamedIndividual
has db xref: nlx_158475
synonym: Relypsa Inc.
synonym: Vifor Pharma
abbrev: RLYP
IAO_0000115: Biopharmaceutical company focused on development and commercialization of non-absorbed polymeric drugs to treat disorders in areas of renal, cardiovascular and metabolic diseases.February 2021 - Relypsa changed its name to Vifor Pharma. Company is focused on development and commercialization of late stage medicines that will change treatment paradigms and improve patients lives.

Renal Physicians Association
type: Resource
type: NamedIndividual
has db xref: nlx_158476
abbrev: RPA
IAO_0000115: An association representing and serving nephrology practitioners in the United States whose members are committed to improving the care of patients with chronic kidney disease (CKD) and related disorders. RPA educates policymakers about issues that affect both patients and nephrology practices. They also work with the Centers for Medicare & Medicaid Services (CMS) on regulatory policies. (Adapted from Wikipedia) Programs focus in the areas of practice management, public policy and quality patient care. They provide timely and relevant programs along with current nephrology tools and resources to make certain members maintain their highest level of professional satisfaction.

Renal Support Network
type: Resource
type: NamedIndividual
has db xref: nlx_158479
abbrev: RSN
IAO_0000115: A nonprofit, patient-focused, patient-run organization that provides non-medical services to those affected by chronic kidney disease (CKD). RSN strives to help patients develop their personal coping skills, special talents, and employability by educating and empowering them and their family members to take control of the course and management of the disease. RSN plays a vital role in providing lawmakers and policymakers with the patient''s perspective on the needs and capabilities of people with CKD.

Rockwell Medical
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_158480
synonym: Rockwell Medical Inc.
synonym: Rockwell Medical Technologies Inc.
abbrev: RMTI
abbrev: Rockwell
IAO_0000115: A fully-integrated biopharmaceutical company targeting end-stage renal disease (ESRD) and chronic kidney disease (CKD) with products and services for the treatment of iron deficiency anemia, secondary hyperparathyroidism and hemodialysis.

Binding Site
type: Organization
type: NamedIndividual
has db xref: nlx_158482
synonym: Binding Site Group Ltd
synonym: Binding Site Inc
synonym: The Binding Site
synonym: The Binding Site Group Ltd
synonym: The Specialist Protein Company
IAO_0000115: Company provides specialist diagnostic products to clinicians and laboratory professionals worldwide. Specialist protein company committed to research, development, manufacture and distribution of immunodiagnostic assays for global laboratory market. Specialized in antibody specificity technology, Binding Site gives clinicians and laboratory staff tools to significantly improve diagnosis and management of those patients with specific cancers and immune disorders. Binding Site manufactures wide range of products for plasma protein analysis including Freelite, Hevylite and SPAplus.

Thrasos Therapeutics
type: Organization
type: NamedIndividual
has db xref: nlx_158489
synonym: Thrasos Innovation Inc.
abbrev: Thrasos
IAO_0000115: Private, clinical stage biotherapeutics company focused on delivering new solutions to individuals affected by kidney disease. They are committed to developing novel approaches to protect, treat and restore kidney function for this patient group. Company has designed specific class of peptide compounds that have shown excellent results in controlling experimental kidney diseases, notably, models of diabetic nephropathy (kidney damage associated with diabetes), and acute kidney injury. These proprietary peptides may therefore be able to prevent and treat acute kidney injury, as well as slow and possibly reverse the progression of diabetic nephropathy. They act to control apoptosis (programmed cell death), inflammation and fibrosis (formation of scar tissue).

University of Lodz; Lodz; Poland
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100005643
has db xref: grid.10789.37
has db xref: ISNI:0000 0000 9730 2769
has db xref: nlx_158123
has db xref: Wikidata:Q137503
synonym: University of Lodz
synonym: University of �d
synonym: Uniwersytet �dzki
IAO_0000115: Public research university founded in 1945 in Łódź, Poland, as a continuation of educational institutions functioning in Łódź in the interwar period — the Teacher Training Institute, the Higher School of Social and Economic Sciences and a division of the Free Polish University.

Boston University; Massachusetts; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100007161
has db xref: grid.189504.1
has db xref: ISNI:0000 0004 1936 7558
has db xref: nlx_75713
has db xref: Wikidata:Q49110
synonym: Boston University
abbrev: BU
IAO_0000115: Private research university in Boston, Massachusetts. The university is nonsectarian but maintains its historical affiliation with the United Methodist Church. It was founded in 1839 by Methodists with its original campus in Newbury, Vermont, before moving to Boston in 1867.

ProteomeXchange
type: Resource
type: NamedIndividual
has db xref: biotools:proteomexchange
has db xref: nlx_158620
has db xref: r3d100012122
synonym: Proteome Exchange
IAO_0000115: A data repository for proteomic data sets. The ProteomeExchange consortium, as a whole, aims to provide a coordinated submission of MS proteomics data to the main existing proteomics repositories, as well as to encourage optimal data dissemination. ProteomeXchange provides access to a number of public databases, and users can access and submit data sets to the consortium's PRIDE database and PASSEL/PeptideAtlas.

Vascular Access Society
type: Resource
type: NamedIndividual
has db xref: nlx_158490
abbrev: VAS
IAO_0000115: A society to raise interest in the field of hemodialysis vascular access, to promote and conduct basic and clinical research and to organize congresses, meetings and courses. The VAS is a multidisciplinary society which is of interest to nephrologists, surgeons, interventional radiologists, dialysis, nurses, vascular and radiological technologists. The VAS organizes an International Congress every two years in one of the countries in Europe. Every year a Vascular Access Course will be held in a European City. The multidisciplinary council of the VAS consists of nephrologists, surgeons and radiologists and representatives from each European country will be asked to join the board.

National Cancer Research Institute
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100008667
has db xref: grid.451262.6
has db xref: ISNI: 0000 0004 0578 6831
has db xref: nlx_143544
has db xref: Wikidata: Q6971241
synonym: NCRI - National Cancer Research Institute
abbrev: NCRI
IAO_0000115: The National Cancer Research Institute (NCRI) is a UK-wide partnership between the government, charity and industry which promotes co-operation in cancer research among the 22 member organizations for the benefit of patients, the public and the scientific community. Cancer affects everyone. One third of people in the UK get cancer at some time in their lives and a quarter of all people die from it. This means that even if we don''t have cancer ourselves, we know someone who does, or soon will.

Vascular Access Society of the Americas
type: Resource
type: NamedIndividual
has db xref: nlx_158492
abbrev: VASA
IAO_0000115: Society devoted to the advancement of the field of dialysis access through research, education and advocacy for patients with end stage kidney disease. They provide vascular access education for physicians, nurses, and other health care professionals and advocate for evidenced-based best clinical practices.

Vasculitis Foundation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100007211
has db xref: grid.453926.f
has db xref: nlx_158493
abbrev: VF
IAO_0000115: An international organization for patients with vasculitis, their families, friends and the health care professionals who care for them, supporting and empowering them through education, awareness and research. The Foundation advocates for early diagnosis and leading edge treatment for all. The Foundation also partners with researchers around the world to determine the cause and discover the cure for vasculitis.

W. L. Gore and Associates
type: Organization
type: NamedIndividual
has db xref: nlx_158494
synonym: W. L. Gore & Associates
synonym: W. L. Gore & Associates Inc.
synonym: W.L. Gore & Associates
synonym: W.L. Gore & Associates Inc.
synonym: W.L. Gore and Associates
abbrev: Gore
IAO_0000115: An American manufacturing company specializing in products derived from fluoropolymers that focuses its efforts in four main areas: electronics, fabrics, industrial and medical products.

European ScreeningPort
type: Organization
type: NamedIndividual
has db xref: nlx_158497
synonym: European Screening Port
synonym: European Screening Port GmbH
synonym: European ScreeningPort GmbH
abbrev: ESP
IAO_0000115: Commercial organization that aims to bridge the gap between academia and the life-sciences industry with a wide ranging experience in pharmaceutical industry R&D covering multiple target classes and therapeutic areas. This deep scientific insight and established links with world class research institutions is applied across their business groups: * Drug Discovery * Biomarker and Translational Research * Enabling Technologies * R&D Information Technologies They measure their performance by successful outcomes for their collaborators, and recognize that an authentic partnership approach is essential in achieving the goal of converting outstanding science into high quality starting points for new medicines.

Sierra Sensors
type: Organization
type: NamedIndividual
has db xref: nlx_158499
synonym: Sierra Sensors Biosensor Technologies
synonym: Sierra Sensors GmbH
IAO_0000115: In 2018 Bruker acquired Sierra Sensors GmbH, based in Hamburg, Germany. Sierra develops and manufactures innovative analytical biosensors based on Surface Plasmon Resonance (SPR) detection. Driven by patented technologies in the areas of SPR detection and microfluidic sample delivery, Sierra instruments are setting a new standard in high-throughput and high-performance label-free analysis.

Spike Sorting Evaluation Project
type: Resource
type: NamedIndividual
has db xref: nlx_151374
abbrev: Spikesorting Evaluation
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023.This project attempts to establish a platform for spike sorting with two different goals: First, to provide a sophisticated benchmark data set which could be used for future publications on this topic. Second, to give researchers using spike sorting software the possibility to evaluate their data under different conditions and compare their results to other spike sorters. Extracellular recordings are a standard procedure to analyzing the activity of neurons. A problem with this kind of recording is the simultaneous recording of not a single neuron but a small local population of neurons. It is not straight-forward to reconstruct the single neuronal activities. To estimate the single neuron activity (the so called spike train) from this multi neuron activity, spike sorting is applied. Many different algorithms for spike sorting were proposed. However, despite many efforts to tackle this problem, it is still difficult to tell under which circumstances which spike sorting algorithm is the best. If you are interested in some basic reading about spike sorting please consult the following references. A review of methods for spike sorting: the detection and classification of neural action potentials M. S. Lewicki (1998), Network: Computation in Neural Systems, Vol. 9, No. 4. (1998), pp. 53-78 Towards reliable spike-train recordings from thousands of neurons with multielectrodes. Einevoll GT, Franke F, Hagen E, Pouzat C, Harris KD (2011), Curr Opin Neurobiol. 2011 Oct 22.

DrugDev
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_158500
synonym: DrugDev Inc.
IAO_0000115: Organization founded to meet a growing, urgent need for streamlining clinical trials that brings together an online network of clinical trial sites, the leading investigator identification and start-up platform, the industry''s best trial optimization system, and the leading grants payment capabilities to transform the way drug developers find, engage and pay doctors to run clinical trials. Specialties include: Site Identification, Protocol Feasibility, Building Investigator Communities, Site Startup, Investigator Payments, Contracts and Essential Documents, Investigator Budget Development

Quantitative Enrichment of Sequence Tags
type: Resource
type: NamedIndividual
has db xref: biotools:quest
has db xref: OMICS_00458
synonym: Quantitative Enrichment of Sequence Tags: QuEST
abbrev: QuEST
IAO_0000115: A Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitation (ChIP-seq) experiments.

NeuroWiki
type: Resource
type: NamedIndividual
has db xref: nlx_158502
IAO_0000115: Curriculum materials for an Introduction to Neurobiology course for undergraduate and graduate students. The course focuses on the analysis of neurons and neural circuits for behavior using the fundamental principles of neuroscience. From the online course syllabus, the 24 units that make up the course may be directly accessed. Each unit contains a reading, links to at least one simulation, and a problem set. A list of all available simulations can be found here: https://neurowiki.case.edu/wiki/Simulations. * 25 simulations are written in JavaScript and will run in any browser. Source code: https://github.com/CWRUChielLab/JSNeuroSim * Pre-compiled executables (Windows, Mac, Linux) are available for 1 desktop simulation, the Nernst Potential Simulator. Source code: https://github.com/CWRUChielLab/Nernst Structure of the Course * Solving problems based on simulations of neuronal components, neurons, and simple circuits to understand how they work. * For advanced students, writing a neuroscience Wikipedia article, critical review, or grant, in stages.

Endocells
type: Organization
type: NamedIndividual
has db xref: nlx_158504
synonym: Endocells SARL
synonym: SARL Endocells
IAO_0000115: This resource no longer in service. Documented on August 12, 2021. French biotech company dedicated to human endocrine cell line production with a first focus on human pancreatic beta cell. Other cell types are being prepared like glucagon cells. The material will be powerful tools for drug discovery, toxicology and cell replacement therapy. Achievements to date * Generated tumoral and non-tumoral human beta cell lines which closely resemble human primary pancreatic beta cells (using technologies which have been first developed and validated using immortalized rat beta cell lines). World first. * Established a robust technology platform which will be used to develop other human endocrine cell lines.

ExAc
type: Resource
type: NamedIndividual
has db xref: nlx_158505
has db xref: r3d100010468
synonym: ExAC Browser
synonym: Exome Aggregation Consortium
abbrev: ExAC
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. An aggregated data platform for genome sequencing data created by a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. The data set provided on this website spans 61,486 unrelated individuals sequenced as part of various disease-specific and population genetic studies. They have removed individuals affected by severe pediatric disease, so this data set should serve as a useful reference set of allele frequencies for severe disease studies. All of the raw data from these projects have been reprocessed through the same pipeline, and jointly variant-called to increase consistency across projects. They ask that you not publish global (genome-wide) analyses of these data until after the ExAC flagship paper has been published, estimated to be in early 2015. If you''re uncertain which category your analyses fall into, please email them. The aggregation and release of summary data from the exomes collected by the Exome Aggregation Consortium has been approved by the Partners IRB (protocol 2013P001477, Genomic approaches to gene discovery in rare neuromuscular diseases).

Antibody Resource Page
type: Resource
type: NamedIndividual
has db xref: nif-0000-00222
has db xref: OMICS_01771
abbrev: ARP
IAO_0000115: A complete guide to antibody research and suppliers. Serving the scientific community since 1997, the Antibody Resource Page is a guide designed by scientists for scientists to find companies that sell catalog antibodies and custom monoclonal and polyclonal antibodies. See our other pages on antibody-related databases, software, and educational websites. If you wish to suggest or update a link, please see our FAQ.

EORTC
type: Organization
type: NamedIndividual
has db xref: grid.434691.d
has db xref: nlx_158510
has db xref: Wikidata: Q50376884
synonym: European Organisation for Research and Treatment of Cancer
synonym: European Organization for Research and Treatment of Cancer
IAO_0000115: An independent pan-European clinical research organization to improve the standards of cancer care through the multidisciplinary multinational efforts of basic scientists and clinicians. The efforts include the testing of more effective therapeutic strategies based on drugs, surgery and/or radiotherapy that are already in use. They also contribute to the development of new drugs and other approaches in partnership with the pharmaceutical industry which is accomplished mainly by conducting large, multicenter, prospective, randomized, phase III clinical trials. The EORTC Network comprises over 300 hospitals and cancer centers in over 30 countries which include some 2,500 collaborators from all disciplines involved in cancer treatment and research. The EORTC Headquarters staff handle some 6,000 new patients enrolled each year in cancer clinical trials, approximately 30 protocols that are permanently open to patient entry, over 50,000 patients who are in follow-up, and a database of more than 180,000 patients. Intergroup collaboration is also promoted to face current challenges of clinical trials aiming at targeted therapies in order to recruit a large number of patients within a reasonable period of time.

Korea Research Institute of Bioscience and Biotechnology; Daejeon; South Korea
type: NamedIndividual
has db xref: nlx_151414
synonym: Korea Research Institute of Bioscience & Biotechnology
synonym: Korea Research Institute of Bioscience & Biotechnology (KRIBB)
synonym: Korea Research Institute of Bioscience and Biotechnology
synonym: KRIBB - Korea Research Institute of Bioscience & Biotechnology
abbrev: KRIBB

PhenoSys
type: Organization
type: NamedIndividual
has db xref: nlx_158513
synonym: PhenoSys GmbH
IAO_0000115: A research- and development-oriented company based in Berlin that engineers and markets technology for animal behavior research offering unique, automated instrumentation. This includes specialized applications of virtual reality and touch screen technology for animal behavior environments and RFID (transponder) operated devices in home cage environments. Their experimental systems are used for behavioral phenotyping, brain research, experimental psychology, and the diagnostic characterization of animal models for translational medicine.

International Alliance of Patients Organizations
type: Resource
type: NamedIndividual
has db xref: nlx_158518
synonym: International Alliance of Patients'' Organizations
abbrev: IAPO
IAO_0000115: A global alliance representing patients of all nations across all disease areas and promoting patient-centered healthcare across the world. They represent people who suffer from diseases, disabilities, illnesses, impairments or syndromes and work with communities of patients to get their voices heard by all involved in healthcare. With the help of their members and collaborating organizations, they work towards patient-centered healthcare throughout the world.

Noldus
type: Organization
type: NamedIndividual
has db xref: grid.425797.a
has db xref: ISNI: 0000 0004 0444 4194
has db xref: nlx_158522
synonym: Noldus Information Technology
synonym: Noldus Information Technology BV
synonym: Noldus IT
IAO_0000115: Commercial organization that develops tools and systems for measurement and analysis of animal and human behavior. They develop instrumented home cage systems, in which rodent behavior and ultrasonic vocalizations can be measured in a non-intrusive manner. Furthermore, they develop computer vision and pattern recognition technology for automated behavior detection. They believe that this approach has significant potential in research on animal models for Autism Spectrum Disorder.

BioSci Consulting
type: Organization
type: NamedIndividual
has db xref: nlx_158523
IAO_0000115: A project manager service focused on creating progress in life science innovation. They can assist in IMI and H2020 proposal preparation, obtaining funding for Small to Medium Enterprises (SMEs), leading a consortium, and have an established network - they know who best can help you.

Assembled Chaos
type: Resource
type: NamedIndividual
has db xref: nlx_158524
IAO_0000115: Blog on how to increase your return on the effort you invest in collaboration. You''ll learn about ways you can maximize your operational efficiency and ways to increase what you get in return.

IDBS
type: Organization
type: NamedIndividual
has db xref: nlx_158525
synonym: ID Business Solutions
synonym: ID Business Solutions Limited
synonym: ID Business Solutions Ltd.
IAO_0000115: Commercial provider of advanced software and solutions that helps R&D teams make discoveries. They provide organizations with the technology they need to securely capture, manage, share and exploit structured and unstructured data. Their technology and domain expertise enables users to link data to data, data to people and people to people to drive innovation, achieve faster time to market and improve margins. Their diverse customer list includes R&D driven international companies in pharmaceuticals, biotechnology, agricultural sciences, chemicals, consumer goods, energy, engineering, food and beverage, and healthcare.

Pash 3.0
type: Resource
type: NamedIndividual
has db xref: biotools:pash
has db xref: OMICS_00586
IAO_0000115: Performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-Seq and methylome mapping by whole-genome bisulfite sequencing.

MEDINA Foundation
type: Resource
type: NamedIndividual
has db xref: nlx_158529
synonym: Fundacion MEDINA
synonym: Fundaci��n Centro de Excelencia en Investigaci��n de Medicamentos Innovadores en Andaluc��a Medina
synonym: Fundaci��n MEDINA
synonym: Fundaci��n MEDINA (Centro de Excelencia en Investigaci��n de Medicamentos Innovadores en Andalucia)
abbrev: MEDINA
IAO_0000115: A non-profit research center established through a public-private alliance between the Regional government of Andalusia, the pharmaceutical company Merck Sharp & Dohme Spain S.A. (MSD), and the University of Granada, that is focused on: # Discovery of new compounds and therapies as new leads for drug development # Contract Research Services: High throughput screening services for lead discovery, ADME/TOX, bioanalysis and metabolomics MEDINA offers 1) natural products screening services for lead discovery on therapeutic targets developed by the customers and 2) compound profiling services for their drug candidates, using a counterscreening panel designed to determine potential risks in cardiovascular safety and drug-drug interactions.

Neurophysiology Imaging Facility
type: Resource
type: NamedIndividual
has db xref: nlx_158530
synonym: Neurophysiology Imaging Facility (NIF)
abbrev: NIF
IAO_0000115: Neurophysiology imaging core facility that provides anatomical and functional MRI scanning for researchers in the National Institute of Mental Health (NIMH), the National Eye Institute (NEI), and the National Institute for Neurological Disorders and Stroke (NINDS). The shared intramural resource centers on a cutting-edge 4.7T vertical bore scanner dedicated to imaging of nonhuman primates.

Biomol-Informatics
type: Organization
type: NamedIndividual
has db xref: grid.432020.7
has db xref: nlx_158539
has db xref: Wikidata Q30254873
synonym: Biomol-Informatics SL
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 12, 2021. Technology based company in Madrid that offers consulting services on Bioinformatics in areas of research, diagnostics and pharmaceutical industry.

Inspiralis
type: Organization
type: NamedIndividual
has db xref: nlx_158540
synonym: Inspiralis Limited
synonym: Inspiralis Ltd
IAO_0000115: Commercial organization supplying topoisimerase products and services to the pharmaceutical industry and academia to aid research in the anti-infectives and anti-cancer markets. Their aim is to provide pharmaceutical companies, and others involved in drug development, with the necessary tools to develop and screen novel anti-infective and anti-cancer compounds. Products All their proteins are expressed as the native sequences without additional tags. The only exception is the M. tuberculosis gyrase which is currently produced with a C-terminal His tag. An untagged version of this protein will be available soon. * Topoisomerase Enzymes and Assay Kits * Specific Gyrase Protein Domains * DNA Substrates and Markers * Antibodies Services * Gel Based Assays * Medium / High Throughput Assay * Investigation protein DNA interaction ReDCaT chip

American Psychological Association
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100006324
has db xref: grid.280937.7
has db xref: ISNI: 0000 0001 2166 7523
has db xref: nlx_143547
has db xref: Wikidata: Q466587
abbrev: APA
IAO_0000115: Based in Washington, D.C., the American Psychological Association (APA) is a scientific and professional organization that represents psychology in the United States. With more than 154,000 members, APA is the largest association of psychologists worldwide. The mission of the APA is to advance the creation, communication and application of psychological knowledge to benefit society and improve people''s lives. The American Psychological Association aspires to excel as a valuable, effective and influential organization advancing psychology as a science, serving as: * A uniting force for the discipline * The major catalyst for the stimulation, growth and dissemination of psychological science and practice * The primary resource for all psychologists * The premier innovator in the education, development, and training of psychological scientists, practitioners and educators * The leading advocate for psychological knowledge and practice informing policy makers and the public to improve public policy and daily living * A principal leader and global partner promoting psychological knowledge and methods to facilitate the resolution of personal, societal and global challenges in diverse, multicultural and international contexts * An effective champion of the application of psychology to promote human rights, health, well being and dignity APA and its affiliate organizations provide a diverse range of scholarships, grants, and awards with the aim of advancing research in psychology. Using our specialized search tool, you can find funding by type, sponsor, topic area, recipient type, and deadline date.

KeytoLead
type: Organization
type: NamedIndividual
has db xref: nlx_158542
synonym: KeytoLead AB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 12, 2021. Commercial organization with expertise in lead generation, such as compound selection, iterative screens, fragment based lead generation (FBLG), HTS evaluation (clustering, scoring and actives selec…

Molecular Discovery
type: Organization
type: NamedIndividual
has db xref: grid.452579.8
has db xref: nlx_158543
has db xref: Wikidata: Q6895943
synonym: Molecular Discovery Ltd
synonym: Molecular Discovery Ltd.
abbrev: MD
IAO_0000115: Commercial organization providing the GRID software to scientists working on the field of drug design. All the products are based on the GRID force field, which is used in connection with experimental design and multivariate analysis tools to transform information into knowledge. The main field of application is drug discovery, property design and prediction by merging molecular modelling techniques and Quantitative structure-activity relationship (QSPR) methods into 3D-QSPR models. The same strategies can also be used in virtual screening, ADME prediction and profile and prediction of human drug metabolism, where selection or prioritization of candidates is required from large collections of compounds to minimize drug failures. Molecular Discovery offers training courses on all MD programs. Workshops and seminars on Drug Design methodologies, DMPK prediction and QSPR are also offered. Consulting agreements are also offered in research areas related with chemometrics and drug discovery. Products * GRID, a program for rational or structure-based design using molecular interaction fields * MetaSite, a program for predicting metabolic hotspots or soft spots and subsequent metabolite formation * Mass-MetaSite, a program for identifying metaoblites based on experimental LC-MSMS data * WebMetaBase, a program for storing, visualising, and data-mining the results from Mass-MetaSite * VolSurf+, a program for modelling pharmacokinetic or ADME properties * SHOP, a program for scaffold replacement * MoKa, a program for modelling pKa and tautomerisation * Pentacle, a program for 3D-QSAR (an update of Almond) * FLAP, a program for virtual screening, pharmacophore modelling, docking, water prediction, and 3D-QSAR

Factorbook
type: Resource
type: NamedIndividual
has db xref: OMICS_00533
IAO_0000115: A Wiki-based database for transcription factor-binding data generated by the ENCODE consortium.

MPS Hamburg
type: Organization
type: NamedIndividual
has db xref: nlx_158544
synonym: MPS Hamburg GmbH
abbrev: MPS
IAO_0000115: Full service Clinical Research Organization (CRO) in Hamburg, Germany, mainly focusing on phase-I and phase-IIa clinical trials. MPS owns 72 bed research clinic with 6 physicians and 15 nurses as permanent staff. MPS is experienced in performing all kind of early stage clinical trials, including first-in-man-trials, medical-devices-trials, nutraceutical and consumer-goods-trials. MPS holds active database of more than 17,000 healthy volunteers, plus hundreds of patients in special populations.

OnTarget Chemistry
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_158546
synonym: OnTarget Chemistry AB
synonym: OT Chemistry
abbrev: OTC
IAO_0000115: A chemistry contract research organization (CRO) that offers synthetic and analytical chemistry services performed by a team of predominately PhD. level chemists with pharma backgrounds. * Synthesis Services: Their main areas of expertise are in Medicinal Chemistry (SAR exploration, parallel chemistry, patent examples), synthesis of reference compounds, metabolites and labeled compounds (including radio-labeled compounds). OT Chemistry also offers drug Development Support chemistry expertise in route scouting and process optimization. * Analytical and Pre-clinical Services: They provide a wide range of analytical and pre-clinical services such as bioanalysis (non-GLP and GLP utilizing UPLC MS/MS), MTS solubility, protein binding studies, stability and degradation studies, metabolic profiling, formulation development, autoradiography and mass balance studies.

Brighton Collaboration
type: Resource
type: NamedIndividual
has db xref: nlx_158550
synonym: Brighton
abbrev: BC
IAO_0000115: A non-profit partnership and global research network providing high quality vaccine safety information. Their mission is to enhance the science of vaccine research by providing standardized, validated, and objective methods for monitoring safety profiles and benefit to risk ratios of vaccines. Products and services to promote high quality vaccine safety research include: * Standardized case definitions of adverse events following immunization * Guidelines for collection, analysis, and presentation of vaccine safety data * Template protocols for vaccine safety research * Automatic Case Classification Tool (ABC tool) * Library of vaccine safety publications * Links to high quality vaccine safety resources * Vaccine Safety Quarterly - Newsletter

EuroRec
type: Organization
type: NamedIndividual
has db xref: grid.424835.c
has db xref: nlx_158552
has db xref: Wikidata: Q17053004
synonym: European Institute for Health Records
synonym: EuroRec - European Institute for Health Records
synonym: EuroRec Institute
IAO_0000115: An independent not-for-profit organization promoting in Europe the use of high quality Electronic Health Record systems (EHRs). One of its main missions is to support, as the European authorized certification body, EHRs certification development, testing and assessment by defining functional and other criteria. EuroRec is organized as a permanent network of National ProRec centers and provides services to industry (developers and vendors), healthcare providers (buyers), policy makers and patients.

Synapse Research Management Partners
type: Organization
type: NamedIndividual
has db xref: nlx_158581
synonym: Synapse Research Management Partners S.L.
IAO_0000115: Commercial organization specialized in the high quality management of complex research and development projects in the biomedical sector. Synapse partners with national and international organizations, both public and private. Their company goes beyond classical project management and brings in added value capabilities in team management, vision management, strategic thinking and project intelligence. Synapse's expertise extends to market knowledge, business planning and valorization of research results.

PENTA-ID
type: Resource
type: NamedIndividual
has db xref: nlx_158553
synonym: Fondazione PENTA
synonym: Fondazione PENTA - for the Treatment and Care of Children with HIV-ONLUS
synonym: PENTA Foundation
IAO_0000115: A Level 1 network for pediatric infectious disease in Europe recognized by the European networks of paediatric research at the European Medicines Agency (EnprEMA) whose activities vary from clinical trials, to cohort studies and training. It is currently developing a portfolio of clinical trials in antimicrobials in children, including antibiotics, antivirals and antifungals.

Bremen Cancer Registry
type: Resource
type: NamedIndividual
has db xref: nlx_158557
synonym: Bremer Krebsregister
abbrev: BKR
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. A population based database collecting incident cases of cancer diagnosed since January 1998 in the population of the Federal state of Bremen. The Registry provides data for the analysis of * age specific time trends and geographical patterns of cancer incidence in men and women * cancer causes (e.g. work-related, environmental and personal risk factors) * epidemiological evaluation of screening programs * survival analysis of cancer patients. Since the incidence year of 2001, the Registry has a completeness level of > 95 %, based on expected values provided by the Robert Koch Institute.

Leibniz Institute for Prevention Research and Epidemiology Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_158559
IAO_0000115: Biobank that contains more than 50,000 blood, urine and saliva samples as well as tissue materials from epidemiological field studies. The samples and DNA collected in various studies are increasingly being used for the investigation of genetic, environmental and life-style associated factors in the etiology and prognosis of cancer and other chronic diseases such as obesity, diabetes and metabolic syndrome.

Korea University; Seoul; South Korea
type: Organization
type: NamedIndividual
has db xref: nlx_91872
IAO_0000115: Korea University is a private research university in Seoul, South Korea. Established in 1905, Korea University is one of the nation oldest and most prominent institutions of higher education. The student body consists of over 20,000 undergraduate students and over 10,000 graduate students. Korea University consists of the Seoul Campus, Sejong Campus and three auxiliary hospitals (Anam Hospital, Guro Hospital, Ansan Hospital).

Mouse Connectome Project
type: Resource
type: NamedIndividual
has db xref: nlx_143548
synonym: UCLA Mouse Project
abbrev: MCP
IAO_0000115: Three-dimensional digital connectome atlas of the C57Black/6J mouse brain and catalog of neural tracer injection cases, which will eventually cover the entire brain. Serial sections of each case are available to view at 10x magnification in the interactive iConnectome viewer. The Image Gallery provides a glimpse into some of the highlights of their data set. Representative images of multi-fluorescent tracer labeling can be viewed, while more in depth examination of these and all other cases can be performed in the iConnectome viewer. Phase 1 of this project involves generating a physical map of the basic global wiring diagram by applying proven, state of the art experimental circuit tracing methods systematically, uniformly, and comprehensively to the structural organization of all major neuronal pathways in the mouse brain. Connectivity imaging data for the whole mouse brain at cellular resolution will be presented within a standard 3D anatomic frame available through the website and accompanied by a comprehensive searchable online database. A Phase 2 goal for the future will allow users to view, search, and generate driving direction-like roadmaps of neuronal pathways linking any and all structures in the nervous system. This could be looked on as a pilot project for more ambitious projects in species with larger brains, such as human, and for providing a reliable framework for more detailed local circuitry mapping projects in the mouse.

UCSF Chimera
type: Resource
type: NamedIndividual
has db xref: nlx_143560
synonym: Chimera - an Extensible Molecular Modeling System
synonym: UCSF Chimera - an Extensible Molecular Modeling System
abbrev: Chimera
IAO_0000115: Software tool for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated. Chimera includes complete documentation and several tutorials.

Resource Identification Portal
type: Resource
type: NamedIndividual
has db xref: nlx_158572
synonym: Resource Identification Initiative Portal
abbrev: RII Portal
IAO_0000115: Portal providing identifiers for Antibodies, Model Organisms, and Tools (software, databases, services) created in support of the Resource Identification Initiative, which aims to promote research resource identification, discovery, and reuse. The portal offers a central location for obtaining and exploring Research Resource Identifiers (RRIDs) - persistent and unique identifiers for referencing a research resource. A critical goal of the RII is the widespread adoption of RRIDs to cite resources in the biomedical literature and other places that reference their generation or use. RRIDs use established community identifiers where they exist, and are cross-referenced in their system where more than one identifier exists for a single resource.

ECM Biosciences
type: Organization
type: NamedIndividual
has db xref: nlx_152351
synonym: ECM Biosciences LLC
IAO_0000115: An Antibody supplier

concentris research management
type: Organization
type: NamedIndividual
has db xref: nlx_158576
synonym: concentris - management for research
synonym: concentris research management gmbh
abbrev: concentris
IAO_0000115: Commercial organization specialized in the management of EU-funded research projects in the HEALTH area. They carry out the non-scientific tasks of funded research projects and provide support and consultancy services for scientists and researchers at universities, in businesses and research institutes from the first project idea to the successful completion. As the project office, it is the point of reference for funded research projects. They support you with the following services: * Fund-raising and project planning * Project management * Financial management * Conference services * Dissemination and project marketing * Training organization

Custodix
type: Organization
type: NamedIndividual
has db xref: grid.423863.8
has db xref: nlx_158577
synonym: Custodix N.V.
synonym: Custodix NV
IAO_0000115: A private limited company that specializes in data protection solutions for eHealth. They are a trusted and reliable Trusted Service Provider (TSP) in the Healthcare sector providing both consultancy and technical privacy protection solutions. Its data protection services are supported by a combination of high-level technical and legal expertise in privacy protection and e-security and a sound experience with a number of advanced e-security solutions such as PKI, VPN, Web Services security frameworks, time-stamping and more. Custodix helps businesses deal with all security and privacy related aspects of modern data management (cf. European Data Protection Directive 95/46/EC, 2001/20/EC, 2005/28/EC, the US HIPAA Privacy Rule, the WHO GCP, GPMP/ICH/135/95, ...) by offering end-to-end solutions for data protection in e-Clinical Trials, disease management and other longitudinal studies. Custodix has an international customer-base, deploying services in Europe, Asia and Australia. Customers are both commercial companies and governmental research organizations. Specialties: CATS - Custodix Anonymization Tool services, TriTob - clinical TRIal TOolBox, PIMS - Patient Identity Management System, PESF - Privacy Enhanced Storage Framework, TTPS - Trusted Third Party Services, FP7 EU Research

Kumamoto University; Kumamoto; Japan
type: NamedIndividual
has db xref: nlx_43885

Genomedics
type: Organization
type: NamedIndividual
has db xref: nlx_158578
synonym: Genomedics health care consultants
synonym: Genomedics S.r.l.
IAO_0000115: A commercial company specialized in the field of clinical governance, research and clinical-epidemiological analysis and development of services and software applications for healthcare. Products and Services * Analysis and development software solutions, web, e-learning * Design and Implementation APP for Smartphone and Tablet (iOS, Android, Windows Phone) * Clinical Intelligence & Clinical Decision Support Systems (CDSS) * Data center services and Application Server Provider * Epidemiology, Surveillance and Health Promotion - Development of studies and epidemiological research

WholeCellKB
type: Resource
type: NamedIndividual
has db xref: nlx_158579
synonym: Mycoplasma genitalium database
synonym: Whole Cell KB
synonym: WholeCellKB-MG
IAO_0000115: A collection of free, open-source model organism databases designed specifically to enable comprehensive, dynamic simulations of entire cells and organisms. WholeCellKB provides comprehensive, quantitative descriptions of individual species including: * Their subcellular organization, * Their chromosome sequences, * The essentiality, location, length, direction, and homologs of each gene, * The organization and promoter of each transcription unit, * The expression and degradation rate of each RNA gene product, * The specific folding and maturation pathway of each RNA and protein species including the localization, N-terminal cleavage, signal sequence, prosthetic groups, disulfide bonds, and chaperone interactions of each protein species, * The subunit composition of each macromolecular complex, * Their genetic code, * The binding sites and footprint of every DNA-binding protein, * The structure, charge, and hydrophobicity of every metabolite, * The stoichiometry, catalysis, coenzymes, energetics, and kinetics of every chemical reaction, * The regulatory strength of each transcription factor on each promoter, * Their chemical composition, and * The composition of its typical SP-4 laboratory growth medium. WholeCellKB currently contains a single database of Mycoplasma genitalium, an extremely small gram-positive bacterium and common human pathogen. This database is the most comprehensive description of any single organism to date, and was used to develop the first whole-cell computational model. Users can download the WholeCellKB source code and content to create and customize - including the content, data model, and user interface - their own model organism database.

PHARMO Institute
type: Organization
type: NamedIndividual
has db xref: grid.418604.f
has db xref: ISNI: 0000 0004 1786 4649
has db xref: nlx_158580
has db xref: Wikidata: Q30281788
synonym: Pharmo Cooperatie UA
synonym: PHARMO Institute for Drug Outcomes Research
abbrev: PHARMO
IAO_0000115: An independent scientific research organization dedicated to the improvement of the use, quality and cost-effectiveness of pharmaceuticals. They collect, maintain and perform research on patient-centric data to derive real-life insights for tailoring of medicines. They maintain a large and high quality database network and work closely with (inter)national medical universities and European databases. Through its studies with longitudinal and real-life patient data, they contribute to risk management, outcomes research and provides solutions for decision makers in market access, health economics and health outcomes domains. Academics from Dutch universities or research institutes are granted the opportunity to perform scientific studies using the PHARMO Database Network.

Proteome Sciences
type: Organization
type: NamedIndividual
has db xref: nlx_158582
synonym: Proteome Science
synonym: Proteome Sciences plc
abbrev: PS
IAO_0000115: Commercial company delivering content for personalized medicine in the areas of Biomarker Services, Biomarker Assays, Isobaric and Isotopic Reagents and Proprietary Biomarkers. A global leader in applied proteomics, they use high sensitivity proprietary technologies to detect biomarkers (differentially expressed proteins in diseases) and to develop rapid assays for testing. The biomarkers discovered in body fluids or tissues are validated, developed and commercialized as diagnostic, prognostic or therapeutic products through strategic alliances and out-licensing.

Pedianet
type: Resource
type: NamedIndividual
has db xref: nlx_158583
synonym: Pedianet project
IAO_0000115: Independent network and system used to collect epidemiological information for clinical research from family paediatricians in Italy. It is based on the transmission of specific data from computerised clinical files. Such data is collected anonymously by a central server in Padua, where it is validated and elaborated.

Kyoto University; Kyoto; Japan
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100005683
has db xref: grid.258799.8
has db xref: ISNI:0000 0004 0372 2033
has db xref: nlx_60798
has db xref: Wikidata:Q336264
abbrev: Kyodai
IAO_0000115: National university in Kyoto, Japan. It is the second oldest Japanese university, one of Asia highest ranked universities and one of Japan National Seven Universities.

Gnubila
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_158585
synonym: Gn??bila
synonym: Gnubila Technology
IAO_0000115: A commercial software and service company operating in Spain, France and Colombia whose main stakeholder is Indra and its main product is the G platform, on top of which they have developed several vertical applications for various industry sectors like banking, healthcare, government and SMB. Since its constitution, gn??bila has constituted an international reference in the development and deployment of Network Service Infrastructures and Platforms for Businesses, Organizations and Individuals, facilitating communication, collaboration and the coordination of applications, data and information. gn??bila Products: * Cloud Application Platform * Cloud TP Platform * Platform as a Service * Development Platform

BioAscent
type: Organization
type: NamedIndividual
has db xref: nlx_158588
synonym: BioAscent Discovery Ltd.
IAO_0000115: Commercial organization that specializes in compound management, compound logistic services, screening compound collection, and compound storage and retrieval. BioAscent enables drug discovery innovation; increasing lead finding opportunities through access to new chemical space; and providing compound management and logistics services that increase the value of existing collections.

ChemAxon
type: Organization
type: NamedIndividual
has db xref: nlx_158589
synonym: ChemAxon Kft.
synonym: ChemAxon Kutat??-Fejleszt Kft.
IAO_0000115: Commercial organization that provides cheminformatics software platforms, applications and services to optimize the value of chemistry information in life science and other R&D. This software enables structure visualization and management, property predictions and calculations, virtual synthesis, screening, clustering and drug design.

Edelris
type: Organization
type: NamedIndividual
has db xref: nlx_158590
IAO_0000115: A commercial medicinal chemistry company dedicated to the design and synthesis of natural product-mimetic screening compounds, Hit-to-Lead & Lead Optimization projects and Custom Synthesis. Aiming at the acceleration of the lead discovery and optimization process in pharma and biotech research organizations, EDELRIS uses its validated chemistry and drug discovery expertise to provide novelty to its customers with exclusive or non-exclusive small molecules and with efficient hit-to-lead optimization capabilities. EDELRIS has a wide range of services and based on its experience in various and complementary fields, the team is capable to deliver innovative solutions to synthetic and medicinal chemistry problems faced by clients.

Lead Discovery Center
type: Organization
type: NamedIndividual
has db xref: nlx_158591
synonym: Lead Discovery Center GmbH
abbrev: LDC
IAO_0000115: Commercial organization active in the field of pharmaceutical research that transforms promising early-stage projects into leads with initial proof-of-concept in animals. Focusing on small molecules, the LDC conducts drug discovery projects originating primarily from academic groups and sustains a preferred partnership with the Max Planck Society. Projects are developed in close collaboration with the project owner. LDC offers core expertise in Automation & Screening, Cellular Biology, Pharmacology and Medicinal Chemistry.

Mercachem
type: Organization
type: NamedIndividual
has db xref: nlx_158592
synonym: Mercachem B.V.
synonym: MercachemSyncom
synonym: Symeres
IAO_0000115: Privately owned European contract research organization offering innovative chemistry, medicinal chemistry and early process research services to accelerate drug discovery and development. They provide a wide range of chemical services specializing in exclusive synthetic and process chemistry services to support research and development programs of companies across the globe. Name changed to Symeres after merger of Mercachem and Syncom., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Pivot Park Screening Centre
type: Organization
type: NamedIndividual
has db xref: nlx_158593
synonym: Pivot Park Screening Center
abbrev: PPSC
IAO_0000115: Commercial organization dedicated to open innovation, providing automated cellular and biochemical in-vitro screening experiments, and ultra-High Throughput Screening (uHTS) services. The Pivot Park facilities include MSD''s former screening centre which comprise two unique robotic systems for in-vitro screening. Because the new screening centre was able to retain a significant number of the original screening staff, it offers a wealth of experience in assay development, screening and automation in a new, open setting.

DCI Tissue and Blood Procurement Shared Resource
type: Resource
type: NamedIndividual
has db xref: nlx_19619
synonym: DCI Tissue Bank
synonym: DCI Tissue Blood Procurement Shared Resource
synonym: Duke Cancer Institute Tissue and Blood Procurement Shared Resource
synonym: Duke Cancer Institute Tissue Bank
synonym: Duke Cancer Institute Tissue Blood Procurement Shared Resource
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Over 10,000 patient consents, 5,000 banking events, and 40,000 biospecimens have been processed to date with storage of both formalin fixed paraffin embedded (FFPE) tissue and frozen tissue located within multiple freezers spanning temperatures in the range of -80 degrees to -180 degrees C depending on protocol requirements. Considerable effort continues to be expended to assure compliance with IRB, NIH and HIPAA best practices and guidelines on banking human tissues. The biorepository in place today is the result of the combined efforts of the Duke Cancer Institute (DCI) Breast SPORE, DCI Shared Resource for Tissue and Blood Procurement, and the Duke University School of Medicine Research Foundation (DUSOM-RF). The DCI and the School of Medicine Research Foundation (SOMRF) have funded the collection of frozen and fixed tissues, both malignant and benign, under an ?????????????????excess tissue????????????????? protocol that utilizes freshly excised tissue that is available for research after the needs of the pathologic workup are met. This program procures tissues from many anatomic sites including breast. Recently Duke''s Institute of Genome Science & Policy (IGSP), under the direction of Drs. Geoff Ginsburg and Tom Burke, initiated a blood collection program that spans several departments and institutes. The Breast SPORE blood collection program served as the pilot for this much larger effort. The Breast SPORE tissue and blood collection effort utilizes much of the same infrastructure and personnel that are also supported by the DCI, SOMRF, and IGSP.

Sygnature Discovery
type: Organization
type: NamedIndividual
has db xref: nlx_158594
synonym: Sygnature Discovery Limited
synonym: Sygnature Discovery Ltd
synonym: Sygnature Discovery Ltd.
abbrev: Sygnature
IAO_0000115: Independent commercial provider of integrated drug discovery with core capabilities including medicinal chemistry, in vitro bioscience, computational chemistry and informatics. They also provide ADME (absorption, distribution, metabolism, and excretion), in vitro toxicology, early safety pharmacology, in vivo efficacy models, ion channel expertise, protein production and X-ray crystallography according to our clients'' specific needs, via long-term strategic alliance partners. They undertake complete drug discovery programs and hit finding, hit-to-lead and lead optimization projects.

Syncom
type: Organization
type: NamedIndividual
has db xref: nlx_158595
synonym: Symeres
synonym: Syncom BV
synonym: Syncom: Contract Research in Organic Chemistry
IAO_0000115: Independent contract research organization / small and medium sized enterprise (CRO/SME) that assists pharma and biotechnology companies with medicinal chemistry programs, providing tailor-made custom synthesis solutions. Primary activities include synthesis of key building blocks, route scouting services, process research activities, scale up, medicinal chemistry services and hit-to-lead optimization. On custom basis they also synthesize metabolites, impurities, reference standards and stable labelled compounds. Their services are backed up by state-of-the-art analytical technologies such as HPLC, GC, LC-MS, GC-MS and NMR. These technologies can be offered as stand-alone analytical services as well. Syncom also has expertise in chiral technology. The firm has designed and synthesized numerous unique scaffolds, yielding many patent applications and clinical candidates. Name changed to Symeres after merger with Mercachem., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Taros
type: Organization
type: NamedIndividual
has db xref: nlx_158596
synonym: Taros Chemicals GmbH
synonym: Taros Chemicals GmbH & Co. KG
synonym: Taros Discovery
IAO_0000115: An independent contract research company that serves the needs of pharmaceutical, chemical, agrochemical and biotech companies, operating state-of-the art lab facilities and supporting the diverse needs of its customers in efficient drug discovery, medicinal chemistry and classical synthetic chemistry. Taros'' scientists combine more than 140 years industrial organic chemistry experience and over 60 years of active drug discovery experience from big pharmas and biotechs. They have expertise across a broad range of therapeutic areas (oncology, respiratory, CNS, cardiovascular, inflammation, pain, metabolism and infectious) and in all small molecule target classes. They have developed TarosGate, a unique software suite putting cost, time and chemistry information at a Project Leader''s finger tips.

Neural-Immune Gene Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157506
abbrev: NIGO
IAO_0000115: Ontology that is a subset of GO directed for neurological and immunological systems. It was created by clipping those GO terms that are not associated to any gene in human, rat and mouse, and by clipping terms not found to be relevant to the neural and/or immune domains.

Office of Rare Diseases Research
type: Resource
type: NamedIndividual
has db xref: nlx_15860
synonym: NIH Office of Rare Diseases Research
abbrev: ORDR
IAO_0000115: Organization which develops and maintains a centralized database on rare disease clinical research supported by the NIH. It also stimulates rare disease research by supporting scientific workshops and symposia, responds to requests for information on highly technical matters and matters of public policy, provides information to the Office of the Director on matters relating to rare diseases and orphan products, and coordinates and serves as a liaison with Federal and non-Federal national and international organizations.

Digital Access to Scholarship at Harvard
type: Resource
type: NamedIndividual
has db xref: nlx_158606
abbrev: DASH
IAO_0000115: Harvard University''s central service for sharing and preserving work. In addition to the scholarly journal articles targeted by Harvard''s several open access resolutions, DASH maybe used to self-archive manuscripts and materials. DASH supports a variety of file formats, and users are encouraged to deposit related materials with manuscripts (including data, images, audio and video files, etc.) When users deposit their work in DASH, it becomes visible to colleagues around the world by virtue of metadata harvesting, Google Scholar, and other indexing services. Higher visibility leads to higher rates of citation and impact. When users post early versions of their work, before publication, they establish intellectual priority sooner. Users act in their own best interests by taking part in the University''s mission to share and preserve the knowledge produced there. Because Harvard now has a prior, non-exclusive license to faculty journal articles in schools with open access policies, those faculty members are required to act accordingly when publishing journal articles, either by attaching an addendum to their publication agreement or obtaining a waiver. They then must deposit the publication in DASH.

FlyTF.org
type: Resource
type: NamedIndividual
has db xref: OMICS_00534
synonym: FlyTF.org - The Drosophila Transcription Factor Database
abbrev: FlyTF
IAO_0000115: A database of genomic and protein data for Drosophila site-specific transcription factors.

Data Scientist Training for Librarians
type: Resource
type: NamedIndividual
has db xref: nlx_158607
synonym: Data Savvy Librarians
abbrev: DST4L
IAO_0000115: An experimental course and blog offered by the Harvard-Smithsonian Center for Astrophysics John G. Wolbach Library and the Harvard Library to train librarians to respond to the growing data needs of their communities. Data science techniques are becoming increasingly important to all fields of scholarship. In the hands-on course, librarians learn the latest tools for extracting, wrangling, storing, analyzing, and visualizing data. By experiencing the research data lifecycle themselves, librarians develop the data savvy skills that can help transform the services they offer. Material will be made available via the DST4L website as it progresses.

SHared Access Research Ecosystem
type: Resource
type: NamedIndividual
has db xref: nlx_158608
synonym: SHared Access Research Ecosystem (SHARE)
abbrev: SHARE
IAO_0000115: A higher education and research community initiative to ensure the preservation of, access to, and reuse of research outputs. SHARE will develop solutions that capitalize on the compelling interest shared by researchers, libraries, universities, funding agencies, and other key stakeholders to maximize research impact, today and in the future. SHARE aims to make the inventory of research assets more discoverable and more accessible, and to enable the research community to build upon these assets in creative and productive ways. ARL, AAU, and APLU strongly believe that ensuring broad and continuing access to research is central to the mission of higher education. Research publications, research data, other research outputs, along with their associated metadata, should be publicly accessible and available for reuse, text mining, data mining, and machine reading. This accelerates further research and discovery.

Wikigenes
type: Resource
type: NamedIndividual
has db xref: nlx_25130
synonym: WikiGenes - Evolutionary Knowledge
abbrev: WikiGenes
IAO_0000115: A wiki knowledge base for the life sciences that combines the collaborative and largely altruistic possibilities of wikis with explicit authorship. Authors are provided credit even while the knowledge can evolve via continual revision and traditional peer review into a rigorous scientific tool.

Committee on Coherence at Scale for Higher Education
type: Resource
type: NamedIndividual
has db xref: nlx_158609
synonym: Committee on Coherence at Scale
IAO_0000115: Committee to foster strategic thinking about how to more rigorously manage the transition from analog to digital in higher education to ensure the programmatic, concerted, and efficient development of large-scale projects that, if built as coherent elements of an emerging digital environment, will significantly enhance scholarly productivity and enrich teaching. The Committee will produce a blueprint for this new environment that is cost effective and sustainable by focusing on the following activities: research and analysis of key large projects and the technology requisite for their correlation; business plans necessary for a coherent, sustainable digital ecology of enormous scale in service to education and the public good; and return on investment, that is, the benefits and transformational aspects of such an undertaking.

HathiTrust
type: Resource
type: NamedIndividual
has db xref: nlx_158610
synonym: HathiTrust Digital Library
IAO_0000115: A partnership of academic and research institutions, offering a collection of millions of titles digitized from libraries around the world. Their goals are: * To build a reliable and increasingly comprehensive digital archive of library materials converted from print that is co-owned and managed by a number of academic institutions. * To dramatically improve access to these materials in ways that, first and foremost, meet the needs of the co-owning institutions. * To help preserve these important human records by creating reliable and accessible electronic representations. * To enable the digital archive to be accessible to persons who have print disabilities. * To stimulate redoubled efforts to coordinate shared storage strategies among libraries, thus reducing long-term capital and operating costs of libraries associated with the storage and care of print collections. * To create and sustain this public good in a way that mitigates the problem of free-riders. * To create a technical framework that is simultaneously responsive to members through the centralized creation of functionality and sufficiently open to the creation of tools and services not created by the central organization.

ZENODO
type: Resource
type: NamedIndividual
has db xref: DOI:10.5281
has db xref: DOI:10.17616/R3QP53
has db xref: DOI:10.25504/FAIRsharing.wy4egf
has db xref: nlx_158614
has db xref: r3d100011858
synonym: Zenodo
IAO_0000115: Repository for all research outputs from across all fields of science in any file format as well as both positive and negative results. They assign all publicly available uploads a Digital Object Identifier (DOI) to make the upload easily and uniquely citeable. They further support harvesting of all content via the OAI-PMH protocol. They promote peer-reviewed openly accessible research, and curate uploads. ZENODO allows users to create their own collection and accept or reject all uploads to it. They allow for uploading under a multitude of different licenses and access levels.

Semantic Automated Discovery and Integration
type: Resource
type: NamedIndividual
has db xref: nlx_143562
synonym: SADI - Semantic Automated Discovery and Integration
synonym: Semantic Automated Discovery and Integration (SADI)
abbrev: SADI
IAO_0000115: Framework for discovery of, and interoperability between, distributed data and analytical resources. It combines GET/POST-based Web Services with standards from the W3C Semantic Web initiative. The objective is to make it easy for data and analytical tool providers to make their resources available on the Semantic Web with minimal disruption to their usual practices. It simply defines an open set of best-practices and conventions, within the spectrum of existing standards, that allow for a high degree of semantic discoverability and interoperability between participating services.

Nutrition and Obesity Research Centers
type: Resource
type: NamedIndividual
has db xref: nlx_158684
abbrev: NORC
IAO_0000115: Portal to research centers and core facilities specifically support obesity research and better understand the relationship between health and nutrition.

IMHRO: International Mental Health Research Organization
type: Resource
type: NamedIndividual
has db xref: nlx_143563
synonym: International Mental Health Research Organization
abbrev: IMHRO
IAO_0000115: International Mental Health Research Organization (IMHRO) is a 501(c)3 organization committed to raising awareness and funding research to find preventions and cures for schizophrenia, depression and bipolar disorder within a generation. We are families and individuals whose lives have been touched by these brain diseasesand who have seen how far mental health research has come in the last decade. Contributors to IMHRO have played a major part. The $135 million they have helped to raise has funded stunning scientific discoveries to help people now and tomorrow.

3DSwap
type: Resource
type: NamedIndividual
has db xref: nlx_143564
synonym: 3D Swap
synonym: 3DSwap - Knowledgebase of proteins involved in 3D domain swapping
synonym: 3DSwap Database
synonym: 3DSwap: Knowledgebase of 3D Domain Swapping in Proteins
IAO_0000115: Curated knowledegbase of protein structures that are reported to be involved in 3-dimensional domain swapping. 3DSwap provides literature curated information and structure related information about 3D domain swapping in proteins. Information about swapping, hinge region, swapped region, extent of swapping, etc. are extracted from original research publications after extensive literature curation.

Stanford University, Center for Interdisciplinary Brain Sciences Research
type: Resource
type: NamedIndividual
has db xref: nif-0000-02075
synonym: Stanford Center for Interdisciplinary Brain Sciences Research
abbrev: CIBSR
IAO_0000115: The Center for Interdisciplinary Brain Sciences Research (CIBSR) at the Stanford University School of Medicine is dedicated to research that will improve the lives and well-being of individuals with disorders of the brain and improve knowledge of healthy brain and behavioral development. CIBSR research staff are dedicated to identifying biological and environmental risk factors, understanding disease pathophysiology and developmental outcomes, and developing new treatments for neurodevelopmental, neurogenetic and neuropsychiatric disorders of childhood onset. Our research studies are truly multi/interdisciplinary as they bring together experts from the fields of psychiatry, neurology, psychology, computer science, biostatistics and genetics to explore and seek answers for complex questions related to brain-behavior relationships. Active research at CIBSR includes: * Mutlimodal imaging of the brain utilizing anatomical and functional magnetic resonance imaging (MRI), diffusion tensor imaging (DTI) and magnetic resonance spectroscopy (MRS). * Behavioral, cognitive, and physiological assessment to address questions concerning the influence of biological and environmental factors on outcome. * The development of new biological and cognitive-behavioral treatments. * Development of brain image analysis methods and software.

Childhood Leukaemia Cell Bank
type: Resource
type: NamedIndividual
has db xref: nlx_143572
synonym: Childhood Leukemia Cell Bank
IAO_0000115: This is a facility for UK-based research into leukemia and other related disorders. The Bank contains viable cells and DNA from children diagnosed with acute leukemia. (diagnostic, treatment and relapse samples) and also HLA- typed normal cord blood donations. Samples can only be obtained from the Cell Bank for approved peer-reviewed and fully costed research projects. To view further information about the Cell Bank, or for instruction on how to apply for samples, please register.

Cleveland Clinic Genomic Medicine Biorepository
type: Resource
type: NamedIndividual
has db xref: nlx_59927
synonym: Cleveland Clinic Genomic Medicine Institute Biorepository
synonym: Cleveland Clinic GMI Biorepository
synonym: Genomic Medicine Biorepository
synonym: Genomic Medicine Institute Biorepository
synonym: GMI Biorepository
abbrev: GMB
IAO_0000115: A biorepository is a place where investigators can deposit and store biological material, in this case samples derived from patients. Moreover, the Genomic Medicine Institute (GMI) takes this basic concept and elevates it to make the Genomic Medicine Biorepository (GMB) a full-service processing and banking laboratory that serves as the foundation for evidence-based research for the GMI, the Cleveland Clinic, and our collaborators. The process relies on a team of multi-disciplinary professionals coordinating their efforts in order to streamline medical research. This begins with dedicated physicians and genetic counselors identifying individuals with specific medical conditions indicating the possibility of genetic involvement. Once identified, biological material (e.g. blood, tissue, or saliva) is collected under the care of the patient''s doctor or by our clinicians and sent to the GMB. Once in the lab, the patient and their samples are assigned a unique identifier (to protect the patient''s personal information) and logged into a central database. This unique identifier accompanies all samples processed and banked for that individual. The specimens are then processed into research-relevant samples using proven laboratory techniques and state-of-the-art quality control practices. These samples include the isolation of DNA and RNA from white blood cells for genetic studies; collection of plasma for proteomic studies; and initiated immortalized cell lines from lymphocytes for in-vitro studies and biochemical research. These cell lines are able to be indefinitely stored in cryogenic suspension and are invaluable as a renewable resource for genetic and biochemical research. The GMB also processes genetic material from various tissues (both fresh and archived). Charis Eng, MD, PhD, Chair and Director of the GMI, has been the faculty oversight person of a human biorepository for the last eight years. Since then, our biorepository has received, cataloged, processed, and …

CCLG
type: Resource
type: NamedIndividual
has db xref: nlx_143573
synonym: Children''s Cancer and Leukaemia Group
synonym: Children''s Cancer and Leukemia Group
synonym: Childrens Cancer and Leukaemia Group
synonym: Childrens Cancer and Leukemia Group
IAO_0000115: THIS RESORUCE IS NO LONGER IN SERVICE. Documented on April 27,2023. CCLG is an association of healthcare professionals involved in the treatment and care of children and younger teenagers with cancer, and underpins all the activity in pediatric oncology in the British Isles. CCLG is committed to research and development in the treatment of cancer in this age group, the ultimate goal of which is to maximize cure while minimizing the early and late side effects of treatment. Provision of information for patients and families is a core activity. The Children''s Cancer and Leukaemia Group was formed in 2006 as a result of the merger of the UK Children''s Cancer Study Group and the UK Childhood Leukaemia Working Party, both of which had been in existence since the 1970s.

Sunnybrook Tumour Bank
type: Resource
type: NamedIndividual
has db xref: nlx_16022
synonym: Sunnybrook Research Institute Tumor bank
synonym: Sunnybrook Research Institute Tumour bank
IAO_0000115: Sunnybrook Research Institute''s tumour bank provides a mechanism for the optimal collection, storage and distribution of human tissue for investigative purposes. We collect both freshly frozen and formalin-fixed paraffin-embedded tumour and normal samples, retrospectively and prospectively (informed consent and confidential consent is obtained from patients before sample collection). We offer the 1. Distribution of tissue and data to interested investigators after approval from the institutional research ethics board and 2. Collaboration with various research investigators. Our mandate is to design, implement and manage the structures and processes to ensure the timely provision of tissue samples and associated data. We are currently building bank on four disease sites: breast, prostate, colorectal, gynecological. We are also creating and maintaining a database with a tissue tracking and inventory system, using TissueMetrix software.

DataCite
type: Organization
type: NamedIndividual
has db xref: grid.475826.a
has db xref: nlx_16255
has db xref: Wikidata: Q821542
synonym: Data Cite
synonym: datacite.org
IAO_0000115: Platform for storing, finding and accessing data that provides a service for data centres to mint DOIs and store associated metadata. Their goals are to establish easier access to scientific research data on the Internet, increase acceptance of research data as legitimate, citable contributions to the scientific record and support data archiving that will permit results to be verified and re-purposed for future study. DataCite is global, with member institutions offering services and advice directly where they are needed by the researchers. While datasets are shared and accessed globally, researchers work within national funding and organizational frameworks. It therefore operates globally, with national representation. The DataCite Metadata Scheme is a list of core metadata properties chosen for the accurate and consistent identification of data for citation and retrieval purposes, along with recommended use instructions.

My Cancer Genome
type: Resource
type: NamedIndividual
has db xref: OMICS_01552
synonym: MyCancerGenome.org
abbrev: MCG
IAO_0000115: A freely available online personalized cancer medicine knowledge resource for physicians, patients, caregivers and researchers that gives up-to-date information on what mutations make cancers grow and related therapeutic implications, including available clinical trials. It is a one-stop tool that matches tumor mutations to therapies, making information accessible and convenient for busy clinicians.

Massachusetts Human Stem Cell Bank
type: Resource
type: NamedIndividual
has db xref: nlx_16360
synonym: UMass Human Stem Cell Bank and Registry
abbrev: MHSCB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 31, 2016. Stem cell research, particularly human embryonic stem cell (hESC) research, holds tremendous promise to discover therapeutic options and perhaps cures for insidious diseases such as cancer, juvenile diabetes, Alzheimer's and Parkinson's. The Massachusetts Human Stem Cell Bank provides the biomedical research community with expertly maintained human ES (hES) and reprogrammed (iPS) cell lines to facilitate studies into the properties and potential therapeutic applications of pluripotent stem cells. The Bank cultures, characterizes and distributes quality controlled hES and iPS cell lines derived in Massachusetts and beyond. The Bank is a 15,000 square foot facility that contains research and training space for visiting investigators. In addition, the Education and Training division provides technical training and programs to educate the community.

Parkinson's Disease Mouse Model Resource
type: Resource
type: NamedIndividual
has db xref: nlx_16393
abbrev: PDMMR
IAO_0000115: The Parkinson's Disease Mouse Model Resource (PDMMR) is funded by the Michael J Fox Foundation to provide genetically engineered mice and information useful for their selection and use. The resource also serves as an archive of genetically stable mouse models. The Repository distributes Parkinson's disease models that are useful for the study of the basic pathophysiology of PD, and for testing new therapies. Also available are research tool strains including transgenics that express marker genes in affected brain regions, and strains with systems for regulating gene expression (e.g. Cre recombinase and tet-inducible promoters) in specific types of neurons.

Liverpool Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_143574
synonym: Cancer Tissue Bank Research Centre
synonym: CTBRC
abbrev: LTB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. It has been incorporated with the LBIH Biobank. The Liverpool Tissue Bank (LTB) collects biological samples (tissue surplus to diagnostic requirement and blood) from patients undergoing surgery or biopsy procedure for the treatment and diagnosis of a wide variety of medical conditions. The main focus of the LTB is collecting samples from patients where cancer is a confirmed or likely diagnosis. These samples are banked to provide an invaluable resource for research groups investigating the molecular mechanisms involved in a range of medical conditions with the aim of devising new treatments and therapies. The Liverpool Tissue Bank (LTB) was formerly known as the Cancer Tissue Bank Research Centre (CTBRC) and changed to the LTB in late 2009. The Tissue Bank was established in 1991 from a charitable donation by the Candis Club, the charitable arm of Candis Magazine. It is a University of Liverpool resource located within the Department of Pathology, School of Cancer Studies. The LTB operates a cost recovery scheme where a charge is made to researchers to cover the costs involved in the collection, storage and processing of biosamples.

Ontology of Physics for Biology
type: Resource
type: NamedIndividual
has db xref: nlx_157536
abbrev: OPB
IAO_0000115: A reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms.

Dr. Donald MacLellan Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_17150
synonym: Moncton Hospital Tissue Bank
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. Part of the Surgery Program, The Moncton Hospital''s Tissue Bank is a support service that recovers, processes, stores and distributes bone for transplantation. Approximately 175 surgical bone donors and 25 cadaver donors are received by The Moncton Hospital Tissue Bank each year. The Tissue Bank consolidates the recovery, processing, testing, storage and distribution of tissues for transplantation to: * Improve the health of individuals; * Provide the required tissue to surgeons for their patients; * Provide the highest quality tissue for transplantation; * Ensure the safety, efficacy and economy in all aspects of tissue banking practice; * Ensure that the quantity and range of tissue meets the clinical demand; * Develop and use outcome measures to ensure quality and safety of tissue provided; * Contribute to the development and implementation of national standards; and * Provide a clinical support service to clinicians in order for them to help the patients achieve their optimum level of functioning. While South-East Regional Health Authority has led the province of New Brunswick in organ donation for decades, only in 2002 did the health authority officially embark on working towards achieving accreditation. In October, 2006, the American Association of Tissue Banks awarded the prestigious accreditation to the Dr. Donald MacLellan Tissue Bank, making this the sixth tissue bank in Canada to hold this achievement. This service will enable SERHA to provide better care to New Brunswicker''s in the event of a trauma or the need for reconstructive surgery.

International Anesthesia Research Society
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100008984
has db xref: grid.428880.e
has db xref: ISNI: 0000 0001 1092 7668
has db xref: nlx_17174
abbrev: IARS
IAO_0000115: The International Anesthesia Research Society is a nonpolitical, not-for-profit medical society founded in 1922 to advance and support scientific research and education related to anesthesia, and to improve patient care through basic research. The IARS contributes nearly $1 million annually to fund anesthesia research; provides a forum for anesthesiology leaders to share information and ideas; maintains a worldwide membership of more than 15,000 physicians, physician residents, and others with doctoral degrees, as well as health professionals in anesthesia-related practice; sponsors the SmartTots initiative in partnership with the FDA; and publishes the monthly Anesthesia & Analgesia journal in print and online. The IARS mission is to encourage, stimulate, and fund ongoing anesthesia-related research projects that will enhance and advance the specialty, and to disseminate current, state-of-the art, basic and clinical research data in all areas of clinical anesthesia, including perioperative medicine, critical care, and pain management. The IARS is focused solely on the advancement and support of education and scientific research related to anesthesiology. To fulfill this mission the Society publishes a monthly scientific journal, Anesthesia & Analgesia, conducts an annual clinical and scientific meeting, funds anesthesia-related research, and sponsors the SmartTots research initiative.

Sasakawa Memorial Health Foundation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100007295
has db xref: grid.481209.6
has db xref: ISNI: 0000 0004 5896 3547
has db xref: nlx_143575
abbrev: SMHF
IAO_0000115: Sasakawa Memorial Health Foundation (SMHF) was established in 1974, with Mr. Ryoichi Sasakawa, founder and first chairman of the Nippon Foundation (TNF) as President, and Professor Morizo Ishidate, father of chemotherapy of Hansen''s Disease (HD) in Japan, as chair. The principal objective of SMHF is to eliminate HD, a disease which has struck fear into human beings for millennia and stigmatized those it touched. SMHF approaches HD not only as a public health problem but also as a social and human issue. Apart from HD, the work of SMHF covers many of issues within the realm of basic health needs. In doing so SMHF has always respected the ownership by the people, of their own health related needs. SMHF believes in sharing resources and knowledge, rather than creating a situation in which the ''haves'' give to the ''have-nots''. Through this we would like to share with you the joy of working together across national borders for the benefit of people in need. Sasakawa Memorial Health Foundation provides grants to projects implemented by non-profit organizations based outside of Japan. Funding Areas: Hansen''s disease (HD), Neglected Tropical Diseases (NTDs), and Palliative Care (For Japan based Applicants Only)

OneLegacy
type: Resource
type: NamedIndividual
has db xref: nlx_17189
synonym: OneLegacy: a donate life organization
IAO_0000115: A non-profit organization dedicated to saving lives through organ and tissue donation in the seven-county greater Los Angeles area. With more than 200 hospitals, 12 transplant centers and a diverse population of 19 million, OneLegacy is the largest organ and tissue recovery organization in the world. OneLegacy saves and heals lives through organ, eye and tissue donation, comforts the families we serve, and inspires our communities to Donate Life. With each day comes a chance for people to say yes to donation and help those on the other side of the bridge, one legacy at a time.

Kyushu University; Fukuoka; Japan
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100004096
has db xref: grid.177174.3
has db xref: ISNI:0000 0001 2242 4849
has db xref: nlx_23378
has db xref: Wikidata:Q1188786
IAO_0000115: Japanese national university located in Fukuoka, in the island of Kyushu.

Arizona Biospecimen Locator
type: Resource
type: NamedIndividual
has db xref: nlx_17349
abbrev: ABL
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.

COBALT: Constraint-based Multiple Alignment Tool
type: Resource
type: NamedIndividual
has db xref: nlx_17358
synonym: Constraint-based Multiple Alignment Tool
synonym: NCBI COBALT
synonym: NCBI Constraint-based Multiple Alignment Tool
IAO_0000115: COBALT is a multiple sequence alignment tool that finds a collection of pairwise constraints derived from conserved domain database, protein motif database, and sequence similarity, using RPS-BLAST, BLASTP, and PHI-BLAST. Pairwise constraints are then incorporated into a progressive multiple alignment. A Linux executable for COBALT, and CDD and PROSITE data used is available at ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/cobalt/ COBALT has reasonable runtime performance and alignment accuracy comparable to or exceeding that of other tools for a broad range of problems.

Multiple Sclerosis Society
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100000381
has db xref: grid.453295.c
has db xref: ISNI: 0000 0001 0665 6519
has db xref: nlx_143577
has db xref: Wikidata: Q6934907
abbrev: MS Society
IAO_0000115: The UK''s leading MS charity that provides information and support, funding research and fighting for change. We''re a democratic organization: one member, one vote. We fund research, give grants, campaign for change, provide information and support, invest in MS specialists and lend a listening ear to those who need it. The UK''s biggest MS charity. * 38,000 members have a say in how we''re run. * 9000 volunteers give a million hours every year. * 550 staff work in all four nations of the UK. * Over 300 branches support people with MS locally. * One aim: to beat MS. Our national offices in England, Scotland, Wales and Northern Ireland and our network of 300 branches support people affected by MS locally.

Pathosystems Resource Integration Center
type: Resource
type: NamedIndividual
has db xref: nlx_17476
has db xref: OMICS_01658
has db xref: r3d100010142
synonym: PathoSystems Resource Integration Center
synonym: PATRIC
IAO_0000115: A Bioinformatics Resource Center bacterial bioinformatics database and analysis resource that provides researchers with an online resource that stores and integrates a variety of data types (e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data) and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. The PATRIC project includes three primary collaborators: the University of Chicago, the University of Manchester, and New City Media. The University of Chicago is providing genome annotations and a PATRIC end-user genome annotation service using their Rapid Annotation using Subsystem Technology (RAST) system. The National Centre for Text Mining (NaCTeM) at the University of Manchester is providing literature-based text mining capability and service. New City Media is providing assistance in website interface development. An FTP server and download tool are available.

BioPharma Storage Facility - Masy Systems
type: Resource
type: NamedIndividual
has db xref: nlx_17515
synonym: BioPharma Storage Facility
abbrev: BioPharma Storage
IAO_0000115: Safe and secure environmentally controlled storage for the biotech, pharmaceutical and medical device industries. Masy provides same-day retrieval and shipping of your biomaterials. Our cost-effective repository space is comprised of multiple chamber styles, from walk-in refrigerators / freezers for large containers, to single-shelf storage units for individual vials. Segregated & unsegregated storage is available. Our sophisticated inventory management system utilizes a precise bar-code inventory track-and-trace system with data safely stored on dedicated servers. Critical data access is secured by password protection. Environmental storage condition information and sample access is limited to customer approved personnel only. Our in-house Validation and Calibration teams allow us to offer unique storage conditions. And, we now offer GMP labeling and distribution of clinical samples. Masy is ISO 9001:2009 Certified and NVLAP ISO/IEC 17025:2005 Accredited. Our state-of-the-art facility is conveniently located less than an hour from Metro-Boston, just 15 minutes from the Devens Commerce Park.

Linkoping University; Linkoping; Sweden
type: University
type: NamedIndividual
has db xref: nlx_158604
synonym: Linkoping University
synonym: Linköping University
synonym: Linköpings Universitet
abbrev: LiU

Demystifying Depression
type: Resource
type: NamedIndividual
has db xref: nlx_33114
IAO_0000115: Demystifying Depression is a wiki book on depression that is downloadable as a PDF file. This book may not have been written by a doctor. The recommendations are not referenced to actual research except in a bibliography. This document should in no way serve as a substitute for medical advice. Experts are welcome to add their comments. Depression is a mood disorder, so start many descriptions of the illness. That is a gross understatement. Depression does indeed seriously affect your mood, but that is just the tip of the iceberg. A clinical depression can be an incapacitating illness, affecting your ability to perform tasks that require concentration and rendering you unable to work. By writing this document we hope to provide you with the knowledge everyone should have about their mental well-being. Depression is not an unavoidable fate. It is physical.

Brain Tumour Foundation of Canada
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100000238
has db xref: grid.478522.e
has db xref: ISNI: 0000 0004 5900 0419
has db xref: nlx_143579
synonym: Brain Tumor Foundation of Canada
IAO_0000115: Brain Tumour Foundation of Canada is a dedicated team of volunteers, patients, survivors, family members, health care professionals and staff, determined to make the journey with a brain tumor one full of hope and support. We work collaboratively to serve the needs of those Canadians affected by all types of brain tumors. Information, education and support is available and research continues into the cause of and a cure for brain tumors. Every year, thousands of Canadians affected by brain tumors find emotional support and comfort while gaining a better understanding and knowledge of their disease through a range of programs and services available across the country. This includes: up-to-date brain tumor information material, numerous education events and support groups. Important brain tumor research is also supported through annual grants, a fellowship and the brain tumour tissue bank. We welcome donations, large or small. Charitable Registration #BN118816339RR0001

CanEuCre
type: Resource
type: NamedIndividual
has db xref: nlx_143587
IAO_0000115: Cre expressing mice under the control of promoters with a design focus on the brain. Each promoter is derived from human sequence, but the resulting expression is assessed in the mouse for the activation of a LacZ reporter gene by the Cre activity. Promoters tested as large MaxiPromoters (BACs inserted into the mouse genome) and MiniPromoters (plasmid-based sequences inserted either into the mouse genome or introduced within AAV viruses). The Cre-related project continues from the Pleiades Promoter Project. Here is the list of genes for which icre/ERT2 mice are currently in development: AGTR1, CARTPT, CLDN5, CLVS2, CRH, GABRA6, HTR1A, HTR1B, KCNA4, KDM5C, MKI67, NEUROD6, NKX6-1, NOV, NPY2R, NR2E1, OLIG2, POU4F2, SLITRK6, SOX1, SOX3, SOX9,, SPRY1, VSX2

ProMPT - Prostate Cancer Mechanisms of Progression and Treatment
type: Resource
type: NamedIndividual
has db xref: nlx_18078
synonym: CamUro-Oncology Biobank
synonym: Prostate Cancer Mechanisms of Progression and Treatment
synonym: Prostate Cancer: Mechanisms of Progression and Treatment
abbrev: ProMPT
IAO_0000115: The MRC and Cancer Funders'' Forum (now National Cancer Research Institute, NCRI) established two cancer collaboratives in 2002, ProMPT and the Southern Collaborative. Their purpose was to increase the critical mass of basic and translational cancer researchers working on prostate cancer. The Collaboratives have both been successful in raising external grant income over the past 5 or 6 years and the current funding is very much geared around infrastructure to help with bio-marker development. This includes the establishment of biorepositories and tissue collections together with appropriate epidemiological and clinical information. The ProMPT collaborative is organized by Professor David Neal, Chair of Surgical Oncology in Cambridge. The other institutions include the Universities of Bristol, Manchester, Newcastle upon Tyne, Sheffield and York. The collaborative is very much working on translational aspects of prostate cancer research and has available to it a wide range of models. The Bristol group is working on epidemiological aspects and IGF, the Manchester group is working on stem cells, the Newcastle group is focused on target identification and validation and new drug development. Sheffield is working on model systems, bone metastasis and angiogenesis, York''s expertise is stem cells, structural biology and prostate specific gene targeting., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

MSG
type: Resource
type: NamedIndividual
has db xref: OMICS_01551
synonym: MSG: Multiplexed Shotgun Genotyping
synonym: Multiplexed shotgun genotyping
synonym: Multiplexed shotgun genotyping (MSG)
IAO_0000115: A pipeline of scripts to assign ancestry to genomic segments using next-gen sequence data. This method can identify recombination breakpoints in a large number of individuals simultaneously at a resolution sufficient for most mapping purposes, such as quantitative trait locus (QTL) mapping and mapping of induced mutations.

NITRC-IR
type: Resource
type: NamedIndividual
has db xref: nlx_18447
has db xref: SCR_015623
synonym: NeuroImaging Tools and Resources Collaboratory Image Repository
synonym: NITRC Image Repository
abbrev: NITRC IR
IAO_0000115: Data repository for neuroimaging data in DlCOM and NIFTI formats. It allows users to search for and freely download publicly available data sets relating to normal subjects and those with diagnoses such as: schizophrenia, ADHD, autism, and Parkinson's disease.XNAT-based image registry that supports both NIfTI and DICOM images to promote re-use and integration of NIH funded data.

InsertionMapper
type: Resource
type: NamedIndividual
has db xref: biotools:insertionmapper
has db xref: OMICS_01547
IAO_0000115: A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. It consists of four independently working modules: Data Preprocessing, Database Modeling, Dimension Deconvolution and Element Mapping. This pipeline tool is applicable to scenarios requiring analysis of the tremendous output of short reads produced in NGS sequencing experiments of targeted genome sequences.

PublicationsList.org
type: Resource
type: NamedIndividual
has db xref: nlx_18649
IAO_0000115: PublicationsList.org exists to let researchers and research organizations maintain a reliable web-based record of their academic output without any fuss. Free for individual use; subscription for additional services and institutional sites. PublicationsList.org was set up to streamline the process of maintaining a professional academic publications list online with an easy to use web front end which any researcher can use to maintain their own, professional looking list of publications, which can be hosted on publicationslist.org, or embedded within a departmental web page. Links to full text preprints, or versions in open access repositories and journal websites can be included. Publicationslist.org now offers solutions for research groups and universities to archive and disseminate their research output. The emphasis on ease of use and intuitive user interaction that appeals so much to individuals provides an effective means for organizations to gather and manage research content without having to worry about user interface design themselves. There is a built in PubMed search interface for finding publications matching your name and selecting and importing the ones you want. All the fields will be fetched automatically from MedLine, including the abstract and keywords where available. In the data entry page there is an area where you can paste an entry from the reference management software and have the form automatically populated. You can also upload a complete bibliography file to add all the papers in one go. The supported formats are: EndNote, Reference Manager, BibTeX, ProCite, US Library of Congress XML (MODS), ISI, with conversions performed by bibutils.

GenomeNet
type: Resource
type: NamedIndividual
has db xref: nlx_18770
IAO_0000115: GenomeNet is a Japanese network of database and computational services for genome research and related research areas in biomedical sciences, operated by the Kyoto University Bioinformatics Center. GenomeNet was established in September 1991 under the Human Genome Program of the then Ministry of Education, Science and Culture (Monbusho). The GenomeNet service has been developed by the Kanehisa Laboratory in Kyoto University as part of the research projects. GenomeNet is operated using the Supercomputer System of the Institute for Chemical Research, Kyoto University. LinkDB is supported by the National Bioscience Database Center of the Japan Science and Technology Agency.

PubMed Central
type: Resource
type: NamedIndividual
has db xref: nlx_18862
has db xref: OMICS_01193
abbrev: PMC
IAO_0000115: Collection of full text archive of biomedical and life sciences journal literature at U.S. National Institutes of Health National Library of Medicine (NIH/NLM). With PubMed Central, NCBI is taking lead in preserving and maintaining open access to electronic literature. Value of PubMed Central, in addition to its role as an archive, lies in what can be done when data from diverse sources is stored in common format in single repository. All articles in PMC are free (sometimes on a delayed basis). Some journals go beyond free, to Open Access.

SeWeR - SEquence analysis using WEb Resources
type: Resource
type: NamedIndividual
has db xref: biotools:sewer
has db xref: nlx_18981
synonym: SEquence analysis using WEb Resources
synonym: SeWeR
IAO_0000115: Sequence analysis using Web Resources (SeWeR) is an integrated, Dynamic HTML (DHTML) interface to commonly used bioinformatics services available on the World Wide Web. It is highly customizable, extendable, platform neutral, completely server-independent and can be hosted as a web page as well as being used as stand-alone software running within a web browser. It doesn''t require any server to host itself. The goal of SeWeR is to turn your web-browser into a powerful sequence-analysis tool. It is written entirely in JavaScript1.2. SeWeR can be downloaded and mirrored freely. The whole package is just around 300K. You can even run it from a floppy. SeWeR is not compatible with Netscape 6. SeWeR now generates graphics. Savvy is a plasmid drawing software that generates plasmid map in the revolutionary Scalable Vector Graphics format from W3C.

GeneCommittee
type: Resource
type: NamedIndividual
has db xref: OMICS_02291
abbrev: geneCommittee
IAO_0000115: Tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification. While the user can work with different gene set collections and several microarray data files to configure specific classification experiments, the tool is able to run several tests in parallel. It is able to render valuable information for diagnostic analyses and clinical management decisions based on systematically evaluating custom hypothesis over different data sets using complementary classifiers, a key aspect in clinical research.

Echelon Biosciences
type: Organization
type: NamedIndividual
has db xref: nlx_152350
synonym: Echelon Biosciences Inc.
synonym: Echelon Biosciences Incorporated
abbrev: EBI
IAO_0000115: An Antibody supplier

DOMEO
type: Resource
type: NamedIndividual
has db xref: nlx_143598
synonym: Document Metadata Organizer
synonym: Document Metadata Organizer Web Annotation Toolkit
synonym: domeo - (Document Metadata Organizer) Web Annotation Toolkit
synonym: Domeo - Web Annotation toolkit
synonym: Domeo Toolkit
synonym: SWAN annotation tool
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. The DOMEO (Document Metadata Organizer) Annotation Tool, is an extensible web component enabling users to visually and efficiently create and share ontology-based stand-off annotation metadata on HTML or XML document targets - and soon images - , using the Annotation Ontology (AO) RDF model. The tool supports manual, fully automated, and semi-automated annotation with complete provenance records, as well as personal or community annotation with access authorization and control. DOMEO is just one of the components of a bigger architecture - The Annotation Framework - that uses Annotation Ontology (AO) as communication mechanism within the platform and with the external world. Acknowledgements Special thanks to Marco Ocana for his valuable contribution in bootstrapping the DOMEO project.

British Columbia Gynaecologic Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_19753
synonym: BC Gynecologic Tissue Bank
synonym: Ovarian Cancer Research Tissue Bank
synonym: OvCaRe Tissue Bank
abbrev: BC Gynaecologic Tissue Bank
IAO_0000115: The OvCaRe Tissue Bank is housed within the Vancouver General Hospital Department of Pathology and the British Columbia Cancer Agency. This bank contains tumour samples from over 1100 patients. The tissue samples in the bank are collected from consenting patients within 30 minutes of surgical excision and stored in a variety of forms, including snap frozen, formalin fixed, and as live cells. As of 2007, serum, plasma, and buffy coat are also being collected for every case within the tissue bank. In addition to providing research material for OvCaRe researchers, the OvCaRe Tumour Bank is more active than any other tumour bank in sending samples to research collaborators and has already contributed to 43 national and international research projects. This and other tissue banks provide the foundation for translational research in medicine. In order for these samples to be used by current technologies such as Illumina whole transcriptome sequencing, the samples must be of extremely high quality. We have currently sent a selection of our samples to The Cancer Genome Atlas Project for analysis and were told by researchers there that our samples were among the best quality that they had encountered around the world. Serum Bank The OvCaRe serum bank is located at the British Columbia Cancer Agency. This bank contains over 10,000 serum samples that have been submitted for CA-125 testing as well as samples collected from patients who have consented to have their tumours submitted to the OvCaRe Tumour Bank. Like the tumour bank, these resources are available to collaborating researchers. Ovarian Cancer Tissue Microarrays The ovarian cancer tissue microarray facility from all available early ovarian cancer cases in the province for the period 1984-2000 (541 samples) was created by Dr. Blake Gilks and is the largest tissue microarray of early ovarian cancer samples. This population based series was generated in the Genetic Pathology Evaluation Center (GPEC), a laboratory support…

eBIRT
type: Resource
type: NamedIndividual
has db xref: nlx_143600
synonym: eBIRT - Biomedical Interactive Resource Tool
synonym: Electronic Biomedical Interactive Resource Tool
IAO_0000115: Venue for research resource discovery offering resource providers a platform to advertise their services and products, as well as investigators a means to locate services for their use. Search results may be refined by resource type, research area or institution.

INMEX
type: Resource
type: NamedIndividual
has db xref: biotools:inmex
has db xref: OMICS_01546
synonym: INMEX - INtegrative Meta-analysis of EXpression data
synonym: INtegrative Meta-analysis of EXpression data
IAO_0000115: A web-based tool to support meta-analysis of multiple gene-expression data sets, as well as to enable integration of data sets from gene expression and metabolomics experiments. INMEX contains three functional modules. The data preparation module supports flexible data processing, annotation and visualization of individual data sets. The statistical analysis module allows researchers to combine multiple data sets based on P-values, effect sizes, rank orders and other features. The significant genes can be examined in functional analysis module for enriched Gene Ontology terms or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, or expression profile visualization. INMEX has built-in support for common gene/metabolite identifiers (IDs), as well as 45 popular microarray platforms for human, mouse and rat. Complex operations are performed through a user-friendly web interface in a step-by-step manner.

CFC International
type: Resource
type: NamedIndividual
has db xref: nlx_20087
IAO_0000115: CFC International is a volunteer, not-for profit, self-help support group for persons and families dealing with Cardio-Facio-Cutaneous Syndrome. Incorporated in 1999 in the state of New York, its membership has grown from 21 families in mainly the USA to now include persons from all around the world. Our mission is to strive to help each other cope with the challenges of raising a child with a rare and often medically involved disorder. We act as a clearinghouse of information on all aspects of CFC Syndrome. We publish a quarterly newsletter, produce a brochure and CFC Parent' '''s Guide, private address book, host a private family computer list serve and also host a website. We host International family conferences and clinics open to families from all over the globe. Our goal is to educate the general public, the medical profession, and government agencies by disseminating information on CFC Syndrome. We work to facilitate research on this very rare syndrome. We have a medical/scientific advisory board consisting of doctors from different regions of the world who have a committed interest in our CFC children. We maintain the most extensive registry for CFC Syndrome patients in the world. The Registry provides resources for the study of CFC Syndrome. It maintains centralized information records on CFC Syndrome cases from around the world. Confidentiality of personal information regarding incidence, genetics, clinical course, and prognosis is provided to professionals and families. The Registry also serves to improve communication of ideas among interested researchers, and to assure rapid distribution of any new information that may benefit patients or their families. As part of this medical registry we are founding members of the Genetic Alliance BioBank. The BioBank contains the largest collection of DNA and tissue samples from CFC patients and their parents.

TagDust
type: Resource
type: NamedIndividual
has db xref: biotools:nexalign
has db xref: biotools:tagdust
has db xref: OMICS_01095
IAO_0000115: A program to eliminate artifactual reads from next-generation sequencing data sets.

PASS-bis
type: Resource
type: NamedIndividual
has db xref: OMICS_00587
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. A bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads.

FAIRsharing
type: Resource
type: NamedIndividual
has db xref: nlx_143602
has db xref: r3d100011250
has db xref: SCR_017615
synonym: BioSharing
IAO_0000115: Web-based, searchable portal of three interlinked registries, containing both in-house and crowdsourced manually curated descriptions of standards, databases and data policies, combined with integrated view across all three types of resource. By registering your resource on FAIRsharing, you gain credit for your work, increase its visibility outside of your direct domain, reduce potential for unnecessary reinvention and proliferation of standards and databases.

UniLib
type: Resource
type: NamedIndividual
has db xref: nlx_20445
synonym: Unified Library Database
synonym: UNILIB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016. The Unified Library Database, or UniLib, takes a library-level view of the EST and SAGE libraries present in NCBI's dbEST, UniGene and SAGEmap resources. This database was initially developed by NCBI in order to track and annotate libraries being generated by NCI's CGAP project. The query bar of the UniLib Library browser provides the most friendly way to navigate through these libraries. When matches to the Library browser query are returned as summaries, full library records can be retrieved through the linked Record retriever.

Friedrich Miescher Institute
type: Organization
type: NamedIndividual
has db xref: grid.482245.d
has db xref: ISNI: 0000 0001 2110 3787
has db xref: nlx_143605
synonym: Friedrich Miescher Institute for Biomedical Research
abbrev: FMI
IAO_0000115: The Friedrich Miescher Institute is devoted to fundamental biomedical research aimed at understanding the basic molecular mechanisms of health and disease. We communicate and patent our findings to enable their translation into medical application. The FMI focuses on the fields of Epigenetics, Signaling & Cancer, and Neurobiology. In these fields, the FMI has gained international recognition as a center of excellence in innovative biomedical research. Training young scientists The Friedrich Miescher Institute contributes to the training of graduate students and postdoctoral fellows. Through its PhD program, which was established as early as 1970, the FMI attracts top international students. The FMI is affiliated with the University of Basel, where most of the graduate students are enrolled and where it contributes to the teaching program. Many FMI alumni have gone on to pursue successful careers in Novartis, in other pharmaceutical companies, or in academic research. Exciting environment for academic and applied research Staff at FMI benefit from a unique scientific environment, allowing researchers, specialists and students to pursue questions that yield new scientific insights. As part of the Novartis Research Foundation, the FMI receives strong core support from the foundation. Funding is supplemented by competitive fellowships and awards from national and international funding agencies. This provides an optimal environment for both academic and applied biomedical research.

NIH Topic Maps - A Topic Database of NIH Funded Grants
type: Resource
type: NamedIndividual
has db xref: nlx_20595
synonym: NIH Map Viewer
synonym: NIH Maps
IAO_0000115: There is a great demand for practical tools that enable scientists to understand the organization of the fields of research of interest to them. This project is an ''unofficial'' (i.e., non-supported by NIH itself) web-based system that helps researchers understand the ''funding landscape'' of a particular field through the use of statistical analysis of the language used in grant applications'' abstracts. Our system is available at https://app.nihmaps.org/, providing both a query- and mapping- based interface for funded NIH-grants from 2007-2010. From its conception, this project has been a highly collaborative team effort. The project''s main driving force has been provided by Ned Talley but has involved ideas, technical support, academic contributions and funding from multiple sources and people.

Wellcome Images
type: Resource
type: NamedIndividual
has db xref: nlx_143611
has db xref: r3d100010779
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023.Digital collection of images, with themes ranging from medical and social history to contemporary healthcare and biomedical science. The collection contains historical images from the Wellcome Library collections, Tibetan Buddhist paintings, ancient Sanskrit manuscripts written on palm leaves, beautifully illuminated Persian books and much more. The Biomedical Collection holds over 40 000 high-quality images from the clinical and biomedical sciences. Selected from the UK''s leading teaching hospitals and research institutions, it covers disease, surgery, general healthcare, sciences from genetics to neuroscience including the full range of imaging techniques. They are always looking for new high quality biomedical images from scientific researchers, clinical photographers and artists in any field of science or medicine. As a contributor you retain your original material and copyright, and receive commission and full credit each time your images are used. The annual Wellcome Images awards (previously known as Biomedical Images Awards) reward contributors for their outstanding work and winners are chosen by a panel of experts. The resulting public exhibitions are always extremely popular and receive widespread acclaim. All images on the Wellcome Images site are available free for use in: * private study and non-commercial research * examination papers * criticism and review, this applies only where there are no multiple copies made * theses submitted by a student at a higher or further education institution for the purposes of securing a degree * personal use by private individuals

bioPIXIE
type: Resource
type: NamedIndividual
has db xref: nlx_20893
synonym: biological Process Inference from eXperimental Interaction Evidence
IAO_0000115: bioPIXIE is a general system for discovery of biological networks through integration of diverse genome-wide functional data. This novel system for biological data integration and visualization, allows you to discover interaction networks and pathways in which your gene(s) (e.g. BNI1, YFL039C) of interest participate. The system is based on a Bayesian algorithm for identification of biological networks based on integrated diverse genomic data. To start using bioPIXIE, enter your genes of interest into the search box. You can use ORF names or aliases. If you enter multiple genes, they can be separated by commas or returns. Press ''submit''. bioPIXIE uses a probabilistic Bayesian algorithm to identify genes that are most likely to be in the same pathway/functional neighborhood as your genes of interest. It then displays biological network for the resulting genes as a graph. The nodes in the graph are genes (clicking on each node will bring up SGD page for that gene) and edges are interactions (clicking on each edge will show evidence used to predict this interaction). Most likely, the first results to load on the results page will be a list of significant Gene Ontology terms. This list is calculated for the genes in the biological network created by the bioPIXIE algorithm. If a gene ontology term appears on this list with a low p-value, it is statistically significantly overrepresented in this biological network. As you move the mouse over genes in the network, interactions involving these genes are highlighted. If you click on any of the highlighted interactions graph, evidence pop-up window will appear. The Evidence pop-up lists all evidence for this interaction, with links to the papers that produced this evidence - clicking these links will bring up the relevant source citation(s) in PubMed. You may need to download the Adobe Scalable Vector Graphic (SVG) plugin to utilize the visualization tool (you will be prompted if you need it).

Guthy-Jackson Repository for Neuromyelitis Optica
type: Resource
type: NamedIndividual
has db xref: nlx_20951
synonym: Neuromyelitis Optica Repository
abbrev: NMO Repository
IAO_0000115: Special collection of Neuromyelitis Optica (NMO) biological samples and data to foster scientific collaboration for NMO Spectrum Disease that will lead to the prevention, clinical treatment programs and a potential cure for Neuromyelitis Optica (NMO) Spectrum Disease. In this initiative, people with NMO can enroll into the repository at ACP''s collection sites located in leading neurology clinics across the US. Participants provide blood samples and information, which will in turn be used by qualified scientists whose research will contribute to the diagnosis, prevention, treatment, and/or cure of NMO. NMO subjects are primarily enrolled through the efforts of a study nurse employed by UTSW. Accelerated Cure Project (ACP), University of Texas Southwestern (UTSW), and Guthy-Jackson will work together to invite people with NMO to participate in the repository. Participants can enroll by visiting one of the ACP repository sites or by accepting an enrollment visit from the UTSW nurse.

Biorepository Alliance of Georgia for Oncology
type: Resource
type: NamedIndividual
has db xref: nlx_20991
synonym: Bio-Repository Alliance of Georgia for Oncology
synonym: Bio-Repository Alliance of Georgia for Oncology Tissue and Tumor Bank
synonym: Georgia Cancer Specimen and Tissue Bank
abbrev: BRAG-Onc
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. The Georgia Cancer Specimen and Tissue Bank is committed to a safe and reliable supply of tissue and cell products for research purposes. Work has begun already to build the state tumor bank initiative with operating sites in several locations through the state. We are confident that our results will yield a strong program that will benefit all Georgians and contribute to significant advances in cancer research and knowledge.

HLASeq
type: Resource
type: NamedIndividual
has db xref: OMICS_01543
IAO_0000115: An open-source software tool for accurate genotyping the human HLA genes from Illumina GA high-throughput sequencing data.

NeuroMatic
type: Resource
type: NamedIndividual
has db xref: biotools:neuromatic
has db xref: nif-0000-00073
IAO_0000115: NeuroMatic is a collection of Igor Pro functions for analyzing electrophysiological data. By allowing users to organize their data into Sets and Groups, NeuroMatic makes it relatively easy to compute transformations and statistical analyses on their data, including scaling, alignment averaging, baseline subtraction, spike detection, stationarity analysis, rise-time computations, etc. Being open source and modular designed, NeuroMatic also allows users to develop their own analysis functions that can be easily incorporated into NeuroMatic's framework. Note, if you have reached this page in search of a freeware tool for neuronal reconstructions, you are more likely to be interested in Neuromantic, a software package that sounds like NeuroMatic, but is not quite the same. Features of NeuroMatic Include * Sorting, Scaling, Averaging, Interpolation * Max / Min / Mean / Level / Rise Time / FWHM / Slope Measurements * Stability / Stationarity Analysis * Event Detection * Waveform Template Matching * Spike Raster Plots * Interspike-Interval and Peri-Stimulus Time (PST) Histograms * Compact Easy-to-Use Interface * Modular design as a basis for your own procedures * Extra space for your own buttons and controls * Import functions for Axograph and Pclamp data * Automatic macro generation for batch processing Supporting Agencies: MRC, Wellcome Trust Spike, Event, Fit, NClamp, Acquisition, spike train, EPSP, IPSP, IPSC, EPSC

FIDEA
type: Resource
type: NamedIndividual
has db xref: OMICS_01539
synonym: Functional Interpretation of Differential Expression Analysis
IAO_0000115: A web server for the functional interpretation of differential expression analysis. It can: * Calculate overrepresentation statistics using KEGG, Interpro, Gene Ontology Molecular Function, Gene Ontology Biological Process, Gene Ontology Cellular Component and GoSlim classifications; * Analyze down-regulated and up-regulated DE genes separately or together as a single set; * Provide interactive graphs and tables that can be modified on the fly according to user defined parameters; the user can set a fold change filter and interactively see the effects on the gene set under examination; * Output publication-ready plot of the graph; * Compare the results of several experiments in any combination.

NGVB SeqMap Database
type: Resource
type: NamedIndividual
has db xref: nlx_21403
abbrev: SeqMap Database
IAO_0000115: SeqMap is a generalized tool to characterize insertion sites that have been predicted from LM/LAM PCR methods. It will automatically identify genome insertion sites and nearby genes characterizing their function. This is an important tool as insertion site analysis is required for gene therapy clinical trials that are using retroviral and lentiviral vectors.

EGAPP
type: Resource
type: NamedIndividual
has db xref: OMICS_01538
synonym: Evaluation of Genomic Applications in Practice and Prevention
synonym: Evaluation of Genomic Applications in Practice and Prevention (EGAPP)
IAO_0000115: Initiative to develop a systematic, evidence-based process for evaluating genetic tests and other applications of genomic technology that are rapidly moving from research to use in clinical practice. A key objective of this process is to provide objective, timely, and credible information that is clearly linked to the scientific evidence on specific applications of genetic and genomic tests. The primary focus of EGAPP activities is an independent, nonfederal expert panel, the EGAPP Working Group. Other components of the EGAPP initiative include a federal interagency, the CDC staff and consultants, and an EGAPP initiative evaluation team.

RatMine
type: Resource
type: NamedIndividual
has db xref: biotools:RatMine
has db xref: nlx_21635
IAO_0000115: RatMine integrates data from RGD, UniProtKB, NCBI, KEGG and other sources to form a web-based data warehouse and tool set tailored for rat based data research. Search RatMine by entering names, identifiers, or keywords for genes, proteins, pathways, papers, etc. Additionally, we support programmatic access to our data through Application Programming Interface - choose from Perl or Java API. RatMine is a data warehouse that integrates many diverse biological data sets. The main focus is R. norvegicus genomics and proteomics. By integrating such data into one place it is possible to construct queries across domains of biological knowledge. The RatMine user interface is designed to go beyond simply looking up an identifier and viewing a report page. Some of the features include: * Quick Search is available just like on other sites, type in an identifier to see a report page. * Template queries are ''canned'' queries that provide a simple form to perform a specific task. You can create your own templates if you log in. * Lists lets you operate on whole lists of data at once. You can upload lists or save them from results tables. We also create useful public lists for everyone to use. * MyMine lets you create an account to save your own queries, bags and templates, as well as marking public templates as favorites.

ITOR Biorepository Services
type: Resource
type: NamedIndividual
has db xref: nlx_21679
synonym: Greenville Hospital System Cancer Biorepository
synonym: Institute for Translational Oncology Research Biorepository
synonym: Institute for Translational Oncology Research Biorepository Services
abbrev: ITOR Biorepository
IAO_0000115: From the type of mutation causing cancer to specific gene expression levels, genetic biomarkers are becoming an indispensable tool for developing new treatment models for cancer. The ITOR Biorepository Services tissue bank initiatives are critical to the continued development of an organized research infrastructure that will attract leading biotechnology and pharmaceutical companies interested in developing the next generation of cancer therapies. Ultimately, by linking the laboratory and clinical settings through innovative research investigations, USC, Greenville Hospital System University Medical Center, and private partners can identify the most novel ways to find and couple these biomarkers to patient drug trials and eventually, the most effective treatments & cures for cancer. The ITOR Biorepository Services Department ����?����������?? in conjunction with the Greenville Hospital System''s surgical oncologists, pathologists and staff ����?����������?? have developed tissue bank sample processing guidelines for frozen tissue, fresh tissue and peripheral blood and include flash freezing in liquid nitrogen within 15 minutes of harvest to maximize cell viability for basic science research. The department has a dedicated staff, including two research nurses and a data coordinator, which facilitate the logistics of tissue handling and submit outcomes data on participating patients. The ITOR Biorepository staff is in the process of adopting a universal consent for all patients of the Greenville Hospital System to have the option of donating excess tissue for research, should they desire. ITOR of GHS has several tissue-based patient initiatives & programs under development and ongoing. At the forefront of cancer care are two specific programs, Total Cancer Care and Caris Target Now.

Canadian Tumour Repository Network
type: Resource
type: NamedIndividual
has db xref: nlx_21725
synonym: Canadian Tumor Repository Network
synonym: CTRNet.ca
abbrev: CTRNet
IAO_0000115: The Canadian Tumour Repository Network (CTRNet) is a not-for-profit consortium of leading provincial tumor banks and programs that furthers Canadian health research. CTRNet provides interested researchers with a streamlined process to obtain quality human tissue and human tissue products from member tumor banks. The benefits of working with CTRNet.ca include: * The ability for researchers to search for quality controlled tissue samples from Canada' '''s leading tumor banks in one central location and for biobanks to display and make their biospecimens available for research users. * Learning opportunities in tissue handling, research design and relevant technology training and innovations. * Invitation to CTRNet workshops and conferences. * A resource for current news links and discussion forums about cancer research and tumor banking. The vision of CTRNet is to create new opportunities for translational cancer research that will improve cancer outcomes in Canada and beyond. Through the creation and maintenance of an online pan-Canadian network, researchers will gain unprecedented access to a new and comprehensive source of tissue and clinical data. The network is a sustainable resource and operates according to the highest scientific and ethical standards for research to benefit all Canadians. Currently CTRNet has the following member banks: * CBCF Tumor Bank Alberta * Manitoba Tumour Bank * Ontario Tumour Bank * British Columbia Cancer Agency Tumour Tissue Repository (BCCA-TTR) * Le r��seau de recherche en cancer du FRSQ * NCIC Clinical Trials Group

One Mind Biospecimen Bank Listing
type: Resource
type: NamedIndividual
has db xref: nlx_143622
synonym: One Mind Biospecimen Banks
synonym: One Mind: One Voice Bio-repository Cosmic Landscape
abbrev: One Mind Biobank
abbrev: One Mind Biobanks
IAO_0000115: International registry of biomaterial supply resources both for transplantation and research. Contributions to this resource are welcome. The database is searchable through NIF and is updated regularly.

Progeria Cell and Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_22169
synonym: PRF Cell & Tissue Bank
synonym: PRF Cell Tissue Bank
synonym: Progeria Cell Tissue Bank
synonym: Progeria Research Foundation Cell and Tissue Bank
synonym: Progeria Research Foundation Cell Tissue Bank
abbrev: PRF Cell and Tissue Bank
IAO_0000115: The PRF Cell & Tissue Bank provides medical researchers with genetic and biological material from Progeria patients and their families, so that research on Progeria and other age-related diseases can be performed. We''ve been hard at work with the families and their physicians to gather these precious biological materials. As you know, Hutchinson-Gilford Progeria Syndrome is an extremely rare condition. Thus while access to cell lines is essential for studying the biology and genetics of the disorder, there are very few cell lines in existence. Because an integral part of PRF''s mission is to stimulate interest in, and NIH funding opportunities for, Progeria research, there is an increased need for cell lines. The PRF Cell Bank will ensure that need is met! The goals of The PRF Cell & Tissue Bank are to promote: * Sufficient availability of cells for approved research projects * Incentive for new research projects * Study of the biochemical basis for Hutchinson-Gilford Progeria Syndrome * Discoveries leading to new treatments for children with Progeria * Discovery of a cure for Progeria

Wright Medical Technology, Inc.
type: Resource
type: NamedIndividual
has db xref: nlx_22299
abbrev: Wright
IAO_0000115: An ISO 9001 certified designer, manufacturing and distributing orthopedic implants and instrumentation worldwide for over 50 years. Wright''s product offerings include large joint implants for the hip and knee; extremity implants for the shoulder, elbow, hand, wrist and foot; and both synthetic and tissue-based bone graft substitute materials. Since its inception, Wright has introduced a number of products that represent new standards in orthopedic technology. From new material technologies to advanced products and instrumentation, Wright is committed to finding solutions to the challenges that face today''s orthopedic professionals.

DCTD
type: Resource
type: NamedIndividual
has db xref: OMICS_01537
synonym: Division of Cancer Treatment and Diagnosis
IAO_0000115: Division of NCI that takes prospective cancer detection and treatment leads, facilitates their paths to clinical application, and expedites the initial and subsequent large-scale testing of new agents, biomarkers, imaging tests, and other therapeutic interventions (radiation, surgery, immunotherapy) in patients. DCTD, like all of NCI, supports many programs that could not be done without government funding - investigators supported by the division engage in scientifically sound, high-risk research that may yield great benefits for patients with cancer, but are too difficult or risky for industry or academia to pursue. This includes a particular emphasis on the development of distinct molecular signatures for cancer, refined molecular assays, and state-of-the-art imaging techniques that will guide oncologic therapy in the future. The division has eight major programs that work together to bring unique molecules, diagnostic tests, and therapeutic interventions from the laboratory bench to the patient bedside: * Cancer Diagnosis Program * Cancer Imaging Program * Cancer Therapy Evaluation Program * Developmental Therapeutics Program * Radiation Research Program * Translational Research Program * Biometrics Research Branch * Office of Cancer Complementary and Alternative Medicine

Integrated Brain Gene Expression
type: Resource
type: NamedIndividual
has db xref: nlx_22354
synonym: Brain Gene Expression
synonym: Integrated BGE
synonym: Integrated Brain Gene Expression View
synonym: NIF Brain Gene Expression
synonym: NIF Integrated Brain Gene Expression
synonym: NIF Integrated Brain Gene Expression View
IAO_0000115: Virtual database indexing brain region gene expression data from mice from: Gene Expression Nervous System Atlas (GENSAT), Allen Mouse Brain Atlas, and Mouse Genome Institute (MGI).

PSI-MOD
type: Resource
type: NamedIndividual
has db xref: nlx_22387
synonym: Proteomics Standards Initiative Protein Modifications
synonym: PSI MOD
synonym: PSI Protein Modifications
abbrev: MOD
IAO_0000115: The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics to facilitate data comparison, exchange and verification. The protein modification workgroup focuses on developing a consensus nomenclature and provide an ontology reconciling in a hierarchical representation the complementary descriptions of residue modifications. The protein modification ontology (PSI-MOD) is available in OBO format or in OBO.xml. A spreadsheet containing the mapping of the descriptive labels used in various databases and search engines, the consensus list of proposed short name for protein modifications established by collaborative effort of mass spectrometry community, and the proposed rules and recommendations for this nomenclature are available. These short names are included in the ontology as synonyms of the corresponding terms.

EVOLUTIONARY FOUNDATIONS FOR THE HUMAN FOREBRAIN
type: Resource
type: NamedIndividual
has db xref: nlx_22479
synonym: First Periodic Table for the Neurosciences
synonym: Periodic Table for the Human Forebrain
abbrev: Evolution of the Human Forebrain
IAO_0000115: Portal on the evolution of the Human Forebrain with schematically depicted sequential age levels of cortical evolution: Staggered Dual Parameter Grid, Growth Rings of the Neocortex, Growth Shells of Thalamus, Major Nuclei of the Thalamus, Dual Parameter - Grid, Types of Neocortical Lamination, and Rolf Hasslers Hexa-Partition of Unit Thalamic Inputs. The cytoarchitectonic subdivisions of both the thalamus and the neocortex are topographically defined in terms of the variables of phylogenetic age and input specificity. The cortical and thalamic parcellations of Brodmann, von Economo and Hassler are each quantitatively correlated to a specific Cartesian coordinate value designating discrete levels for both age and input basic parameters. The variable of phylogenetic age is represented in the cortex by the five circumferential growth rings demonstrated by Sanides, plus an additional growth ring detected intermediate to the fifth and sixth age levels and designated as prekoniocortex. The paleocortex and the archaecortex are the two primordial neocortical precursors that form the mammalian neocortex. In contrast to the arrangement in the planar cortex, six phylogenetically distinct growth shells are detected in the three-dimensional thalamus and are designated after the corresponding schematic levels of Rolf Hassler''s paradigm of hexapartition of unit-thalamic inputs. The subthalamus and the epithalamus analogously represent the primordial diencephalic precursors of the mammalian dorsal thalamus, Both the neocortex and the dorsal thalamus evolved in response to the necessity for a more comprehensive blending of inputs from differing neuraxial levels. Unlike the age variable, the parameter of input specificity is most readily apparent in the dorsal thalamus; which is the site of termination for each major forebrain input. Accordingly, the fourteen individual units of the parameter of input specificity are designated after each of the specific input classifications projec…

DC-Research.eu - Dendritic Cell Research Knowledge Portal
type: Resource
type: NamedIndividual
has db xref: nlx_143631
abbrev: DC-RESEARCH.EU
IAO_0000115: An open knowledge resource for the dendritic cell research community, this index of research assets and expertise is designed to support translational research by providing annotations and interrelations on materials, datasets, tools, techniques, persons and organizations. The content of DC-RESEARCH.EU can be accessed by researchers through its website and can be accessed programmatically: the information in DC-RESEARCH.EU is represented through machine processable languages, proper of the Semantic Web (RDF and RDFa). To submit to the dc-thera directory please contact: dc-research_at_leafbioscience.com

BC Cancer Agency
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100005614
has db xref: grid.248762.d
has db xref: ISNI: 0000 0001 0702 3000
has db xref: nlx_143635
has db xref: Wikidata: Q4835275
synonym: British Columbia Cancer Agency
abbrev: BCCA
IAO_0000115: A portal that provides a province-wide, population-based cancer control program for the residents of British Columbia and the Yukon. The BC Cancer Agency''s mandate covers the spectrum of cancer care, from prevention and screening, to diagnosis, treatment, and through to rehabilitation. The BC Cancer Agency''s mandate is driven by a three-fold mission: 1. To reduce the incidence of cancer; 2. To reduce the mortality rate of people with cancer; 3. To improve the quality of life of people living with cancer. This mission drives everything we do, including providing screening, diagnosis and care, setting treatment standards, and conducting research into causes of, and cures for, cancer. The BC Cancer Agency operates five regional cancer centers, providing assessment and diagnostic services, chemotherapy, radiation therapy, and supportive care. Each of the BC Cancer Agency''s centers delivers cancer treatment based on provincial standards and guidelines established by the Agency. We work in partnership with communities to provide a network of chemotherapy clinics so patients can receive care closer to home. Research is an essential part of the BC Cancer Agency''s mission to not only find the causes of cancer, but to find better treatments for prolonged life and better quality of life. With direct links between the BC Cancer Agency''s physicians and researchers at our five centers, the Deeley Research Centre (located in Victoria) and the BC Cancer Agency''s Research Centre (located in Vancouver), we can quickly translate new discoveries into clinical applications. The BC Cancer Agency''s Research Centre includes eight specialty laboratories including the Genome Sciences Centre, and the Terry Fox Laboratory. The BC Cancer Foundation raises funds for cancer research and enhancements to care at the BC Cancer Agency.

Medical Education and Research Institute - MERI
type: Resource
type: NamedIndividual
has db xref: nlx_22603
synonym: Medical Education & Research Institute
synonym: Medical Education and Research Institute
abbrev: MERI
IAO_0000115: A nonprofit medical teaching and training school in Memphis, Tennessee qualified under section 501 (c) (3) of the Internal Revenue Code. The MERI conducts state-of-the-art, hands-on educational courses for physicians, nurses and other medical professionals from across the country and around the world. At the MERI, medical professionals are introduced to the latest innovations in medicine, and have the opportunity to learn first-hand about the most up-to-date medical techniques and technologies. The MERI supports research in all specialties by providing the sponsor with the most effective environment for achieving maximal outcomes for their studies. Through our Mobile MERI unit, we are proud to provide courses and support to our sponsors off-site anywhere in the continental United States. Our dedicated course specialists offer customer service, provide safe and efficient transport of equipment and ensure a quality training and educational experience at the off-site location.

Hapmix
type: Resource
type: NamedIndividual
has db xref: nlx_22768
has db xref: OMICS_02082
abbrev: HAPMIX
IAO_0000115: Software application that uses genotyping data from SNP arrays for accurately inferring chromosomal segments of distinct continental ancestry in admixed populations, using dense genetic data. (entry from Genetic Analysis Software)

University at Buffalo SMBS Department of Pharmacology and Toxicology
type: Organization
type: NamedIndividual
has db xref: nif-0000-02077
synonym: UB SMBS Dept. of Pharmacology and Toxicology
IAO_0000115: The Department of Pharmacology and Toxicology strives to maintain excellence in the areas of research, teaching and service to the School, University, and Community. The Department offers a program of didactic course work and research training leading to the degree of Doctor of Philosophy in Pharmacology, either through the Interdisciplinary Graduate Program in Biomedical Sciences (IGPBS) or through the Medical Scientist Training Program (MSTP). Pharmacology and Toxicology have similar basic principles and often utilize similar experimental methods and approaches to address a wide range of biomedical and health-related questions. Both are sciences that are basic not only to medicine, but also to pharmacy, nursing, dentistry, public health, and veterinary medicine. Additional programs are offered for the Bachelor of Science, or a combined Bachelor of Science / Master of Science in Pharmacology and Toxicology, and a Master of Arts in Pharmacology. The graduate programs are structured to provide the candidate with a broad training in basic areas of pharmacology as well as a degree of expertise in one research area including: Neuropharmacology, Psychopharmacology, Toxicology, Molecular and Cellular Pharmacology, Clinical Pharmacology

Boston University Medical Campus; Massachusetts; USA
type: NamedIndividual
has db xref: nlx_46771
abbrev: BUMC
IAO_0000115: Boston University Medical Campus; Massachusetts; USA

Segway - a way to segment the genome
type: Resource
type: NamedIndividual
has db xref: biotools:segway
has db xref: nlx_22911
synonym: Segway
IAO_0000115: The free Segway software package contains a novel method for analyzing multiple tracks of functional genomics data. The method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling. Segway uses the Graphical Models Toolkit (GMTK) for efficient DBN inference. The software has extensive documentation and was designed from the outset with external users in mind.

BamView
type: Resource
type: NamedIndividual
has db xref: biotools:bamview
has db xref: nlx_22933
has db xref: OMICS_00878
IAO_0000115: A free interactive display of read alignments in BAM data files that can be launched with Java Web Start or downloaded. This interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence can be used in a number of contexts including SNP calling and structural annotation. It has been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features. The source code is available as part of the Artemis code which can be downloaded from GitHub.

Accelerated Cure Project MS Repository
type: Resource
type: NamedIndividual
has db xref: nlx_22946
synonym: Accelerated Cure Project Repository
synonym: ACP Repository
synonym: Multiple Sclerosis (MS) Repository
IAO_0000115: A repository of biological samples and data from people with multiple sclerosis, selected other demyelinating diseases, and unaffected controls. The repository not only provides much-needed samples and data to researchers studying MS and other diseases, but also aggregates the results from all of these studies so that they can be analyzed collectively, leading to new findings and breakthroughs. The repository collects blood, DNA, and imaging once per year. The repository currently includes samples and data from over 2,700 subjects with Multiple Sclerosis, Neuromyelitis Optica, Acute Disseminated Encephalomyelitis, Transverse Myelitis, Optic Neuritis, and Clinically Isolated Syndromes, as well as controls. Blood samples are provided as aliquots as serum, plasma, DNA, RNA, and lymphocytes and each sample is accompanied by more than 40 pages of clinical and epidemiological data contributed by the subject and the enrolling neurologist.

svmvia
type: Resource
type: NamedIndividual
has db xref: nlx_23153
IAO_0000115: Software that implements the full regularization path optimization algorithm for training a support vector machine. The support vector machine algorithm has a single hyperparameter C that regularizes the learned model. Recently, Hastie et al. (2004) described an algorithm for finding the SVM solution for all possible values of this regularization parameter. An efficient C++ implementation of this algorithm is presented. For large values of C, it is often faster to find the entire regularization path than to train a single model.

Online Nucleosomes Position Prediction by Genomic Sequence
type: Resource
type: NamedIndividual
has db xref: nlx_23258
synonym: Nucleosomes Position Prediction
IAO_0000115: This tool allows you to submit a genomic sequence and to recieve a prediction of the nucleosomes positions on it, based on the nucleosome-DNA interaction model that we developed in these papers: * Segal et al., A Genomic Code for Nucleosome Positioning, Nature 2006 * Field et al., Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals, PLoS Comp Biol. 2008 * Kaplan et al., The DNA-Encoded Nucleosome Organization of a Eukaryotic Genome, Nature 2008 We recommend using the latest version of the model (Version 3), which is applicable to all species. Paste in a sequence to analyze or upload file. You can provide multiple sequences in fasta format (separate sequences by lines starting with ''>'' followed by the sequence name). The length of each sequence must be between 147bp and 40kb bp. Note: Due to boundary effects, we highly recommend that you add at least 5000 bp of flanking sequence around your sequence of interest. You can generate the nucleosomes positioning predictions on your own machine using our executable and wrapping Perl scripts.

Integrated Biobank of Luxembourg
type: Resource
type: NamedIndividual
has db xref: nlx_23314
abbrev: IBBL
IAO_0000115: An independent, not-for-profit biobanking and biotechnology foundation designed to facilitate new, high quality medical research. The IBBL collects, stores, and analyzes biological samples and associated data, which are then made available to research organizations investigating new treatments for diseases. It houses a biospecimen collection and biorepository that contains high quality tissues and maintains quality control of the specimens and the clinical data associated with the tissue samples, while maintaining biobanking ethical standards. It also provides biorefinery analyses and research services that can make analytes from tissues (e.g. DNA, RNA and protein), maintains technology for high throughput gene sequencing and gene expression, and conducts biospecimen research. An informatics platform maintains the clinical and biospecimens data in a secure fashion for additional analysis. Samples are collected by IBBL personnel from hospitals in a targeted manner. The IBBL collaborates with research and health organizations in North America, Europe and the Middle East, and with the major international biobanking societies.

International Biologics, LLC
type: Resource
type: NamedIndividual
has db xref: nlx_23433
synonym: International Biologics
IAO_0000115: International Biologics is a fully accredited American Association of Tissue Banks (����??AATB����??) Tissue Bank and Processing Facility --- Accreditation #00162. It receives 100% of it''s donor tissue from federally licensed Organ Procurement Organizations (OPO����??s) and other AATB accredited donor sources. International Biologics provides multitudinous bone and soft tissue allografts. Clinical applications for these products include: Orthopedic, Spine, Joint Restoration, Oral Maxillofacial, Podiatry, Periodontal, Urology, Trauma The collection and distribution of donated tissue including soft tissue, bone tissue and organ donation of kidneys, livers and hearts (collectively tissue) are controlled by the Government. Organ Procurement Organizations (OPOs) have long been established in every state to recover tissue from donors. Because there is a very short period following death before tissue breaks down rendering it useless for implantation, OPOs maintain round-the-clock presences in hospitals including grief counseling through procurement personnel. OPO tissue is heavily federally regulated and is therefore the most highly sought tissue because it is universally understood to be the safest tissue for transplant. International Biologics has long-term high-volume OPO tissue supply contracts making it one of the largest recipients of cadaveric bone and soft tissue in the world. International Biologics processes its tissue within a state-of-the-art facility located in Scottsdale, Arizona. The facility includes nine -86C ultra low temperature freezers, 14 tray lyophilization, and four validated class 1000 clean rooms including CNC.

Canadian Biosample Repository
type: Resource
type: NamedIndividual
has db xref: nlx_23447
abbrev: CBSR
IAO_0000115: Biosample processing, management, storage and retrieval infrastructure that operates on a cost-recovery basis to investigators. Services are available to Research Ethics Board (REB) approved studies. They accept any human tissue from appropriately consented subjects for processing to DNA, RNA, serum, plasma, peripheral blood cells, fixed tissue, and tissue blocks. Once your samples have been collected and processed, CBSR will provide short and long-term sample storage, and retrieval(typically within 24hrs) upon request. Their storage services include robust robotic systems for sample aliquoting, tracking, storage, and retrieval to ensure chain of custody on all samples. Their temperature monitoring system ensures that all samples are maintained at the chosen temperature, and provides regulatory-grade audit trail for all samples.

Canadian Breast Cancer Foundation Tumor Bank
type: Resource
type: NamedIndividual
has db xref: nlx_143637
synonym: Alberta Research Tumor Bank
synonym: ARTB
synonym: Canadian Breast Cancer Foundation Alberta Research Tumor Bank
synonym: CBCF Tumor Bank
abbrev: CBCF TB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented May 18, 2022. A tumor bank that provides a large collection of cancer specimens, from breast and other cancers, annotated with clinical information. The CBCF TB enables researchers to address unanswered questions concerning the prognosis and treatment of breast cancer and other cancers. The CBCF TB website is also directed to participants interested in donating tumor tissue or blood. Biological specimens such as blood, urine, bone marrow, and ascites (fluid that sometimes collects in the abdomen) contain genetic information, just as tumor tissue does. These samples can be used in studies that may help researchers see how people with certain genetic make-ups respond to certain treatments. It can also explain why different people have different health problems. CBCF TB, formerly ARTB, was created by a merger of components of two existing Tumor-banking initiatives, the CLS Repository in Calgary and the Tumor bank of the PolyomX Program in Edmonton.

Canadian Breast Cancer Foundation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100000147
has db xref: grid.453374.2
has db xref: ISNI: 0000 0004 0473 5688
has db xref: nlx_143638
synonym: Fondation canadienne du cancer du sein
abbrev: CBCF
IAO_0000115: The Canadian Breast Cancer Foundation is the leading national volunteer-based organization in Canada dedicated to creating a future without breast cancer. Established in 1986 by a dedicated group of volunteers, the Foundation works collaboratively to fund, support and advocate for: * Relevant and innovative research, * Meaningful education and awareness programs, * Early diagnosis and effective treatment * A positive quality of life for those living with breast cancer. Our fundraising through our annual Canadian Breast Cancer Foundation CIBC Run for the Cure, special events, corporate sponsorship and donations has enabled the Foundation to allocate millions of dollars in grants for breast cancer projects and services since our inception. Addressing the needs of Canadians from coast to coast, the Canadian Breast Cancer Foundation has regional offices in British Columbia/Yukon Territory, Prairies/NWT, Ontario and the Atlantic Region. The Foundation''s central office is located in Toronto. Charitable Registration No. 12799 3608 RR0001

AIDS and Cancer Specimen Resource
type: Resource
type: NamedIndividual
has db xref: nlx_23946
synonym: ACSR - AIDS and Cancer Specimen Resource
abbrev: ACSR
IAO_0000115: A biorepository for HIV-infected human biospecimens from a wide spectrum of HIV-related or associated diseases, including cancer, and from appropriate HIV-negative controls. The ACSR has formalin-fixed paraffin embedded biospecimens, fresh frozen biospecimens, malignant cell suspensions, fine needle aspirates, and cell lines from patients with HIV-related malignancies. It also contains serum, plasma, urine, bone marrow, cervical and anal specimens, saliva, semen, and multi-site autopsy speicmens from patients with HIV-related malignancies including those who have participated in clinical trials. The ACSR has an associated databank that contains prognostic, staging, outcome and treatment data on patients from whom tissues were obtained. The ACSR database contains more than 300,000 individual biospecimens with associated clinical information. Biospecimens are entered into the ACSR database by processing type, disease category, and number of cases defined by disease category.

University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA
type: NamedIndividual
has db xref: nlx_144410
synonym: University of North Carolina at Chapel Hill School of Medicine
synonym: University of North Carolina School of Medicine
abbrev: UNC School of Medicine

NCBI Structure
type: Resource
type: NamedIndividual
has db xref: nlx_23947
has db xref: r3d100010927
IAO_0000115: Database of three-dimensional structures of macromolecules that allows the user to retrieve structures for specific molecule types as well as structures for genes and proteins of interest. Three main databases comprise Structure-The Molecular Modeling Database; Conserved Domains and Protein Classification; and the BioSystems Database. Structure also links to the PubChem databases to connect biological activity data to the macromolecular structures. Users can locate structural templates for proteins and interactively view structures and sequence data to closely examine sequence-structure relationships. * Macromolecular structures: The three-dimensional structures of biomolecules provide a wealth of information on their biological function and evolutionary relationships. The Molecular Modeling Database (MMDB), as part of the Entrez system, facilitates access to structure data by connecting them with associated literature, protein and nucleic acid sequences, chemicals, biomolecular interactions, and more. It is possible, for example, to find 3D structures for homologs of a protein of interest by following the Related Structure link in an Entrez Protein sequence record. * Conserved domains and protein classification: Conserved domains are functional units within a protein that act as building blocks in molecular evolution and recombine in various arrangements to make proteins with different functions. The Conserved Domain Database (CDD) brings together several collections of multiple sequence alignments representing conserved domains, in addition to NCBI-curated domains that use 3D-structure information explicitly to define domain boundaries and provide insights into sequence/structure/function relationships. * Small molecules and their biological activity: The PubChem project provides information on the biological activities of small molecules and is a component of NIH' '''s Molecular Libraries Roadmap Initiative. PubChem includes three databases: PCSubstance, PCBioAss…

BrainSpan
type: Resource
type: NamedIndividual
has db xref: nlx_2397
has db xref: nlx_23971
has db xref: nlx_37081
has db xref: nlx_86215
has db xref: nlx_98194
synonym: BrainSpan - Exon microarray summarized to genes
synonym: BrainSpan: RNA-Seq exons
IAO_0000115: Atlas of developing human brain for studying transcriptional mechanisms involved in human brain development. One of the BrainSpan datasets, Exon microarray summarized to genes, is presented. It is a downloadable archive of files containing normalized RNA-Seq expression values for analysis.

Diabetes Wiki
type: Resource
type: NamedIndividual
has db xref: nlx_24030
IAO_0000115: Diabetes Wiki is a wiki where people with diabetes share personal stories, and build a database of helpful information. Categories include News, What is Diabetes?, Managing Diabetes, Impact of Diabetes, and more. Additionally, contribute to blog posts and the forum.

Canadian Virtual Brain Tumour Bank
type: Resource
type: NamedIndividual
has db xref: nlx_24047
synonym: Canadian Virtual Brain Tumor Bank
abbrev: CVBTB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. The mission of the Canadian Virtual Brain Tumour Bank (CVBTB) is to facilitate clinical, molecular and translational research through the provision of well-characterized tissue linked to clinical data and to become a standardized national tissue resource whereby scientific needs are met, addressed and accelerated through a common public accessible core the CVBTB. Recognizing the need to encourage systemic banking of brain tumor tissues throughout the country and to link banks of brain tumor tissue samples with academic and scientific institutions that require these samples, the CVBTB was established. Under the sponsorship of Schering Plough Canada Inc. and in association with the Canadian Brain Tumour Consortium (CBTC), the CVBTB looks to act as a resource for all researchers to provide them with information on the types of brain tumor tissue samples available and to direct them to the tumor tissue banking sites holding these samples. The CVBTB also looks to provide information on standard operating procedures regarding aspects of tumor tissue banking such as tissue accrual, storage and shipment and the processing of blood samples such as serum and lymphocytes. The CVBTB currently consists of four brain tumour tissue banking sites (Toronto Western Hospital - Toronto, Ontario; London Health Sciences Centre - London, Ontario; McGill University - Montreal, Quebec; University of Calgary - Calgary, Alberta) and is continuously looking for more institutions to be a part of the CVBTB. If your institution would like to become a part of the CVBTB, please contact the CVBTB coordinator.

UAB Comprehensive Cancer Center Tissue Procurement Shared Facility
type: Resource
type: NamedIndividual
has db xref: nlx_24048
synonym: UAB Comprehensive Cancer Center TPSF
synonym: UAB Tissue Procurement Shared Facility
synonym: UAB TPSF
abbrev: TPSF
IAO_0000115: The Tissue Procurement Shared Facility (TPSF) of the Comprehensive Cancer Center operates as a prospective service to collect, from UAB associated hospitals, normal, malignant, benign, and diseased fresh human tissues and fluids which are then preserved appropriate to protocol. The TPSF can provide normal, malignant, benign, or diseased remnant human tissues and/or fluids from surgical resections, autopsies, or clinical procedures for IRB-approved researchers. The preservation can include fresh storage in media or saline, snap-frozen storage in liquid nitrogen, freezing in OCT for frozen section preparation, or preservation in a fixative of choice. The TPSF can also provide procurement of control tissues including uninvolved tissues or matched tissues from patients with benign disease processes. The histology laboratory can provide paraffin blocks and/or stained or unstained slides. In addition, investigators can obtain access to rare tissues through the national Cooperative Human Tissue Network (CHTN). Although the facility operates as a prospective service specializing in the preparation of samples to protocol, limited banked frozen and paraffin-embedded samples may be available. Investigators are required to complete an application and provide a copy of their IRB approval as well as a brief description of the project for which the requested samples will be utilized. Samples are provided for research purposes only. Processing fees are to offset processing costs and should be included in all grant applications.

PerM
type: Resource
type: NamedIndividual
has db xref: biotools:perm
has db xref: OMICS_00675
synonym: PERiodic seed Mapping
synonym: Periodic seed Mapping
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms. It capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads.Efficient mapping of short sequencing reads with periodic full sensitive spaced seeds.

Alberta Cancer Foundation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100000001
has db xref: grid.427879.7
has db xref: nlx_143639
abbrev: ACF
IAO_0000115: The Alberta Cancer Foundation is more than a charity. It''s a movement for cancer-free lives today, tomorrow and forever. It''s a movement of those who know a cancer-free future is possible and who won''t settle for some day. It''s a movement of those who stand with Albertans who have no choice but to stand up to cancer. It''s a movement of those who know something can be done and are willing to do it. For those facing cancer today, in honour of those lost to cancer, and for generations to come, we promise progress. Our mission is to deliver progress in cancer research, prevention, treatment and care by generating community investment for Alberta''s coordinated research strategy, the Cross Cancer Institute, Tom Baker Cancer Centre and 15 other cancer centres throughout the province. The Alberta Cancer Foundation is a Registered Charity - Business Number 11878 0477 RR0001. Your dollar fights cancer on every front: research, prevention, screening, early diagnosis, education, treatment and care.

Cancer Research Network of the FRSQ
type: Resource
type: NamedIndividual
has db xref: nlx_143641
synonym: FRSQ Cancer Research Network
synonym: RRCancer-BTD
synonym: R��seau de recherche en cancer
synonym: R��seau de recherche sur le cancer
synonym: R��seau de recherche sur le cancer du FRSQ
abbrev: RRCancer
IAO_0000115: An infrastructure to allow Quebec researchers to have at their disposal tumor banks and the services that support large scale research in genomics and proteomics. The database and the tissue bank of the research network was created to allow rapid access to biological samples and their clinical data. It is spread out over many hospital institutions (in Montreal, Quebec and Sherbrooke). The members of the RRCancer-BTD supply normal, benign and malignant samples from routine surgeries and blood tests. Blood and tissue samples are collected by the provincial biobanks on a regular basis and are coded, classified and stored. The samples can be supplied to a researcher either fresh or frozen or blocks of paraffin or on slices. The sharing of information and biological material is managed according to ethical rules and contributes to increasing the value of research in Quebec. The network has mobilized a significant number of researchers in the area of cancer that unite their efforts to pursue high caliber multidisciplinary research. They are a group of researchers from many different Qu��bec Universities all working in the branch of cancer research. They are located in four hospital centers in Quebec, namely the University of Montreal Hospital Centre (CHUM), the University of Quebec Hospital Centre (CHUQ), the University of Sherbrooke Hospital Centre (CHUS) and the McGill University Hospital Centre (CUSM), as well as in the affiliated research and university centers (Sacr��-Coeur, Maisonneuve-Rosemont and the Montreal Jewish Hospital). The collaborative efforts created and maintained in this network have allowed transfer of knowledge and the sharing of cutting edge technologies. RRCancer favors multidisciplinary cancer research in both fundamental and clinical scopes. The network is based on the desire researchers to work together to prevent cancer and improve therapeutic strategies, all the while continuing the very important task of raining new specialists and graduate s…

Biobanking and Biomolecular Resources Research Infrastructure (BBMRI)
type: Resource
type: NamedIndividual
has db xref: nlx_24389
synonym: BBMRI: Biobanking and Biomolecular Resources Research Infrastructure
synonym: BBMRI: Biobanking Biomolecular Resources Research Infrastructure
synonym: Biobanking and Biomolecular Resources Research Infrastructure
synonym: Biobanking Biomolecular Resources Research Infrastructure
synonym: Biobanking Biomolecular Resources Research Infrastructure (BBMRI)
abbrev: BBMRI
IAO_0000115: BBMRI is a pan-European and internationally broadly accessible research infrastructure and a network of existing and de novo biobanks and biomolecular resources. The infrastructure will include samples from patients and healthy persons, representing different European populations (with links to epidemiological and health care information), molecular genomic resources and biocomputational tools to optimally exploit this resource for global biomedical research. During the past 3 years BBMRI has grown into a 53-member consortium with over 280 associated organizations (largely biobanks) from over 30 countries, making it the largest research infrastructure project in Europe. During the preparatory phase the concept of a functional pan-European biobank was formulated and has now been presented to Member States of the European Union and for associated states for approval and funding. BBMRI will form an interface between specimens and data (from patients and European populations) and top-level biological and medical research. This can only be achieved through a distributed research infrastructure with operational units in all participating Member States. BBMRI will be implemented under the ERIC (European Research Infrastructure Consortium) legal entity. BBMRI-ERIC foresees headquarters (central coordination) in Graz, Austria, responsible for coordination of the activities of National Nodes established in participating countries. BBMRI is in the process of submitting its application to the European Commission for a legal status under the ERIC regulation, with an expected start date at the end of 2011. Major synergism, gain of statistical power and economy of scale will be achieved by interlinking, standardizing and harmonizing - sometimes even just cross-referencing - a large variety of well-qualified, up-to date, existing and de novo national resources. The network should cover (1) major European biobanks with blood, serum, tissue or other biological samples, (2) molecular …

Bangalore Brain Bank
type: Resource
type: NamedIndividual
has db xref: nlx_24619
synonym: Human Brain Tissue Repository of Bangalore
synonym: NIMHANS HBTR
synonym: NIMHANS Human Brain Tissue Repository
abbrev: HBTR
abbrev: NIMHANS Brain Bank
IAO_0000115: A National Facility to promote research in Neurobiology using human nervous tissues. The brain tissues collected with informed consent of close relatives within 4-24 hours following death are frozen for Biochemical, Immuno-histochemical and Molecular Biological studies. A large number of formalin fixed brain tissues from various Neurological, Neurosurgical and Psychiatric disorders are also available for study.

Roslin Wellcome Trust Tick Cell Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_24657
IAO_0000115: The world''s largest collection of tick cell lines, enabling scientists to carry out advanced research. This biobank is establishing a collection of all the continuous cell lines derived from ixodid and argasid ticks of medical and veterinary importance available worldwide now and in future. Ticks are blood feeding arthropods which transmit many human and animal diseases. Research into prevention and cure of these diseases, which are caused by viruses, bacteria and protozoa, is greatly assisted by the use of cell culture systems which enable study of both how tick cells function, and how and why ticks transmit these disease-causing pathogens. Cell lines will always be shipped to recipient laboratories as growing cultures, since we cannot guarantee successful resuscitation of frozen stabilates. Tick cells in culture can tolerate the range of temperatures experienced during transit by air for up to a week. Training: We will provide training in tick cell line care and maintenance. This is an essential component of successful transfer of tick cells to, and their establishment in, laboratories with little or no previous experience of tick cell culture. Recipient scientists (preferably the person who will actually look after the cells) can visit the biobank for between 2 days and 2 weeks, depending on their level of previous experience, to be trained in the specific approach and methods for tick cell cultivation. Establishment of new cell lines: In response to requests and on receipt of suitable starting material (engorged female or moulting nymphal ticks), we will attempt to establish new cell lines from tick species or strains which are not already represented in the collection. Deposition of new tick cell lines: We invite researchers anywhere in the world who have established new tick cell lines to deposit samples for safekeeping free of charge and, if requested, for distribution alongside the existing biobank portfolio.

Virtual Fly Brain
type: Resource
type: NamedIndividual
has db xref: nlx_143644
synonym: VFB
synonym: VirtualFlyBrain.org
IAO_0000115: An interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of the adult Drosophila melanogaster brain.

Phelan-McDermid Syndrome International Registry
type: Resource
type: NamedIndividual
has db xref: nlx_143654
abbrev: PMS International Registry
IAO_0000115: International registry that consolidates information from individuals with Phelan-McDermid Syndrome into a single database, which will be utilized by researchers to understand Phelan-McDermid Syndrome better. In order to accelerate translational efforts (moving from basic laboratory research to meaningful health outcomes, such as therapies and treatments) related to Phelan-McDermid Syndrome, PMSF is funding the Phelan-McDermid Syndrome International Registry. The Registry is important for characterizing and understanding the syndrome better. Not only will the Registry provide valuable information for families and doctors to make the best care decisions possible, it will be important to help researchers decide what are the most important challenges to address. The Registry will also help scientists find out if there are any PMS patients who might be a good match for their research studies. Collecting information from PMS patients is very important, but protecting the privacy of people affected by PMS is also extremely important. In order to protect your privacy, Patient Crossroads (the company that designed the registry software) has designed many safeguards. Your child''s information will be de-identified so no one who looks at the data can identify you or your child. Your child''s information will be assigned a code. If a researcher is interested in learning more about your child, the researcher will ask the Patient Crossroads/PMSIR genetic counselor to contact you. A scientist will not be able to receive any identifying information about your child unless you give explicit consent for your child''s identity to be released to that researcher. BE PART OF OUR INTERNATIONAL REGISTRY The Registry will provide valuable information for families and doctors to make the best care decisions possible, and it will help researchers decide what are the most important challenges to address in PMS. Establishing the registry addresses two important scientific needs. First, scienti…

Mercury
type: Resource
type: NamedIndividual
has db xref: OMICS_02290
synonym: Illumina Mercury pipeline
IAO_0000115: An automated, flexible, and extensible analysis workflow that provides accurate and reproducible genomic results at scales ranging from individuals to large cohorts. The analysis pipeline is deployed in local hardware and the Amazon Web Services cloud via the DNAnexus platform.

Open Connectome Project
type: Resource
type: NamedIndividual
has db xref: nlx_143645
has db xref: SciRes_000189
synonym: Open Connectome Project: Collectively reverse-engineering the brain one synapse at a time
synonym: Open Connectome Project: Collectively reverse-engineering the brain one synapse at a time.
synonym: openconnectomeproject
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. Connectomes repository to facilitate the analysis of connectome data by providing a unified front for connectomics research. With a focus on Electron Microscopy (EM) data and various forms of Magnetic Resonance (MR) data, the project aims to make state-of-the-art neuroscience open to anybody with computer access, regardless of knowledge, training, background, etc. Open science means open to view, play, analyze, contribute, anything. Access to high resolution neuroanatomical images that can be used to explore connectomes and programmatic access to this data for human and machine annotation are provided, with a long-term goal of reconstructing the neural circuits comprising an entire brain. This project aims to bring the most state-of-the-art scientific data in the world to the hands of anybody with internet access, so collectively, we can begin to unravel connectomes. Services: * Data Hosting - Their Bruster (brain-cluster) is large enough to store nearly any modern connectome data set. Contact them to make your data available to others for any purpose, including gaining access to state-of-the-art analysis and machine vision pipelines. * Web Viewing - Collaborative Annotation Toolkit for Massive Amounts of Image Data (CATMAID) is designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface is inspired by Google Maps, enhanced to allow the exploration of 3D image data. View the fork of the code or go directly to view the data. * Volume Cutout Service - RESTful API that enables you to select any arbitrary volume of the 3d database (3ddb), and receive a link to download an HDF5 file (for matlab, C, C++, or C#) or a NumPy pickle (for python). Use some other programming language? Just let them know. * Annotation Database - Spatially co-registered volumetric annotations are compactly stored for efficient queries such as: find all synapses, or whi…

Osiris Therapeutics
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100007075
has db xref: grid.436931.a
has db xref: ISNI: 0000 0004 0418 0643
has db xref: nlx_24773
has db xref: Wikidata: Q7106872
synonym: Osiris Therapeutics Inc
synonym: Osiris Therapeutics Inc.
synonym: Smith and Nephew
IAO_0000115: Stem cell company focused on developing and marketing products to treat medical conditions in the inflammatory, autoimmune, orthopedic and cardiovascular areas. Now part of Smith and Nephew.

Society in Science - The Branco Weiss Fellowship
type: Resource
type: NamedIndividual
has db xref: nlx_24860
synonym: Society in Science: The Branco Weiss Fellowship
abbrev: Branco Weiss Fellowship
IAO_0000115: Society in Science The Branco Weiss Fellowship provides young researchers around the world with a generous personal grant, giving them the freedom to work on whatever topic they choose anywhere in the world, for a maximum duration of five years. This research funding is designed to support postdoctoral researchers after their PhD and before their first faculty appointment. Those in current postdoctoral positions are also eligible. Society in Science was initiated and financed by the Swiss entrepreneur Dr. Branco Weiss, who passed away in October 2010. The program is coordinated by the Swiss Federal Institute of Technology Zurich (ETH).

LifePoint, Inc.
type: Resource
type: NamedIndividual
has db xref: nlx_24872
abbrev: LifePoint
IAO_0000115: Certified by the federal government, LifePoint is the designated Organ Procurement Organization (OPO) for organ recovery services in South Carolina, excepting Aiken and Edgefield counties. LifePoint actively provides organ, tissue and ocular donor services to 62 hospitals throughout the state. We offer professional education about donation to the hospital staff members in order to maximize the amount and quality of donated organs and tissues. LifePoint also helps support and educate families at an emotionally devastating time, so they can make well-informed decisions about organ and tissue donation. Whether they decide for or against donation, our aim is to assure that they will feel they have made the right decision in the months and years to come.

CDP
type: Resource
type: NamedIndividual
has db xref: OMICS_01536
synonym: Cancer Diagnosis Program
IAO_0000115: National program to improve the diagnosis and assessment of cancer by moving scientific knowledge into clinical practice by coordinating and funding resources and research for the development of innovative in vitro diagnostics, novel diagnostic technologies and appropriate human specimens. The Cancer Diagnosis Program is divided into four branches: Biorepository and Biospecimen Research Branch (BBRB), Diagnostic Biomarkers and Technology Branch (DBTB), Diagnostics Evaluation Branch (DEB), and the Pathology Investigation and Resources Branch (PIRB).

CB-Commander
type: Resource
type: NamedIndividual
has db xref: OMICS_01534
IAO_0000115: A plugin based software tool that tries to integrate high throughput sequencing algorithms. It allows researchers to design and execute their experiments through a user friendly interface, enabling users to integrate di erent components of an experiment, e.g. algorithms and converters, into one graphically interfaced application that is very easy to use when working on remote servers as well as local computers. The graphical user interface facilitates a visual design of experiments by using a block diagram to represent the components (algorithms, converters, etc.) of an experiment as a pipeline. The users can easily modify this pipeline.

CURE - Digestive Diseases Research Center
type: Resource
type: NamedIndividual
has db xref: nlx_152337
IAO_0000115: Center whose interests and activities encompass several facets of gastrointestinal regulatory physiology and cell biology. It provides an infrastructure to support basic, translational and clinical research and to facilitate interdisciplinary research and training activities in digestive diseases.

Yogo Data Management System
type: Resource
type: NamedIndividual
has db xref: nlx_25179
synonym: Yogo
synonym: Yogo Data Management Framework
synonym: Yogo Framework
IAO_0000115: A set of software tools created to rapidly build scientific data-management applications. These applications will enhance the process of data annotation, analysis, and web publication. The system provides a set of easy-to-use software tools for data sharing by the scientific community. It enables researchers to build their own custom-designed data management systems. The problem of scientific data management rests on several challenges. These include flexible data storage, a way to share the stored data, tools to curate the data, and history of the data to show provenance. The Yogo Framework gives you the ability to build scientific data management applications that address all of these challenges. The Yogo software is being developed as part of the NeuroSys project. All tools created as part of the Yogo Data Management Framework are open source and released under an OSI approved license.

All In The Mind
type: Resource
type: NamedIndividual
has db xref: nlx_25223
IAO_0000115: Radio National''s weekly foray into all things mental a program (podcast) about the mind, brain and behavior, hosted by Lynne Malcolm (previously by Natasha Mitchell). From dreaming to depression, addiction to artificial intelligence, consciousness to coma, psychoanalysis to psychopathy, free will to forgetting ��All in the Mind��explores the human condition through the mind''s eye. All in the Mind brings together unexpected voices, themes and ideas and engages with both leading thinkers and personal stories. Psychology and human behavior are only part of the equation. The program''s scope is considerably broader and explores themes in science, religion, health, philosophy, education, history and pop culture, with the mind as the key focus.

American Donor Services
type: Resource
type: NamedIndividual
has db xref: nlx_25368
synonym: American Donor Services Inc.
abbrev: ADS
IAO_0000115: American Donor Services (ADS) is an independent, non-profit organization specializing in tissue donation. Its mission is to improve lives through the gift of donation. ADS honors the spirit of donation by providing caring support to donor families, employing competent staff, and partnering with organizations that are dedicated to the innovative use of tissue for transplantation and research. We are registered with the Food and Drug Administration (FDA). ADS is also accredited with the American Association of Tissue Banks (AATB) and employs dedicated and experienced leadership and staff to sustain our program. The fundamental objective of ADS is to provide the opportunity of donation to individuals who have designated themselves as a donor and families who have the inclination and the potential to have their loved one become a tissue donor. ADS is dedicated to the cause of all donations and as such will support all other organizations in their parallel undertakings. We are committed to providing the best possible serivce to our Donor Families, Hospitals, Medical Donate Life Examiners, Coroners and Funeral Professionals.

Life Alaska Donor Services, Inc.
type: Resource
type: NamedIndividual
has db xref: nlx_25780
synonym: Life Alaska Donor Services
abbrev: Life Alaska
IAO_0000115: Life Alaska Donor Services is the tissue donation organization serving the state of Alaska, offering the option of donation to families who have suffered a death in Alaska. Life Alaska was established in 1991 as the state''s tissue donation program. Since that time, Life Alaska has had many donors and has supplied thousands of tissues for transplantation to Alaskan patients. Life Alaska works in partnership with the federally designated Organ Procurement Organization in Washington (LifeCenter Northwest) to provide education on tissue and organ donation throughout the state. Tissue donations have taken place across the state, from Barrow to Ketchikan. The age criteria for transplantable tissues and organs are generally from birth to 80 years of age, with patients of any age being candidates for research. Tissues donated to Life Alaska are first offered to Alaskan patients and physicians before being made available outside the state. Organs are shared using the federally mandated national sharing system operated by the United Network for Organ Sharing and are first offered to transplant centers in the Pacific northwest.

AIDS and HIV Research
type: Resource
type: NamedIndividual
has db xref: nlx_143646
IAO_0000115: AIDS and HIV Research is a disease-related portal that includes Articles, News, Jobs, Free Journals, Links, Forum, Structures, Labs & Rankings. * AIDS and HIV research links are profiled and rated. You can rate each website and view the websites in a number of categories including portals, blogs, databases, software and several other categories. Below you will find the top 10 rated AIDS and HIV research links. * Recent AIDS and HIV research literature is highlighted. We have taken the entire set of AIDS and HIV research articles and arranged them according to their previous or expected citation rate. This allows you to quickly identify the most important articles in the field. * Recent AIDS and HIV research news and press releases are highlighted. We scour over 20,000 news sources to bring you the latest AIDS and HIV research news. * AIDS and HIV research laboratories are featured. We have actually profiled nearly 99% of all AIDS and HIV research laboratories. We have also ranked all labs based upon the citation rating of the papers of the principal investigator. Laboratories may alter information on each lab page including picture, publications, affiliation, and biography. You will find the top 20 AIDS and HIV research laboratories.

University of North Carolina at Charlotte; North Carolina; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100010942
has db xref: grid.266859.6
has db xref: ISNI:0000 0000 8598 2218
has db xref: nlx_155458
has db xref: Wikidata:Q1783178
synonym: Charlotte
synonym: UNC Charlotte
synonym: University of North Carolina at Charlotte
abbrev: UNCC
IAO_0000115: Public research university in Charlotte, North Carolina.

Biobank Graz
type: Resource
type: NamedIndividual
has db xref: nlx_25894
IAO_0000115: Biobank Graz is a non-profit central Medical University of Graz (MUG) service facility that provides the logistics and infrastructure to optimally support MUG research teams in the collection, processing and storage of biological samples and their associated data. In the course of this, special attention is given to sample and data quality and to the protection of the individual rights of patients. Samples from selected patients at the Graz LKH-University Clinical Centre, who have signed an informed consent declaration, are deposited in Biobank Graz. This means that excess tissue and blood samples are collected and placed in storage. The samples are harvested in the course of routine interventions undertaken by the different departments and institutes of the Graz LKH-University Clinical Centre and approved for use in research projects only after the completion of all necessary laboratory and histopathological analyses. No additional material is removed: in other words, there are no associated drawbacks whatsoever for the patients involved. Biobank Graz operates a quality management system according to ISO 9001:2008 and offers the following services for the processing and storage of biological samples and the handling of data: * Consistently high sample quality through the processing of samples using standardized methods in accordance with written working instructions (SOPs) * Efficient use of resources through the building of shared infrastructure and the development of optimized processes * A high degree of reliability provided by the storage of samples in 24/7 - monitored storage systems. * Processing and storage of all data in accordance with data protection legislation. Biobank Graz comprises both population-based and disease-focused collections of biological materials. It currently contains approx. 3.8 mio samples from approx. 1.2 mio patients representing a nonselected patient group characteristic of central Europe. Because the Institute of Pathology was, unti…

Kickstarter
type: Resource
type: NamedIndividual
has db xref: nlx_143647
IAO_0000115: Kickstarter is the world''s largest funding platform for creative projects. Every week, tens of thousands of amazing people pledge millions of dollars to projects from the worlds of music, film, art, technology, design, food, publishing and other creative fields. A new form of commerce and patronage. This is not about investment or lending. Project creators keep 100% ownership and control over their work. Instead, they offer products and experiences that are unique to each project. All or nothing funding. On Kickstarter, a project must reach its funding goal before time runs out or no money changes hands. Why? It protects everyone involved. Creators aren''t expected to develop their project without necessary funds, and it allows anyone to test concepts without risk. Each and every project is the independent creation of someone like you. Projects are big and small, serious and whimsical, traditional and experimental. They''re inspiring, entertaining and unbelievably diverse. We hope you agree... Welcome to Kickstarter!

StRAnGER
type: Resource
type: NamedIndividual
has db xref: nlx_25932
synonym: Statistical Ranking of ANotated Genomic Experimental Results
IAO_0000115: StRAnGER (Statistical Ranking of ANotated Genomic Experimental Results) is a web application for the automated statistical analysis of annotated gene profiling experiments, exploiting controlled biological vocabularies, like the Gene Ontology or the KEGG pathways terms. Starting from annotated lists of differentially expressed genes StRAnGER repartitions and reorders the initial distribution of terms to define a new distribution of elements where each element pools terms holding the same enrichment score. The elements are then prioritized according to StRAnGER' '''s algorithm and, by applying bootstrapping techniques, a corrected measure of the statistical significance of these elements is derived, enabling the selection of terms mapped to these elements, unambiguously associated with respective significant gene sets. Besides their high statistical score, another selection criterion for the terms is the number of their members, something that incurs a biological prioritization in line with a Systems Biology context. Platform: Online tool

UCSF DNA Bank
type: Resource
type: NamedIndividual
has db xref: nlx_26337
IAO_0000115: The DNA Bank accepts the clinical samples from projects that have been approved by the Committee on Human Research (CHR). Genomic DNA isolation is performed utilizing standardized and quality controlled Gentra Systems'' PureGene DNA isolation system or Qiagen Kits. The quantity and quality of the genomic DNA isolate is determined by 260/280 UV spectrophotometery. Following isolation and quality assessment, DNA can be aliquoted into a normalized concentration. The preparation of aliquots serves to allow ready distribution of DNA samples to both the client laboratory and their collaborators and to preclude excessive routine freezing and thawing of the primary DNA isolate, a practice which is well known to result in notable degradation of genomic DNA stocks. All samples are stored in alarmed Revco ultra-low freezers at -80����?����?����?��������C. All of the ultra-low freezer units utilized by the DNA Bank are monitored by a temperature sensitive alarm system that provides 24 hour oversight. In the event of a power outage, all freezers are on an emergency back-up electrical generator.

BSRD
type: Resource
type: NamedIndividual
has db xref: biotools:bsrd
has db xref: OMICS_01533
synonym: Bacterial Small Regulatory RNA Database
synonym: BSRD - Bacterial Small Regulatory RNA Database
IAO_0000115: A repository for bacterial small regulatory RNA. They welcome you to submit new experimental validated sRNA targets.

DER Finder
type: Resource
type: NamedIndividual
has db xref: biotools:derfinder
has db xref: OMICS_02208
synonym: derfinder
IAO_0000115: R package for differential expression analysis of RNA-seq data.

Cell Type Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_26501
synonym: Cell Ontology
synonym: cellontology.org
synonym: Obo-cell-type
abbrev: CL
IAO_0000115: Ontology designed as a structured controlled vocabulary for cell types. It was constructed for use by the model organism and other bioinformatics databases. It includes cell types from prokaryotes, mammals, and fungi. The ontology is available in the formats adopted by the Open Biological Ontologies umbrella and is designed to be used in the context of model organism genome and other biological databases.

Store-a-Tooth Stem Cell Bank
type: Resource
type: NamedIndividual
has db xref: nlx_26572
synonym: Store-a-Tooth - Stem Cells for Life
abbrev: Store-A-Tooth
IAO_0000115: Provia Laboratories Inc. offers Store-A-Tooth, the industry-leading dental stem cell banking service for preserving the stem cells found in baby teeth and wisdom teeth. Store-A-Tooth is a service that provides you the opportunity to store the stem cells inside of teeth that come out. Eligible teeth include baby teeth, wisdom teeth, and other healthy teeth that need to be surgically extracted during the normal course of dental care. Store-A-Tooth has been available since 2006 from dentists across the U.S. At the core of our tooth transport device is the Save-A-Tooth device, which is FDA-approved and ADA accepted for the preservation of avulsed teeth. We use Save-A-Tooth for tooth collection and transport to ensure optimal viability of your sample for processing and cryopreservation. Our laboratory is FDA-registered, CLIA-certified, and AABB-accredited.

N-Browse
type: Resource
type: NamedIndividual
has db xref: nlx_26609
synonym: N-Browse.PNG
synonym: NBrowse
IAO_0000115: Interactive graphical browser for biological networks and molecular interaction data. The N-Browse server at NYU currently provides access to a variety of large-scale functional genomic datasets from several species.

Webvision - The Organization of the Retina and Visual System
type: Resource
type: NamedIndividual
has db xref: nlx_26732
synonym: Webvision - The Organization of the Retina Visual System
abbrev: Webvision
IAO_0000115: Online textbook that has evolved into an interactive, dynamic blog that covers all things related to the bioscience of the visual system. It summarizes recent advances in knowledge and understanding of the visual system through dedicated chapters and evolving discussion to serve as a clearing house for all things related to retina and vision science.

Creative Biomart
type: Organization
type: NamedIndividual
has db xref: nlx_152336
IAO_0000115: An Antibody supplier

UC San Diego Biorepository
type: Resource
type: NamedIndividual
has db xref: nlx_26921
synonym: UC San Diego Moores Cancer Center Biorepository
synonym: UCSD Biorepository
synonym: UCSD Moores Cancer Center Biorepository
synonym: University of California San Diego Moores Cancer Center Biorepository
IAO_0000115: The Biorepository contains plasma, serum, RNA stabilized buffy coat, urine, viable tumor samples, and formalin-fixed paraffin-embedded tumor; all with associated clinical information. These can be provided to investigators with Cancer Sample Banking Committee approval (IRB approval is also required for projects requesting ongoing sample collection or clinical annotation.) Urine and blood-derived specimens are available from a wide variety of cancer cases and cancer-free controls. Tumor sample availability is more limited and predominately from breast and gastrointestinal malignancies. Samples are collected from consented subjects and de-identified clinical information on the subjects is collected over time. Subjects are consented for research germ line genotyping. Access to the clinical annotation is determined based on need as justified in each investigator''s request or protocol. Anonymized samples from the biorepository are available compliant with UCSD HRPP exempt category 4.

Janelia Research
type: Organization
type: NamedIndividual
has db xref: nlx_26970
synonym: HHMI Janelia Farm Research Campus
synonym: Janelia
synonym: Janelia Farm
synonym: Janelia Farm Research Campus
synonym: Janelia Research Campus
IAO_0000115: HHMI Center for integrated teams of lab scientists and tool builders to share methods, results, and tools with the scientific community. Janelia Research campus is a research campus of the Howard Hughes Medical Institute located in Ashburn, Virginia.

START Tumor Bank
type: Resource
type: NamedIndividual
has db xref: nlx_27097
synonym: South Texas Accelerated Research Therapeutics Tumor Bank
synonym: South Texas Tumor Bank
IAO_0000115: Biospecimen repository for tumor specimens, available to all researchers actively engaged in cancer research whether they are in University, Academic, or Pharmaceutical industry, with a goal to accelerate the discovery and development of new agents for the treatment and cure of cancer. The START tumor bank was created to make tumor tissue gifted by patients receiving care or treatment at The START Center available to all researchers involved in developing a better understanding of the biology of cancer or those engaged in the discovery of new therapies. The START Tumor Bank is a department within the PK Department and handles skin and tumor biopsies required by clinical trial protocols. A member of the PK Department is present during biopsy procedures for immediate processing of the sample for the trial. Additionally, the Tumor Bank collects and banks the tumor tissues of patients who consent. This tissue is then stored for future use by researchers developing new therapies.

National Resource for Network Biology
type: Resource
type: NamedIndividual
has db xref: nlx_27231
abbrev: NRNB
IAO_0000115: Biomedical technology research center that develops new algorithms, visualizations and conceptual frameworks to study biological networks at multiple levels and scales, from protein-protein and genetic interactions to cell-cell communication and vast social networks. They are developing freely available, open-source suite of software technology that broadly enables network-based visualization, analysis, and biomedical discovery for NIH-funded researchers. This software is enabling researchers to assemble large-scale biological data into models of networks and pathways and to use these networks to better understand how biological systems operate under normal conditions and how they fail in disease. The National Resource for Network Biology is organized around the following key components: Technology Research and Development, Driving Biomedical Projects, Outreach, Training and Dissemination of Tools. The NRNB supports several types of training events, including both virtual and live workshops; tutorials sessions for clinicians, biologists and bioinformaticians; presentations and demonstrations at conferences; online tutorials and webcasts; and annual symposium.

Broadband Forum
type: Resource
type: NamedIndividual
has db xref: nif-0000-30225
IAO_0000115: The Broadband Forum is the central organization driving broadband wireline solutions and empowering converged packet networks worldwide to better meet the needs of vendors, service providers and their customers. They develop multi-service broadband packet networking specifications addressing interoperability, architecture and management. Their work enables home, business and converged broadband services, encompassing customer, access and backbone networks. Keywords: Vendor, Service, Broadband, Wireline, Forum, Network,

SFARI - Simons Foundation Autism Research Initiative
type: Resource
type: NamedIndividual
has db xref: nlx_27321
synonym: Simons Foundation Autism Research Initiative
abbrev: SFARI
IAO_0000115: Launched in 2005, the Simons Foundation Autism Research Initiative (SFARI) is a research campaign within the Simons Foundation''s overall suite of programs. SFARI''s mission is to improve the diagnosis and treatment of autism spectrum disorders by funding, catalyzing and driving innovative research of the greatest quality and relevance. Although SFARI''s priority is to benefit individuals challenged by these disorders, its efforts are certain to yield insights into the neural mechanisms of fundamental human capabilities, thereby promoting the broader mission of the Simons Foundation to advance the frontiers of research in the basic sciences and mathematics. Autism spectrum disorders are a set of complex developmental disorders characterized by persistent deficits in social communication and interaction, as well as restricted behaviors, interests or activities. The Centers for Disease Control and Prevention estimates that roughly 1 in 110 children in the U.S. have autism, with many more boys affected than girls. These disorders cost the U.S. economy an estimated $35 billion dollars each year in direct care costs and lost productivity, and extract an incalculable human toll.

TFSEARCH: Searching Transcription Factor Binding Sites
type: Resource
type: NamedIndividual
has db xref: nlx_27602
synonym: TFSEARCH
synonym: TFSEARCH: DNA Transcription Factor Binding Site Prediction
synonym: Transcriptional Factor Search
IAO_0000115: The TFSEARCH searches highly correlated sequence fragments against TFMATRIX transcription factor binding site profile database in the "TRANSFAC" databases developed at GBF-Braunschweig, Germany. The TFSEARCH program was written by Yutaka Akiyama (Kyoto University, currently at RWCP) in 1995.

RefGenome
type: Resource
type: NamedIndividual
has db xref: nlx_27840
synonym: Reference Genome Annotation Project
synonym: Reference Genome Project
IAO_0000115: The GO Consortium coordinates an effort to maximize and optimize the GO annotation of a large and representative set of key genomes, known as ''reference genomes''. The goal of the Reference Genome Annotation project is to completely annotate twelve reference genomes so that those annotations may be used to effectively seed the automatic annotation efforts of other genomes. With more and more genomes being sequenced, we are in the middle of an explosion of genomic information. The limited resources to manually annotate the growing number of sequenced genomes imply that automatic annotation will be the method of choice for many groups. The Reference Genome project has two primary goals: to increase the depth and breadth of annotations for genes in each of the organisms in the project, and to create data sets and tools that enable other genome annotation efforts to infer GO annotations for homologous genes in their organisms. In addition, the project has several important incidental benefits, such as increasing annotation consistency across genome databases, and providing important improvements to the GO''s logical structure and biological content. All GO annotations from this project are included in the gene association files that each group submits to GO. Annotations can also be viewed using the GO search engine and browser AmiGO. Annotated families can be viewed with the homolog set browser.

CHB-MIT Scalp EEG Database
type: Resource
type: NamedIndividual
has db xref: nlx_28050
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 22, 2022. Data set collected at the Children''s Hospital Boston, of EEG recordings from pediatric subjects with intractable seizures. Subjects were monitored for up to several days following withdrawal of anti-seizure medication in order to characterize their seizures and assess their candidacy for surgical intervention. All signals were sampled at 256 samples per second with 16-bit resolution. Most files contain 23 EEG signals (24 or 26 in a few cases).

Donor Alliance
type: Resource
type: NamedIndividual
has db xref: nlx_28218
IAO_0000115: Donor Alliance is one of 58 not-for-profit organ recovery organizations federally designated by the U.S. Department of Health & Human Services to facilitate the donation and recovery of organs for people needing transplants. Additionally, Donor Alliance is a recognized leader in facilitating the donation and recovery of transplantable tissues in Colorado and most of Wyoming. Our goal is to save the lives of people in need. To achieve this, Donor Alliance employs effective family approach and recovery programs in more than 100 hospitals in Colorado and Wyoming. Additionally, Donor Alliance dedicates time, funding and effort toward increasing the number of registered organ and tissue donors through active public awareness and educational programs and grassroots public relations campaigns.

Scientific American Cross-Check
type: Resource
type: NamedIndividual
has db xref: nlx_144217
synonym: Scientific American - Cross-Check
abbrev: SA Cross-Check
IAO_0000115: Every week, John Horgan takes a puckish, provocative look at breaking science. A former staff writer at Scientific American, he is the author of four books, the most recent of which is The End of War (to be published by McSweeney''s Books January 17, 2012). He currently directs the Center for Science Writings at Stevens Institute of Technology. He lives in New York State''s Hudson Highlands, where he plays ice hockey each winter to hone his cross-checking skills.

Artemis: Genome Browser and Annotation Tool
type: Resource
type: NamedIndividual
has db xref: biotools:artemis
has db xref: nlx_28554
has db xref: OMICS_00903
abbrev: Artemis
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Free genome browser and annotation tool that allows visualization of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. Artemis is free software and is distributed under the terms of the GNU General Public License. Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.

PeaKDEck
type: Resource
type: NamedIndividual
has db xref: OMICS_02207
IAO_0000115: A peak-calling software program for DNAseI-seq data.

Medpedia
type: Resource
type: NamedIndividual
has db xref: nlx_28592
IAO_0000115: Medpedia is an open platform connecting people and information to advance medicine. This wiki is the collaborative encyclopedia and resource for information about health, medicine and the body. Only physicians and Ph.D.s are allowed to edit the Articles on Medpedia after they create an account and are approved as an Editor. Non-Editors can create an account and then suggest changes that must be approved by an Editor before going live on the site. To suggest changes, click the link Suggest Changes at the top of Article Pages. Intended Uses and Benefits: * Reference source for both medical professionals and the lay-public covering information about health, medicine and the body * Forum for individuals and groups to be recognized for their areas of expertise * Clearinghouse of bio-medical journal articles, data, research, and educational materials * Forum for debating emerging issues * Platform for advancing medical knowledge Medpedia Portals - Adult Primary Care, Allergy and Immunology, Anatomy, Cardiology, Emergency Medicine, Endocrinology, Epidemiology, Gastroenterology and Hepatology, General Medicine, Infectious Diseases, Internal Medicine, Neurology & Neurobiology, Nutrition, OB/GYN and Reproductive Health, Oncology, Orthopedics, Pathology, Pediatrics, Pharmacology, Psychiatry, Public Health, Pulmonology, Rheumatology, Women''s Health In association with Harvard Medical School, Stanford School of Medicine, Berkeley School of Public Health, University of Michigan Medical School and other leading global health organizations, Medpedia will be a commons for the gathering of the information and people critical to health care.

University of Minnesota Tissue Procurement Facility
type: Resource
type: NamedIndividual
has db xref: nlx_28712
synonym: Tissue Procurement Facility
synonym: UMN TPF
synonym: University of Minnesota Tissue Bank
abbrev: TPF
IAO_0000115: Procure and distribute human tissue and other biological samples in support of basic, translational, and clinical cancer research at the University of Minnesota. The TPF is a centralized resource with standardized patient consent, sample collection, processing, storage, quality control, distribution, and electronic record maintenance. Since the 1996 inception of the TPF, over 61,000 tissue samples including well-preserved samples of malignant and benign tumors, organ-matched normal tissue, and other types of diseased tissues, have been collected from surgical specimens obtained at the University of Minnesota Medical Center-Fairview (UMMC-F) University Campus. Surgical pathologists are intellectually engaged in TPF functions, providing researchers with specimen-oriented medical consultation to facilitate research productivity. Prior to surgery, TPF personnel identify and consent patients for procurement of tissue, blood, urine, saliva, and ascites fluid. Within the integrated working environment of the surgical pathology laboratory, freshly obtained tissues not needed for diagnosis are selected and provided by pathologists to TPF personnel. Tissue samples are then assigned an independent code and processed. TPF staff can also work with researchers to individualize the procurement of tissues to fit specific research needs.

NEALS Sample Repository
type: Resource
type: NamedIndividual
has db xref: nlx_143662
synonym: ALS Biofluid Repository
synonym: NEALS Biofluid Repository
synonym: Northeast ALS Consortium Sample Repository
IAO_0000115: Repository of serum, plasma, cerebrospinal fluid (CSF), whole blood, extracted DNA, and urine samples from NEALS and Massachusetts General Hospital Neurology Clinical Trials Unit (NCTU) research studies of amyotrophic lateral sclerosis (ALS). Samples from this repository are available to researchers for the purpose of furthering the understanding of ALS or developing disease biomarkers. Applications will be accepted at any time, but the committee meets bi-monthly to review applications. The application requires a brief description and scientific justification for the use of the samples. Priority will be given to members of NEALS and investigators from sites that participated in the collection of samples. Investigators must provide IRB approval from their institution. Applications may be submitted to: mghneuroclinicaltrialsunit (at) partners.org (please cc: tlincoln (at) partners.org) NEALS collects an administrative fee of $1,000 at the time of application submission to offset processing costs. If an application for samples is denied, 80% of the administrative fee will be returned. The administrative fee is waived for NEALS members. Checks may be made payable to: The Northeast ALS Consortium.

South Texas Blood and Tissue Center
type: Resource
type: NamedIndividual
has db xref: nlx_28900
synonym: South Texas Blood & Tissue Center
abbrev: STBTC
IAO_0000115: A non-profit, community resource that works with volunteer donors to provide the highest quality blood and tissue components to patients. They collect and test more than 200,000 components of life-saving blood and tissue each year from volunteers all over South Texas. Because patients are in constant need of blood, blood components, and/or tissue, donors are essential. By using cutting-edge technology, the team of dedicated professionals have helped save hundreds of thousands of lives over more than 35 years. They are a member of the American Association of Blood Banks (AABB); American Association of Tissue Banks (AATB) and America''s Blood Centers (ABC). We are also one of the first blood centers in the country to be registered by the International Standards Organization.

New Life Generation, Inc.
type: Resource
type: NamedIndividual
has db xref: nlx_60029
abbrev: New Life Generation
IAO_0000115: New Life Generation is a not-for-profit tissue agency headquartered in Indianapolis, Indiana. We recognize our responsibility to recover, process, store and distribute human tissues in a professional manner that is of service to the medical community, ensures safety of transplantable tissue, and increases the availability of quality allograft tissue. While our primary focus is tissue donation, we recognize that donation also includes organ, bone marrow, blood, and blood products.

Transplant Services Center
type: Resource
type: NamedIndividual
has db xref: nlx_28938
IAO_0000115: Transplant Services Center is a clinical and academic service center of UT Southwestern Medical Center which completes the Circle of Care from donation to transplantation by providing a full service tissue bank which procures, processes, stores and distributes tissue allografts. These transplantable tissues include corneas, sclera, skin, musculoskeletal and cardiovascular allografts, which restore function, improve the quality of life and in some cases even save lives. Transplant Services Center provides services to hospitals and physicians throughout Texas, the nation and on occasion worldwide. The mission of the Transplant Services Center is to * provide quality tissue grafts for transplantation, teaching, research and medical need that is responsive and appropriate to both the recipient need and the donor family; * to promote public and professional education to increase donor awareness; * and to contribute to advancements in transplantation technology.

University of Pennsylvania; Philadelphia; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100006920
has db xref: grid.25879.31
has db xref: ISNI:0000 0004 1936 8972
has db xref: nlx_24937
has db xref: SCR_022445
has db xref: Wikidata:Q49117
synonym: University of Pennsylvania
abbrev: Penn State
abbrev: UPenn
IAO_0000115: University of Pennsylvania is private Ivy League research university located in University City neighborhood of Philadelphia, Pennsylvania. Established in 1740, UPenn has 4 undergraduate schools and 12 graduate schools.

Nevada Donor Network, Inc.
type: Resource
type: NamedIndividual
has db xref: nlx_28947
synonym: Nevada Donor Network
abbrev: NDN
IAO_0000115: Nevada Donor Network (NDN) is a federally designated, not-for-profit organ, tissue, and eye procurement organization. NDN is responsible for the coordination, recovery, and distribution of donated human organs and tissues for transplantation and medical research throughout the Las Vegas area. In addition, NDN participates in national organ and tissue sharing in an effort to meet the ever-growing needs of patients awaiting transplantation therapy. NDN is one of the few organ procurement agencies in the country to manage the recovery of organs, tissues, and eyes in the same facility, making Nevada progressive in the field of organ and tissue procurement. NDN is certified by the Department of Health and Human Services and the Center for Medicare and Medicaid Services (CMS). The Network is accredited by the Eye Bank Association of America (EBAA), the American Society for Histocompatibility and Immunogenetics (ASHI), the Clinical Laboratory Improvement Act (CLIA), and the American Association of Tissue Banks (AATB).

Zebrafinch Brain Architecture Project
type: Resource
type: NamedIndividual
has db xref: nlx_143663
IAO_0000115: Atlas of high resolution Nissl stained digital images of the brain of the zebra finch, the mainstay of songbird research. The cytoarchitectural high resolution photographs and atlas presented here aim at facilitating electrode placement, connectional studies, and cytoarchitectonic analysis. This initial atlas is not in stereotaxic coordinate space. It is intended to complement the stereotaxic atlases of Akutegawa and Konishi, and that of Nixdorf and Bischof. (Akutagawa E. and Konishi M., stereotaxic atalas of the brain of zebra finch, unpublished. and Nixdorf-Bergweiler B. E. and Bischof H. J., A Stereotaxic Atlas of the Brain Of the Zebra Finch, Taeniopygia Guttata, http://www.ncbi.nlm.nih.gov.) The zebra finch has proven to be the most widely used model organism for the study of the neurological and behavioral development of birdsong. A unique strength of this research area is its integrative nature, encompassing field studies and ethologically grounded behavioral biology, as well as neurophysiological and molecular levels of analysis. The availability of dimensionally accurate and detailed atlases and photographs of the brain of male and female animals, as well as of the brain during development, can be expected to play an important role in this research program. Traditionally, atlases for the zebra finch brain have only been available in printed format, with the limitation of low image resolution of the cell stained sections. The advantages of a digital atlas over a traditional paper-based atlas are three-fold. * The digital atlas can be viewed at multiple resolutions. At low magnification, it provides an overview of brain sections and regions, while at higher magnification, it shows exquisite details of the cytoarchitectural structure. * It allows digital re-slicing of the brain. The original photographs of brain were taken in certain selected planes of section. However, the brains are seldom sliced in exactly the same plane in real experiments. Re-slicing prov…

BOLD
type: Resource
type: NamedIndividual
has db xref: DOI:10.5883
has db xref: DOI:10.17616/R3PP7J
has db xref: DOI:10.25504/FAIRsharing.en9npn
has db xref: nlx_29236
has db xref: r3d100010129
synonym: Barcode of Life Data Systems
synonym: Barcode of Life Database
synonym: Barcode of Life Database Systems
synonym: BOLD : The Barcode of Life Data System
synonym: BOLD Systems
IAO_0000115: DNA barcode data with an online workbench that supports data validation, annotation, and publication for specimen, distributional, and molecular data. The data platform consists of three main modules, a data portal, a database of barcode clusters, and data collection workbench. The Public Data Portal provides access to all public barcode data which consists of data generated using the Workbench module as well as data mined from other sources. The Barcode Index Number (BIN) system assigns a unique identifier to each sequence cluster of COI, providing an interim taxonomic system for species in the animal kingdom. The workbench module integrates secure databases with analytical tools to provide a private collaborative environment for researchers to collect, analyze, and publish barcode data and ancillary DNA sequences. This platform also provides an annotation framework that supports tagging and commenting on records and their components (i.e. taxonomy, images, and sequences), allowing for community-based validation of barcode data. By providing specialized services, it aids in the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances. Public data records include record identifiers, taxonomy, specimen details, collection information and sequence data. Data that has been publicly released through BOLD can be retrieved manually through the BOLD public interface or automatically through BOLD web services. BOLD analytical tools are available for any data set that exists in BOLD (including publicly available data). Analytical tools can be accessed through the BOLD Project Console under the headings Sequences Analysis or Specimen Aggregates. Some examples include Taxon ID Tree, Alignment Viewer, Distribution Maps, and Image Library.

Scholarometer
type: Resource
type: NamedIndividual
has db xref: nlx_29330
IAO_0000115: Scholarometer (beta) is a social tool to facilitate citation analysis and help evaluate the impact of an author''s publications. It is a social (crowdsourcing) application that leverages the wisdom of the crowds. Scholarometer makes visualization of author and discipline networks available on the web site. It requires users to tag their queries with one or more discipline names, choosing from predefined ISI subject categories or arbitrary tags. This generates annotations that go into a database, which collects statistics about the various disciplines, such as average number of citations per paper, average number of papers per authors, etc. This data is publicly available. Scholarometer users can save the finding into formats appropriate for local reference management software (e.g., EndNote), or for social publication sharing systems (e.g., BibSonomy). Currently, our system supports the following export formats: BibTex (BIB), RefMan (RIS), EndNote (ENW), comma-separated values (CSV), tab-separated values (XLS), and BibJSON. Export data is dynamically generated in response to any filter, merge or delete actions performed by the user. Since Scholarometer is a browser extension that provides a smart interface for Google Scholar, it does not have the limitations of server based citation analysis tools that sit between the user and Google Scholar. At the same time Scholarometer is not an application, such as Publish or Perish, and therefore it is platform independent and runs on every system that supports the Firefox or the Chrome browser. Still, Scholarometer uses Google Scholar, which provides the most comprehensive source of citation data across the sciences and social sciences. Scholarometer provides a RESTful web API so that other developers can make use of our crowdsourced data. Select the method on the left panel to see corresponding documentation. The extension/add-on code is available in the Mozilla Firefox Add-ons and Google Chrome Extensions repositories. Addi…

OECI - Tubafrost: The European Human Frozen Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_36384
synonym: OECI TuBaFrost
synonym: OECI-TuBaFrost
synonym: OECI-TuBaFrost database
synonym: Tubafrost - The European Human Frozen Tissue Bank
synonym: TuBaFrost biobank
synonym: Tubafrost Central Database
abbrev: Tubafrost
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. In this web site you will find the central European database of OECI-TuBaFrost collecting the information of biobanks or in the project support environment on human material; i.e., frozen tumor tissue specimens, pathology blocks, blood samples in different forms, cell lines, Tissue Micro Arrays, etc. Our goal is by centralizing the tumor tissues information to facilitate the search of doctors / researchers for tumor materials, which they need for their cancer research there with facilitating cancer research. OECI members only can participate in the OECI-TuBaFrost exchange platform, or those introduced by an OECI member. We are a group of pathology and research departments as well as bio-bankers in clinical based biobanking based in comprehensive cancer centers or hospitals with a competence in comprehensive cancer care across Europe. Each participating institute is involved in cancer research resulting in innovative procedures, new drugs, improved diagnosis and new insights in disease development. The overall result is better care and treatment for cancer patients. To maximize the scientific value of the human tissue samples, information about the clinical status of the patient in combination with the quality and type of samples is very important. A TuBaFrost electronic database will securely store all this information. Within the closed project supporting environments, the data collected will include: * Diagnosis - identification of the type of cancer * Type of tissue collected - the origin, i.e. breast, skin, colorectal * Quality of tissue collected - collection and storage details The tissue is stored in the hospital where the donor was diagnosed/treated. It stays there until it is used or sent to another hospital or research center within the TuBaFrost group. The electronic database will track samples throughout the network. The tissue is not sold. The exchange of tissue to other hospitals is …

Cincinnati Biobank Core Facility
type: Resource
type: NamedIndividual
has db xref: nlx_29770
synonym: Cincinnati Biobank
synonym: Cincinnati Children's Hospital Medical Center Discover Together Biobank
synonym: Cincinnati Childrens Biobank
synonym: Discover Together Biobank
IAO_0000115: Provides access to services for standardized and centralized acquisition, processing, storage and distribution of biospecimens for research. Services include biospecimen storage, serum and plasma processing, preparation of kits for sample collection and shipping, automated DNA/RNA extraction from blood, saliva, tissue and other materials, biofluid collection, processing and storage, tissue collection, processing and storage.Home to Better Outcomes for Children (BofC) biorepository.

OHSU Biolibrary
type: Resource
type: NamedIndividual
has db xref: nlx_29846
synonym: OCTRI - OHSU Biolobrary
synonym: Oregon Health and Science University Biolibrary
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023.A Joint Project between Oregon Clinical and Translational Research Institute (OCTRI) and the Knight Cancer Institute, the OHSU Biolibrary provides information on campus collections of biospecimens originating from OHSU patients. The Biolibrary Search Engine is a user-friendly, online search tool that allows OHSU researchers to search for suitable biospecimen samples. As of October 2010, the Biolibrary Search Engine contains data on over 500,000 biospecimens. The Search Engine accesses data from the OHSU Cancer Registry, the Department of Pathology, and the OCTRI Research Data Warehouse. You must be connected to the OHSU network to access the Search Engine. The Search Engine is accessible on Internet Explorer through WTS connection to the OHSU network.

Brain Architecture Project
type: Resource
type: NamedIndividual
has db xref: nlx_143664
synonym: BrainArchitecture
synonym: BrainArchitecture.org
IAO_0000115: Evolving portal that will provide interactive tools and resources to allow researchers, clinicians, and students to discover, analyze, and visualize what is known about the brain's organization, and what the evidence is for that knowledge. This project has a current experimental focus: creating the first brainwide mesoscopic connectivity diagram in the mouse. Related efforts for the human brain currently focus on literature mining and an Online Brain Atlas Reconciliation Tool. The primary goal of the Brain Architecture Project is to assemble available knowledge about the structure of the nervous system, with an ultimate emphasis on the human CNS. Such information is currently scattered in research articles, textbooks, electronic databases and datasets, and even as samples on laboratory shelves. Pooling the knowledge across these heterogeneous materials - even simply getting to know what we know - is a complex challenge that requires an interdisciplinary approach and the contributions and support of the greater community. Their approach can be divided into 4 major thrusts: * Literature Curation and Text Mining * Computational Analysis * Resource Development * Experimental Efforts

PubChem
type: Resource
type: NamedIndividual
has db xref: biotools:pubchem
has db xref: nlx_29861
has db xref: nlx_42691
has db xref: OMICS_01587
has db xref: r3d100010538
IAO_0000115: Collection of information about chemical structures and biological properties of small molecules and siRNA reagents hosted by the National Center for Biotechnology Information (NCBI).

OBO Relation Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_33226
synonym: OBO RO
synonym: Relation Ontology
abbrev: OBO REL
abbrev: RO
IAO_0000115: The OBO Relation Ontology is an ontology of core relations for use by OBO Foundry ontologies. To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena. The OBO Relation ontology is undergoing substantial changes: * Core domain-independent relations will live in BFO * Biology specific relations (defined in terms of core relations) will live in RO

Novus Biologicals
type: Organization
type: NamedIndividual
has db xref: grid.420893.4
has db xref: ISNI: 0000 0004 0627 4379
has db xref: nlx_143665
has db xref: nlx_152382
has db xref: Wikidata: Q7065122
synonym: Novus
synonym: Novus Biologics LLC
IAO_0000115: Commercial antibody vendor which supplies antibodies and other products to life science researchers.

Ochsner Blood Bank
type: Resource
type: NamedIndividual
has db xref: nlx_30312
IAO_0000115: The primary blood supplier for Ochsner Medical Center, Ochsner Health Center - Kenner, Ochsner Health Center - West Bank, Ochsner Baptist Health Center, Ochsner St. Anne General Hospital and Lady of the Sea General Hospital in Cut Off. In addition, Ochsner Blood Bank participates in blood-resource sharing with other local community hospitals. Ochsner Blood Bank''s mission is to provide an adequate and safe blood supply for the hospitals and communities Ochsner serves. More than 45,000 blood components were transfused just last year. There''s also supporting information that indicates there will be a significant increase in transfusions for the current year. Blood replacement removes some of the costs of blood, but more importantly it provides patients with a safe and adequate blood supply. It''s likewise insurance that blood will be readily available should the need arise. If you happen to need blood during a hospital stay, please consider asking your family and friends to replace the blood that was transfused. Ochsner offers a blood replacement plan that takes care of everything. It even provides coverage for your family members, or other designated individuals, to receive the replacement units for up to one year should they need them.

Wikikidney.org
type: Resource
type: NamedIndividual
has db xref: nlx_30377
synonym: Wiki.Nephron.org
synonym: Wikikidney
IAO_0000115: Wikikidney.org is an effort to prevent kidney diseases and achieve better outcomes in those who have end stage renal disease. Our mission is to use this medium to make the public more aware of kidney disease in a sincere effort to prevent it when we can, and to help our colleagues achieve good outcomes in those who already have end stage renal disease. Our role is to provide as much information as possible to patients, professionals and the general public, with the hopes that this education will be a motivating factor in making the necessary changes to prevent or stall chronic kidney disease. After nearly two decades of seeing patients with end stage renal disease, it is apparent that much of what we deal with can be delayed or prevented altogether. Several medical trials and innovations in the last several years have confirmed these observations, and form the basis of this website. A major element in preventing renal illness is simply early detection, and for this one needs education. As the Internet expands and becomes more and more a tool of everyday life, we will have the ability to access and distribute information like no other generation before us. Qualified readers are encouraged to contribute to existing articles and to create articles of their own. Contents * 1 Kidney Resources - NIC * 2 Especially for Patients * 3 General Kidney Resources * 4 Issues in Nephrology * 5 Clinical Wiki Projects * 6 Be an author, editor or reviewer on wikikidney * 7 Clinical Trials * 8 Newsdesk Top Stories * 9 Essential Physician Resources * 10 Organizations * 11 Government Agencies * 12 Vendor and other Sites * 13 Patents * 14 Index

Brown University Rhode Island Biobank Core Facility
type: Resource
type: NamedIndividual
has db xref: ABRF_167
has db xref: nlx_30512
synonym: Brown University Rhode Island Biobank Cryogenic Core Facility
synonym: Rhode Island Biobank
synonym: RI BioBank
abbrev: RIBB
IAO_0000115: Cryogenic facility for human tissue and fluid samples under management of Brown University Division of Biology and Medicine and supports biomedical research on Brown campus and across affiliated hospitals of Warren Alpert Medical School.

KLI Theory Lab
type: Resource
type: NamedIndividual
has db xref: nlx_143667
synonym: KLI Theory Lab: A powerful scientific database
synonym: Konrad Lorenz Institute Theory Lab
IAO_0000115: The primary aim of the KLI Theory Lab is to highlight interconnections between topics of problems of research on evolution and cognition that look theoretically or methodologically promising. Quite often such correlations remain unrecognized because of the disciplinary closure that characterizes the organization of the scientific enterprise. * Introductory Resources: Introductory texts to various relevant disciplines, provided by the Konrad Lorenz Institute include: ** Introduction to Artificial Intelligence ** Introduction to Artificial Life ** Introduction to Cognitive Science ** Introduction to Cultural Evolution ** Introduction to Developmental Biology ** Introduction to Epistemology & Philosophy of Science ** Introduction to Ethology & Sociobiology ** Introduction to Evolutionary Biology ** Introduction to Evolutionary Epistemology ** Introduction to Genetic Epistemology ** Introduction to History and Social Sciences ** Introduction to Normative Issues ** Introduction to Philosophy of Biology ** Introduction to Philosophy of Mind ** Introduction to Theoretical Biology * Reference Database: The KLI Theory Lab contains a vast collection of research papers that have been selected based on their significance and quality. ** Search references: The search page allows you to search for references and to narrow down your search based on keywords. Results are ordered by relevance. ** Browse references: All references in the database, ordered by date of publication.

Myeloma Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_30783
synonym: MMRC Model: Myeloma Tissue Bank
synonym: Multiple Myeloma Research Constortium Tissue Bank
abbrev: MMRC Tissue Bank
IAO_0000115: Until recently, a scarcity of high-quality myeloma tissue has posed one of the greatest challenges in advancing myeloma research and drug development. Now, with the successful establishment of the MMRC Tissue Bank, researchers for the first time have access to the critical mass of high-quality tissue needed to rapidly validate novel and combination therapies for myeloma. The MMRC Tissue Bank is the only resource of its kind that integrates myeloma tissue samples with corresponding genomic and clinical data. To date, the MMRC Tissue Bank has accrued more than 2,700 samples with matching peripheral blood samples, with ongoing collection of tissue samples at Member Institutions nationwide. To further accelerate accrual, the MMRC has also launched a direct-to-patient program to enable myeloma patients to donate their tissue to the MMRC Tissue Bank. Notably, all tissue accrued into the MMRC Tissue Bank is uniformly collected and stored in adherence with Good Laboratory Practices (GLP) standards and under the governance of more than 50 standard operating procedures. The MMRC has also established a quality assurance unit that performs weekly internal quality assurance reviews and issues quarterly quality assurance reports. In addition, the MMRC Tissue Bank has been audited twice by external organizations since its inception last year. With these stringent practices in place, the MMRC has ensured that all tissue samples in the MMRC Tissue Bank are of the very highest-quality and, as such, has quickly become the premier resource for industry seeking fresh tissue samples to initiate strong validation work.

Gephi
type: Resource
type: NamedIndividual
has db xref: nlx_31183
IAO_0000115: Open-source software for network visualization and analysis helping data analysts to intuitively reveal patterns and trends, highlight outliers and tells stories with their data. It uses a 3D render engine to display large graphs in real-time and to speed up the exploration. Gephi combines built-in functionalities and flexible architecture to: explore, analyze, spatialize, filter, cluterize, manipulate and export all types of networks. Gephi runs on Windows, Linux and Mac OS X. Gephi is based on a visualize-and-manipulate paradigm which allow any user to discover networks and data properties. Moreover, it is designed to follow the chain of a case study, from data file to nice printable maps. It is open-source and free (GNU General Public License). Applications: * Exploratory Data Analysis: intuition-oriented analysis by networks manipulations in real time. * Link Analysis: revealing the underlying structures of associations between objects, in particular in scale-free networks. * Social Network Analysis: easy creation of social data connectors to map community organizations and small-world networks. * Biological Network analysis: representing patterns of biological data. * Poster creation: scientific work promotion with hi-quality printable maps. Gephi 0.7 architecture is modular and therefore allows developers to add and extend functionalities with ease. New features like Metrics, Layout, Filters, Data sources and more can be easily packaged in plugins and shared. The built-in Plugins Center automatically gets the list of plugins available from the Gephi Plugin portal and takes care of all software updates. Download, comment, and rate plugins provided by community members and third-party companies, or post your own contributions!

TAGS
type: Resource
type: NamedIndividual
has db xref: biotools:tags
has db xref: nlx_31187
IAO_0000115: Software tool for gene set enrichment analysis for expression time series, which can incorporate existing knowledge and analyze the dynamic property of a group of genes that have functional or structural associations. The installation file is for Windows., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

US Biomax
type: Resource
type: NamedIndividual
has db xref: nlx_31395
synonym: US Biomax Inc.
IAO_0000115: Our robust searchable Tissue Bank database at US Biomax contains normal, non-cancerous disease and cancer samples, just a fraction of total paraffin tissue bank. Use advanced search function to define your search. Some of them have H&E images. Our tissue repository, tissue bank has huge paraffin tissue blocks, a large selection of histology tissue section slides of human cancer, normal tissue, rhesus and cynomolgus normal fresh frozen tissue as well as paraffin blocks and slides. It has also normal human organs in paraffin embedded tissue blocks as well as rhesus and cynomolgus monkey normal organ tissues. Snap frozen (fresh frozen) tissue of rhesus/cynomolgus monkey are also available. We also provide tissue array, custom tissue microarray (with samples you provided or from our tissue bank) as well as OEM services. Other products/services available include tissue microarray, paraffin tissue sections, histology services and quantitative telomerase detection kit.

Cosmo Bio Co
type: Organization
type: NamedIndividual
has db xref: grid.461874.8
has db xref: ISNI: 0000 0004 0513 0496
has db xref: nlx_152334
synonym: Cosmo Bio Co. Ltd.
IAO_0000115: An Antibody supplier

St. Louis University Department of Neurology and Psychiatry
type: Organization
type: NamedIndividual
has db xref: nlx_144149
synonym: SLU Department of Neurology & Psychiatry
synonym: St. Louis University Department of Neurology & Psychiatry
synonym: St. Louis University Department of Neurology Psychiatry
abbrev: SLU DNP
IAO_0000115: The Department of Neurology & Psychiatry aims to 1) provide the best psychiatric and neurological care to patients and their families, 2) discover and investigate new treatments for psychiatric and nervous system disorders, 3) study psychosocial processes in psychiatric and neurological illness, and 4) educate the next generation of practitioners, as well as our patients and the lay community. The Department of Neurology & Psychiatry (DNP) was established on June 1, 2007. The Department has 34 faculty members and is planning continued expansion. There are 7 psychiatrists, 18 neurologists, 4 child neurologists, and 5 NIH-supported PhD investigators. The DNP is one of five departments in the country that combines the disciplines of neurology and psychiatry. We are unique in having two strong residency programs and are the only that attempts to establish a new paradigm in care of patients with neurological and psychiatric disease through co-management initiatives. * Division of Psychiatry: The Psychiatrists work within four areas: Adult, Geriatric, Community, and Forensic Psychiatry. * Division of Neurology: The division has an extremely active stroke/intensive care and general neurology service. We are expanding services in neurocritical care and interventional neurology. * Education: The DNP has approximately 25 residents/fellows in each discipline. * Research: The DNP has robust programs in clinical, basic, and translational research. We emphasize 3 areas in this overview of the DNP. ** Clinical Research Unit ** Psychosocial Processes Group ** Translational Neuromuscular Disease VISION STATEMENT All members of the Saint Louis University Department of Neurology & Psychiatry will collaborate to support state-of-the-art neurological and psychiatric education, compassionate patient care, and a growing research enterprise. The Department will develop the most exciting intellectual environment in the Nation for investigation, treatment, and training in psychiatry and neur…

LifeShare Transplant
type: Resource
type: NamedIndividual
has db xref: nlx_31426
synonym: LifeShare Transplant Donor Services of Oklahoma
abbrev: LifeShare
IAO_0000115: LifeShare Transplant Donor Services of Oklahoma strives to recover healthy, transplantable organs and tissues through careful screening and management of donors to provide the maximum number of lifesaving/life-enhancing organs and tissues for patients awaiting transplantation in Oklahoma. It is committed to providing a better quality of life for those people who require organ or tissue transplantation, while respecting and honoring those families who share the gift of life. LifeShare emphasizes a person''s decision to be an organ and tissue donor and whenever possible will honor the decision of the individual to donate. It works hard to provide education to the state of Oklahoma about organ, eye and tissue donation. Education is provided to medical professionals who identify and care for potential organ and tissue donors, and recognize donation as continuing to care for the patient and their family. LifeShare strongly supports research and development to improve the quality and availability of organs and tissues for transplantation and the success of human transplantation in general. It is also committed to providing support and comfort to grieving families who have suffered great loss.

Taxonomy
type: Resource
type: NamedIndividual
has db xref: nlx_31444
synonym: Taxonomy via SRS
IAO_0000115: The taxonomy database of the International Sequence Database Collaboration contains the names of all organisms that are represented in the sequence databases with at least one nucleotide or protein sequence. The database is available via the EBI SRS server of ftp.

Alzheimer Society of Ireland
type: Organization
type: NamedIndividual
has db xref: grid.496983.9
has db xref: nlx_143672
synonym: Alzheimer''s Society of Ireland
synonym: Alzheimers Society of Ireland
IAO_0000115: The Alzheimer Society of Ireland is the leading dementia specific service provider in Ireland. The Society is a company limited by guarantee and a registered charity - CHY 7868. The Society was founded in 1982 by a small group of people who were caring for a family member with Alzheimer''s Disease or a related dementia. Today, it is a national voluntary organization with an extensive national network of branches, regional offices and services that aims to provide people with all forms of dementia, their families and carers with the necessary support to maximize their quality of life. As the major dementia-specific service provider in Ireland, The Society''s network includes over 100 dementia specific services such as day care centers, home care services, carer support groups, social clubs, a national respite center and an advocacy service. The Society also operates the Alzheimer National Helpline Service offering information and support to anyone affected by Alzheimer''s disease / dementia at 1800 341 341. For a full list of services in your area please see the We Can Help section. The Society comprises over 2,500 members, 300 volunteers and over 700 full and part-time staff. The Society has 6 regional offices and a network of Branches around the country. A number of core functions are operated through our national office including information, policy and research, fundraising, public relations, training and finance.

Ray Truant Lab
type: Resource
type: NamedIndividual
has db xref: nlx_31488
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 21, 2013. Laboratory portal of Ray Truant, PhD. It provides an image gallery and videos.

BioStorage Technologies
type: Resource
type: NamedIndividual
has db xref: nlx_31526
synonym: BioStorage Technologies Inc.
IAO_0000115: At BioStorage Technologies, our mission is to provide our clients with world class, biorepository services, exceeding clients����?? expectations of service, value and quality while setting the industry standard for the storage, management & logistics of samples. Offering onsite or outsourced management of sample assets, BioStorage Technologies manages the complete life-cycle of samples. With a team of global sample experts, state-of-the-art temperature-controlled storage facilities, and a real-time web-based sample intelligence and tracking system, the company supports customers in maximizing opportunities, minimizing risk and reducing the cost of sample management. The unique advantages of BioStorage Technologies * Consulting����??Expert consulting on Good Storage Practices, global transport standards, standard operating procedures and business continuity planning to mitigate risk and optimize your resources * Consolidation����??Comprehensive management of the sample lifecycle through consolidation of sample data into one technology system for faster retrieval, more flexible tracking and enhanced security * Control����??Enhanced control of sample asset data within one technology system, ISISS, for faster go/no-go decisions and expansion into future research * Compliance����??Improved chain of custody of your samples and easier audit trail tracking for adherence to quality and regulatory compliance standards in order to support product approvals * Cost-Reduction����??Reduced cost of sample management and increased project ROI through more efficient sample and data management processes, enabling you to refocus resources on your core competencies BioStorage Technologies, Inc. was founded in 2002 and is privately held and headquartered in North America in Indianapolis, Indiana with an additional full-service site in Europe near Frankfurt, Germany.

Alzheimers Disease International
type: Resource
type: NamedIndividual
has db xref: nlx_143673
synonym: Alzheimer''s Disease International
abbrev: ADI
IAO_0000115: Alzheimer''s Disease International (ADI) believes that the key to winning the fight against dementia lies in a unique combination of Global Solutions and local knowledge. As such, it works locally, by empowering Alzheimer associations to promote and offer care and support for people with dementia and their carers, while working globally to focus attention on dementia. Our board is composed of people from around the world, and our staff team is based in London. ADI is the international federation of Alzheimer associations around the world, in official relations with the World Health Organization. Each member is the Alzheimer association in their country who support people with dementia and their families. ADI''s vision is an improved quality of life for people with dementia and their families throughout the world. ADI runs the Alzheimer University, a series of practical workshops aimed at helping the staff and volunteers of Alzheimer associations build and strengthen their organisations. ADI holds an annual international conference which is the longest running international conference on dementia. The conference is a unique multi-disciplinary event which unites people with an interest in dementia from around the world. World Alzheimer''s Day, celebrated on September 21 each year, is an opportunity to raise global awareness about dementia and its impact on families and the important work of our members throughout the world. Medical research is also important, and some of ADI''s member Alzheimer associations actively support research in their own countries. More information about research can be found on the web sites of Alzheimer''s Association (USA), Alzheimer''s Society (UK), Alzheimer Society of Canada, or the association in your country. For the fourth year, the Fondation M��d��ric Alzheimer and ADI are running Alzheimer''s Awards for evidence-based psychosocial interventions for people with dementia and their carers.

Duke Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_31838
synonym: DTRI Biobanking
synonym: Duke Translational Research Institute Biobanking
IAO_0000115: The Duke Biobank is an institutional resource that combines well-annotated clinical data with a standardized, regulation compliant, cost efficient repository for both fluid and tissue, connected via information systems to a large scale, long-term biobank in Kannapolis, in order to foster breakthroughs in research; while ensuring the strictest adherence to ethical standards and regulations. Our goal is to work with investigators to maintain biorepository collections which are in compliance with all relevant local, regional and national and IRB biobanking standards. Capabilities * Provide expert consultation in planning and design of biobanking programs * Access, process, aliquot, store and distribute a wide array of liquid and tissue biological samples * Maintain informatics capabilities to accurately and efficiently track samples and link to clinical and laboratory assay data * Use the Duke Biobanking Guidelines document (in development) as guidance on scientific, ethical/legal, and operational to ensure quality and standardization of biospecimen collection * Minimize redundancy of infrastructure, as appropriate, across Duke Medicine. Duke University offers both on- and off-campus options for investigators seeking biobanking services. Our biobanking facilities are: * The Center for Human Genetics (CHG). Serves as the primary on-campus biobank for liquid sample storage for Duke Medicine, and as a portal between Duke and the LabCorp Biobank. * Duke Hospital South Tissue Bank. Serves as a sample portal for the Duke Biobank, and as the primary facility for tissue storage for Duke Medicine. ** DCCC Tissue & Blood Procurement ** IGSP Biospecimen Repository * LabCorp Biorepository. Located in Kannapolis, NC, this is the preferred storage center for large-scale, infrequently accessed sample collections

UAB Alzheimer's Disease Center
type: Resource
type: NamedIndividual
has db xref: nlx_143674
synonym: University of Alabama at Birmingham Alzheimer's Disease Center
abbrev: ADC
abbrev: UAB ADC
IAO_0000115: The UAB Alzheimer's Disease Center provides comprehensive treatment for Alzheimer's patients while also promoting research for the prevention and cure of Alzheimer's disease and related disorders. The ADC is an interdisciplinary program of scientists working in areas including neurology, psychiatry, genetics, and psychology. The Center provides comprehensive treatment and promotes research for the prevention and/or cure of Alzheimer's disease and other related disorders with memory loss and impaired cognition. A major emphasis of research is the maintenance of a clinical research database comprised of neurological, medical, and neuropsychological test data from participants seen in the ADRC Clinical study since 1999, many of whom have been followed for several years in the study.

Duke Biospecimen Repository
type: Resource
type: NamedIndividual
has db xref: nlx_32022
synonym: Duke IGSP Biospecimen Repository
synonym: Duke-IGSP Biospecimen Repository
IAO_0000115: The Duke Institute for Genome Sciences & Policy (IGSP), in partnership with the Duke University School of Medicine Research Foundation and Department of Pathology (SOMRF), has established the Duke IGSP Biospecimen Repository as a centralized and accessible biological resource for Duke Investigators and research programs. The Repository is a standardized, regulatory-compliant and privacy protected repository for fluid and tissue biospecimens, and enables Duke investigators to reduce costs, and eliminate redundancies and significant risks associated with alternative biobanking practices, while facilitating integration of clinical trials and translational research programs with molecular profiling technologies. In order to ensure sample and data integrity and comparability, the Biorepository is developing, evaluating, and implementing evidence-based biobanking ''best practices''. Centralization of activities to a dedicated and expert staff and facility allows small and large research programs to reduce costs through elimination of redundancies and achieving efficiencies and economies of scale. The Duke-IGSP Biorepository is committed to ensuring appropriate consent, approved use, and protection of privacy through compliance with HIPAA regulations and IRB guidelines. The Duke-IGSP Biospecimen Repository will facilitate the integration of clinical research programs with molecular profiling technologies, enabling large-scale ''omic'' research programs that will inform and drive the development of new generations of targeted diagnostics, therapies, and preventions, which in turn will transform clinical outcomes.

Babel
type: Resource
type: NamedIndividual
has db xref: OMICS_01530
synonym: babel: Ribosome profiling data analysis
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documentedt on January 10, 2023. Software that implements babel routines for identifying unusual ribosome protected fragment counts given mRNA counts, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Neuroscience News: Neuroscience Books
type: Resource
type: NamedIndividual
has db xref: nlx_143833
abbrev: Neuroscience Books
IAO_0000115: Favorite and most desired neuroscience books, and books in fields related to neuroscience, listed by Neuroscience News staff members. You may search for books or browse by category. If you don''t see your favorite neuroscience books, or related science books for sale on the site, they want you to let them know which neuroscience books they should include.

qvality - Nonparametric estimation of posterior error probabilities
type: Resource
type: NamedIndividual
has db xref: nlx_32652
synonym: qvality
IAO_0000115: qvality estimates q-values and posterior error probabilities directly from score distributions. The method can be accessed via a web interface or downloaded as stand-alone software (C++ source code and binaries are available under MIT license). The qvality web server allows you to use qvality to compute posterior error probability and q-values for your data. There are two input modes: *Input the empirical score distribution and a corresponding null score distribution. The two inputs do not have to contain the same numbers of scores. *Input only the empirical p-value distribution. In this case, you must use p-values rather than raw scores. In either mode, the output is the same: a three-column file in which the first column contains sorted observed scores, the second column contains estimated q-values, and the third column contains estimated posterior error probabilities. Qvality is a C++ program for estimating two types of standard statistical confidence measures: the q-value, which is an analog of the p-value that incorporates multiple testing correction, and the posterior error probability (PEP, also known as the local false discovery rate), which corresponds to the probability that a given observation is drawn from the null distribution. In computing q-values, qvality employs a standard bootstrap procedure to estimate the prior probability of a score being from the null distribution; for PEP estimation, qvality relies upon non-parametric logistic regression. Relative to other tools for estimating statistical confidence measures, qvality is unique in its ability to estimate both types of scores directly from a null distribution, without requiring the user to calculate p-values.

GeneDB Gmorsitans
type: Resource
type: NamedIndividual
has db xref: nlx_32209
synonym: Glossina morsitans GeneDB
abbrev: GeneDB G. morsitans
IAO_0000115: As of 12th March 2009, GeneDB provides access to the transcriptome of the Tsetse fly Glossina morsitans morsitans, the biological vector of African trypanosomiases. The current data set includes: >>7,015 contigs comprised of ESTs from Trypanosoma brucei infected midgut tissue (Lehane et al, Genome Biol. 2003;4(10):R63) >>7,493 contigs comprised of ESTs from salivary gland tissue >>18,404 contigs comprised of EST pooled from a range of different tissue- and developmental stage-specific libraries: head (2,700 ESTs), midgut (21,662 ESTs), reproductive organs (3, 438 ESTs), salivary gland (27,426 ESTs), larvae (2,304 ESTs), pupae (2,304 ESTs), fatbody (20,257 ESTs) (Attardo et al, Insect Molecular Biology 2006, 15(4):411-424), male and female whole bodies (19,968 ESTs). These data include the midgut and salivary gland ESTs used in the library specific clustering for the contig sets listed above. Initial automated annotations of product descriptions were manually revised by participants in two community annotation jamborees held under the auspice of the International Glossina Genome Initiative (IGGI) with funding by TDR. A Glossina morsitans morsitans genome project is currently also underway. To date, 2.4M capillary shotgun reads have been produced and the initial assembly is available to download via the ftp server and for blast analysis.

KamTek Biorepository
type: Resource
type: NamedIndividual
has db xref: nlx_32371
synonym: KamTek Bio-Repository
synonym: KamTek Inc Bio-Repository
synonym: KamTek Inc Biorepository
synonym: KTI Biorepository
abbrev: KTI Bio-Repository
IAO_0000115: Biorepository promoting the safe handling, receipt, processing, storage, inventory control, packaging and distribution for all types of infectious and non-infectious biological specimens and reagents. The facility houses ultra-low mechanical freezers, vapor-phase liquid nitrogen freezers and mechanical walk-in freezer and cold rooms. A multi-purpose computerized security system provides around-the-clock secure access, intrusion and fire detection, and electronic monitoring of all freezers and critical building functions. In the past, KamTek managed NIH-NIAID Reference reagent Repository that stored and distributed over 2000 different reagent products including antisera against a wide variety of viruses and other infectious organisms, as well as viral antigens, allergenic, mycoplasma, and immunologic reagents. The NIAID Repository was designated World Health Organization (WHO) Collaborating Center for Antiviral Drugs and Interferon and responsible for the international distribution of the WHO Interferon reference standards. In addition, other government agencies and private sector clients use our repository and there is provision to accommodate new clients as well. BIO-SPECIMEN REPOSITORY SERVICES: * Bio-specimen Acquisition * Bio-specimen Processing * Cryo-preservation * Cryo-storage and Maintenance of Bio-Repository * Shipments * Inventory of stored biological samples * Database management of inventory for each project

PDBe - Protein Data Bank in Europe
type: Resource
type: NamedIndividual
has db xref: biotools:pdbe
has db xref: nlx_32372
has db xref: r3d100012791
synonym: Macromolecular Structure Database
synonym: PDBe
synonym: Protein Data Bank Europe
synonym: Protein Data Bank in Europe
synonym: Protein DataBank Europe
synonym: Protein DataBank in Europe
IAO_0000115: The European resource for the collection, organization and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - they work to collate, maintain and provide access to the global repository of macromolecular structure data. The main objectives of the work at PDBe are: * to provide an integrated resource of high-quality macromolecular structures and related data and make it available to the biomedical community via intuitive user interfaces. * to maintain in-house expertise in all the major structure-determination techniques (X-ray, NMR and EM) in order to stay abreast of technical and methodological developments in these fields, and to work with the community on issues of mutual interest (such as data representation, harvesting, formats and standards, or validation of structural data). * to provide high-quality deposition and annotation facilities for structural data as one of the wwPDB deposition sites. Several sophisticated tools are also available for the structural analysis of macromolecules.

UniProtKB Keywords
type: Resource
type: NamedIndividual
has db xref: nlx_32497
abbrev: SP KW
IAO_0000115: UniProtKB entries are tagged with keywords that can be used to retrieve particular subsets of entries. There are 10 categories of keywords: Biological process Cellular component Coding sequence diversity Developmental stage Disease Domain Ligand Molecular function Post-translation modification Technical term You may browse by hierarchy, search in Keywords, or list all keywords. By default, searching the keywords will look for matches in both name and definition.

MicroBrightfield, Inc.
type: Organization
type: NamedIndividual
has db xref: grid.421345.5
has db xref: nif-0000-00110
has db xref: Wikidata: Q6714719
synonym: mbf Bioscience
synonym: MicroBrightfield
abbrev: MBF
IAO_0000115: A provider for commercial products for analyzing neuronal morphology, stereology, etc.

Charge Czar: Peptide charge state determination for low-resolution tandem mass spectra
type: Resource
type: NamedIndividual
has db xref: nlx_32529
synonym: Charge Czar
synonym: ChargeCzar
IAO_0000115: Charge Czar is a software tool that uses a support vector machine to discriminate between +2- and +3-charged tandem mass spectra, with the goal of reducing database search time by eliminating the need to search twice with each spectrum. Charge Czar is written in Python and ANSI C. Source code for the latest version, as well as some pre-compiled versions for popular platforms (Linux, Cygwin) can be downloaded after you have agreed to the license agreement. Mass spectrometry is a particularly useful technology for the rapid and robust identification of peptides and proteins in complex mixtures. Peptide sequences can be identified by correlating their observed tandem mass spectra (MS/MS) with theoretical spectra of peptides from a sequence database. Unfortunately, to perform this search the charge of the peptide must be known, and current charge-state-determination algorithms only discriminate singly- from multiply-charged spectra: distinguishing +2 from +3, for example, is unreliable. Thus, search software is forced to search multiply-charged spectra multiple times. To minimize this inefficiency, we present a support vector machine (SVM) that quickly and reliably classifies multiply-charged spectra as having either a +2 or +3 precursor peptide ion. By classifying multiply-charged spectra, we obtain a 40% reduction in search time while maintaining an average of 99% of peptide and 99% of protein identifications originally obtained from these spectra.

bcbio-nextgen
type: Resource
type: NamedIndividual
has db xref: BioTools:bcbio-nextgen
has db xref: biotools:bcbio-nextgen
has db xref: OMICS_01121
IAO_0000115: A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis.

Center for Organ Recovery and Education - CORE
type: Resource
type: NamedIndividual
has db xref: nlx_32737
synonym: Center for Organ Recovery & Education
synonym: Center for Organ Recovery and Education
synonym: Pittsburgh Transplant Foundation
synonym: Transplant Organ Procurement Foundation of Western Pennsylvania
abbrev: CORE
IAO_0000115: The Center for Organ Recovery & Education (CORE) is one of 58 federally designated agencies in the United States known as a not-for-profit organ procurement organization (OPO). CORE is dedicated to promoting donation, education and research for the purpose of saving and improving the quality of life through organ, tissue and corneal transplantation. An innovative, responsive OPO, CORE plays a pivotal role between potential donors and patients awaiting transplantation. In addition to talking with families about the opportunity to donate, CORE coordinates the surgical recovery of organs, tissue and corneas, as well as the computerized matching of donated organs and placement of corneas. In 1995, CORE created the first donor card database in Pennsylvania. In 1996, the organization added tissue recovery and eye banking services to its organ recovery component. It enhanced its line of services by opening an internal laboratory in 1997, where CORE performs the necessary tests to help determine if the organs, tissue and corneas are healthy for transplantation. Since its inception more than 30 years ago, CORE has helped to provide more than 300,000 organs, tissue and corneas for transplantation. The chances for renewed health provided through CORE would not be possible without those who have said yes to donation.

UVA Center for Research in Reproduction Ligand Assay and Analysis Core
type: Resource
type: NamedIndividual
has db xref: nif-0000-00225
synonym: Ligand and Analysis Assay Core
IAO_0000115: This Core at the University of Virginia employs state-of-the-art methods to quantitate peptide and steroid reproductive hormones in blood and tissue. It also develops new methodology, prepares labeled reagents for immunoassays, immunocytochemistry and binding studies and assists in the transfer of technology to participating investigators. Available services: AMH ELISA, 3-ALPHA DIOL G ELISA (ON HOLD), ANDROSTENEDIONE RIA, CORTISOL HUMAN IMMULITE, CORTICOSTERONE RIA, DHEA ELISA, DHEA-SO4 HUMAN IMMULITE, DHT NON EXTRACTION RIA (ON HOLD), ESTRADIOL HUMAN & MOUSE BECKMAN COULTER RIA, ESTRADIOL RAT SIEMENS RIA, ESTRONE- RIA, FSH HUMAN IMMULITE, IGF-1 HUMAN IMMULITE, INHIBIN-A ELISA, INHIBIN-B ELISA, INSULIN HUMAN IMMULITE, LH HUMAN IMMULITE, MOUSE FSH RIA, MOUSE LH SANDWICH IRMA, PROGESTERONE RIA, PROINSULIN RIA, PROLACTIN HUMAN IMMULITE, 17a-OH-PROGESTERONE RIA, RAT FSH RIA, RAT LH SANDWICH IRMA, SHBG HUMAN IMMULITE, TESTOSTERONE RIA, SENSITIVE ESTRADIOL HUMAN & RAT RIA, SENSITIVE PROGESTERONE RIA, SENSITIVE TESTOSTERONE - RIA

ReproTech, Ltd.
type: Resource
type: NamedIndividual
has db xref: nlx_32918
synonym: ReproTech Limited
abbrev: RTL
IAO_0000115: Established in 1990 as a long term storage cryobank, ReproTech, Ltd. is dedicated to offering safe and effective shipment and long term storage of reproductive tissue that has been originally cryopreserved at another laboratory or cryobank. It is the intent of RTL to provide the physician and client depositors with quality services that fully comply with industry and government Standards and/or Regulations. Our Locations: Florida, Minnesota, Nevada, US Network Administration ReproTech, Ltd. (RTL) is a one-stop resource specializing in effective solutions to the challenges faced in today''s ever changing field of Reproductive Medicine. ReproTech''s experienced staff provides expert consultation services for long term storage of reproductive tissues and donor program management to assist in compliance with regulatory agencies.

Simbios
type: Resource
type: NamedIndividual
has db xref: nlx_33018
synonym: physics-based Simulation of Biological Structures
synonym: Simbios - NIH Center for Biomedical Computation at Stanford
IAO_0000115: Simbios is the NIH Center for physics-based Simulation of Biological Structures. Simbios provides infrastructure, software, and training to help biomedical researchers understand biological form and function as they create novel drugs, synthetic tissues, medical devices, and surgical interventions. Simbios is investigating a wide scale of biological structures - from molecules to organisms. Driving biological problems include RNA folding, protein folding, myosin dynamics, cardiovascular dynamics, and neuromuscular biomechanics. Investigators interested in collaborating with Simbios can apply for NIH funding. To encourage collaboration in building accurate biological models and simulations, Simbios also provides the biomedical community with https://simtk.org, a free, secure, distributed, development system for projects. Projects may include models, software, data, documentation, publications, and graphics and have automatic backups and off-site storage. Projects may be public or private and have project-specific mailing lists, forums, bug & feature databases, news, blogs, and source-code repositories. Simbios is developing and disseminating the SimTK core simulation toolkit, (simtk.org/home/simtkcore). SimTK core is open-source software developed by experienced professionals. The software includes advanced capabilities for modeling the geometry and physics of biological systems. To ensure utility and accuracy, the software and training material is being developed and tested in close collaboration with biomedical scientists. Simbios has developed OpenSim, an application for advanced neuromuscular modeling that uses the SimTK toolkit, and is making it openly available at simtk.org/home/opensim. Simbios also publishes the Biomedical Computation Review, a magazine devoted to the science and tools in biocomputation, aimed at the community which encompasses the diverse biocomputation disciplines. To help researchers find high quality software and tools Simbios has also es…

SIDER
type: Resource
type: NamedIndividual
has db xref: biotools:sider
has db xref: nlx_33359
has db xref: OMICS_01588
has db xref: r3d100012791
synonym: Side Effect Resource
synonym: SIDER: Side Effect Resource
IAO_0000115: Database containing information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. The available information include side effect frequency, drug and side effect classifications as well as links to further information, for example drug-target relations. The SIDER Side Effect Resource represents an effort to aggregate dispersed public information on side effects. To our knowledge, no such resource exist in machine-readable form despite the importance of research on drugs and their effects. The creation of this resource was motivated by the many requests for data that we received related to our paper (Campillos, Kuhn et al., Science, 2008, 321(5886):263-6.) on the utilization of side effects for drug target prediction. Inclusion of side effects as readouts for drug treatment should have many applications and we hope to be able to enhance the respective research with this resource. You may browse the drugs by name, browse the side effects by name, download the current version of SIDER, or use the search interface.

Ludwig Boltzman Tumour Bank
type: Resource
type: NamedIndividual
has db xref: nlx_33431
synonym: Ludwig Boltzmann Gesellschaft Tumor Bank
abbrev: Ludwig Boltzmann Tumor Bank
IAO_0000115: As a basis for the experimental cluster projects, and for further future projects a collection of various biological specimens of cancer patients shall be established. All participating Ludwig Boltzmann Institutes (LBIs) are supplying biological specimens from tumor patients and clinical documentation. At the LBI for Gynecology and Gynecologic Oncology a tumor bank for biological specimens from gynecologic cancer patients already exists. All the procedures for sample processing and storage are well established. Existing equipment for storing tissue specimens at -196 degrees C can be used. Materials from the following malignant diseases are collected: Breast cancer Colorectal cancer Neuroendocrine tumors (NET) (Small cell lung cancer (SCLC) and Carcinoid tumors) Types of biological materials: Tissue (fresh frozen) Bone marrow Blood (serum/plasma/cell fractions) Pleural effusions Ascitic fluids Sputum Bronchial lavage Stool The biological specimens are initially processed at the respective LBIs or at their connected lab facilities. Enrichment of blood samples for disseminated tumor cells is done at the LBI for Gynecology and Gynecologic oncology. Long time storage of all materials is done at appropriate temperatures at the same institution. This LBI also coordinates the logistics. All relevant sample-specific and clinical data are surveyed at the respective LBIs and stored centralized in an on-line data bank in anonymized form, respecting all relevant regulations on data protection and security.

WardWiki
type: Resource
type: NamedIndividual
has db xref: nlx_33631
synonym: WardWiki - Foundation Doctor Helper
synonym: WardWiki.com
synonym: WardWiki.com - Foundation Doctor Helper
IAO_0000115: Wardwiki is a wiki designed to give free advice to foundation doctors (also know as interns) to help with practical issues as they arise on hospital wards. Despite the proliferation of medical websites and expensive courses there remains a large gap in provision of practical, experience based guidance to help foundation doctors survive the first two years on the wards. You may search for topics of interest but there are also sections including Popular Topics, Popular Categories, Top 25 articles, and Featured article. It is the responsibility of each foundation doctor to ensure their actions, referrals and prescriptions are accurate. These pages are written and maintained to the best ability of the contributing authors. We encourage any contributions be well founded, accurate, in good faith, without endorsement of medical products or opinions, and not to breach existing copyright. WardWiki cannot accept liability for adverse events that may arise directly or indirectly from advice given.

Russia 2045: Brain Reverse Engineering Lab
type: Resource
type: NamedIndividual
has db xref: nlx_33794
abbrev: Brain Reverse Engineering
IAO_0000115: The internet-laboratory will present records (publications) of the group of theorist researches, who joined their efforts for collective intellectual works with the goal to understand the mechanisms of operation of human brain in general and in all details, which are necessary for the subsequent artificial re-creation of these mechanisms. The main initial task of the laboratory will be creation of open-access scientific, technological and engineering internet-resource in a form of a specialized database of knowledge on mechanisms of brain work. It is supposed that as a result of the planned work at the end of 2015 the project''s team will elaborate the full detailed description of the mechanisms of human brain. It will be possible to use this description to make (in yrs. 2018-2020) a full scale working analog of the human brain, based on technological (not biological) informational elements and devices. At the present stage the team for the project is under formation. It will include 21 persons of an advanced research level with background in physics and biophysics. The whole work will be divided into overlapping zones of responsibility. All basic elements of the project will be discussed in detail at general sessions of the team and in local group consultations. * Preliminary stage (2011-2012): The main working instrument of the project at this stage will be the internet-laboratory. * The working stage (2013-2015): The forming of the program and of the methods of work will proceed in the course of the preliminary stage of the project. To apply for taking part in the project please write to: shkolamozg (at) ru.ru (Only serious suggestions will be considered).

Lifesharing Tissue Services
type: Resource
type: NamedIndividual
has db xref: nlx_35424
synonym: Lifesharing Tissue Bank
IAO_0000115: Lifesharing Tissue Services provides the opportunity to improve and extend lives through the procurement, processing, storage and distribution of human tissue for transplantation and research. Originally established in 1984 to support the Burn Center at UCSD Medical Center, Lifesharing Tissue Services is a non-profit organization serving San Diego and Imperial counties in Southern California. The majority of tissues recovered by Lifesharing Tissue Services stay in this region to enable physicians to provide the best possible care for critically ill patients. Tissue grafting not only reduces pain and speeds recovery, but it also improves a patient''s quality of life. Fully accredited by the American Association of Tissue Banks (AATB) and the Food and Drug Administration (FDA), Lifesharing Tissue Services works to ensure the highest quality of tissue and technical service. Lifesharing is a member of the United Network for Organ Sharing (UNOS).

EpiGRAPH
type: Resource
type: NamedIndividual
has db xref: biotools:epigraph
has db xref: OMICS_00633
IAO_0000115: A software for genome and epigenome analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Biospecimens/Biorepositories: Rare Disease-HUB (RD-HUB)
type: Resource
type: NamedIndividual
has db xref: nlx_143682
synonym: Biospecimens / Biorepositories: Rare Disease-HUB
synonym: Biospecimens/Biorepositories: Rare Disease-HUB
synonym: Rare Disease-HUB
abbrev: RD-HUB
IAO_0000115: A database of biospecimens collected, stored, and distributed by biorepositories in the United States and around the globe. Its goals are: To help and assist interested parties and investigators search, locate, and identify desired biospecimens needed for their research; to facilitate collaboration and sharing of material and data among investigators across the globe; to accelerate research to facilitate the discovery of new treatments, therapeutics and eventually cures for rare diseases as well as common diseases; to identify, locate and increase the awareness of existing biorepositories across the globe; and to link the RD-HUB with the Global Rare Diseases Patient Registry and Data Repository (GRDR).

FigShare
type: Resource
type: NamedIndividual
has db xref: DOI:10.6084
has db xref: DOI:10.17616/R3PK5R
has db xref: DOI:10.25504/FAIRsharing.drtwnh
has db xref: nlx_34569
has db xref: r3d100010066
synonym: Fig share
synonym: Figshare
abbrev: figshare
IAO_0000115: Repository for all data, figures, theses, publications, posters, presentations, filesets, videos, datasets, negative data in a citable, shareable and discoverable manner with Digital Object Identifiers. Allows to upload any file format to be made visualisable in the browser so that figures, datasets, media, papers, posters, presentations and filesets can be disseminated in a way that the current scholarly publishing model does not allow. Features integration with ORCID, Symplectic Elements, can import items from Github and is a source tracked by Altmetric.com. Figshare gives users unlimited public space and 1GB of private storage space for free. Data are digitally preserved by CLOCKSS. Supported by Digital Science, a division of Macmillan Publishers Limited, as a community-based, open science project that retains its autonomy.

NeuroPod
type: Resource
type: NamedIndividual
has db xref: nlx_34737
synonym: NeuroPod Podcasts
IAO_0000115: NeuroPod is the neuroscience podcast from Nature, produced in association with the Dana Foundation. Each month, join us as we delve into the latest research on the brain, from its molecular makings to the mysteries of the mind. We''ll also be bringing you the latest news from neuroscience conferences around the globe, along with special reports on hot areas in neuroscience.

Donor Network of Arizona
type: Resource
type: NamedIndividual
has db xref: nlx_34837
abbrev: DNA
IAO_0000115: Donor Network of Arizona is the federally designated, not-for-profit, organ procurement organization for the state of Arizona and a tissue and eye recovery organization. DNA serves five organ transplant centers in Arizona with the combined capacity to perform heart, lung, kidney, pancreas and liver transplants. * Our Mission: We make the most of life through the gift of organ and tissue donation. * Our Vision: We challenge ourselves and others everyday to realize Arizona''s potential to save and improve lives. DNA shares organs regionally and nationally through the United Network for Organ Sharing''s (UNOS) national network. DNA is accredited by the Association of Organ Procurement Organization, American Association of Tissue Banks and the Eye Bank Association of America.

Wales Cancer Bank
type: Resource
type: NamedIndividual
has db xref: nlx_34879
IAO_0000115: The Wales Cancer Bank aims to collect samples of tumour, normal tissue and blood from all patients in Wales who are undergoing an operation to remove tissue where cancer is a possible diagnosis. These samples will be banked to build up a research resource that will be used by research groups to help understand the molecular mechanisms involved in cancer and work towards the selection of optimum targeted treatment for individuals. The Wales Cancer Bank is licensed by the Human Tissue Authority (license 12107) to store human tissue for research and has ethics approval from the Wales Multicentre Research Ethics Committee to collect and issue samples for cancer related research.

M2Gen Biorepository
type: Organization
type: NamedIndividual
has db xref: nlx_35112
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The M2Gen Biorepository offers the world's largest cancer-focused tissue biobank linked to longitudinal clinical and molecular data. We provide well-annotated, high quality tissue and clinical data to support research and clinical partnerships. M2Gen's Biorepository team includes dedicated pathologists, biobanking specialists and licensed laboratory staff. Quality control assessment is performed by board-certified pathologists.

Genopole
type: Resource
type: NamedIndividual
has db xref: nlx_35123
IAO_0000115: Genopole is France''s leading biotech-and biotherapy-dedicated science and business park. The Genopole project was initiated in 1998 in the town of Evry-Corbeil, under the impetus of the French government, Ile-de-France Regional Council, Essonne County Council and the French Muscular Dystrophy Association (Association Francaise contre les Myopathies, AFM); the goal was to create France''s first ever science and business park dedicated to genomics, genetics and biotech and help the country to catch up with its international rivals in these fields. Its threefold mission is 1. to develop a high-level research campus in genomics and post-genomics, focused on gene therapy in collaboration with the University Evry Val d''Essonne; 2. encourage the start-up and foster the development of biotech companies in the Paris region by providing personalized advice and support, including financial assistance and 3. create a biopark in Evry-Corbeil in collaboration with the research campus. In addition to constant support from its founding members and other partners, Genopole''s success is largely based on the novelty of its approach: bringing together public-and private-sector research labs, university teaching facilities and life science start-ups on a single campus in EvryCorbeil. In collaboration with France''s national research institutes and the Paris Ile-de-France region''s universities, Genopole hosts and equips academic research units specializing in genetics, genomics and related sciences. Genopole also stimulates scientific life on the biopark by coordinating and organizing high-level teaching & training programs, seminars, symposia, business clubs and much more.

Nathan S. Kline Institute for Psychiatric Research; New York; USA
type: Organization
type: NamedIndividual
has db xref: grid.250263.0
has db xref: ISNI: 0000 0001 2189 4777
has db xref: nlx_151961
has db xref: Wikidata: Q6969183
synonym: Nathan Kline Institute
synonym: Nathan Kline Institute for Psychiatric Research
synonym: Nathan S. Kline Institute for Psychiatric Research
abbrev: NKI
IAO_0000115: New York State-funded research Institute, located in Orangeburg, New York.

Stony Brook University Department of Neurobiology and Behavior
type: Organization
type: NamedIndividual
has db xref: nif-0000-02085
synonym: SBU Department of Neurobiology and Behavior
synonym: SBU Dept. of Neurobiology and Behavior
IAO_0000115: The Department of Neurobiology currently has 18 faculty with substantial research strengths in neural development, circuit function, computation, cellular communication through receptors, channels and synapses and neurological and psychiatric diseases. The Department offers a university-wide predoctoral training program designed to provide broad training opportunities for students interested in careers in the neurosciences. Students can enter from their undergraduate training or through the MD/PhD program. The graduate program provides a broad educational background in neurobiology, experience in teaching, and the opportunity to pursue original doctoral research in one of over 40 laboratories. The program includes scientists at SUNY Stony Brook, recently ranked number two in the Graham/Diamond study of public research institutions, at Cold Spring Harbor Laboratories, an internationally renowned private research institute, and at Brookhaven National Laboratory, a multidisciplinary research facility of the U.S. Department of Energy. Total research grant funding for the primary faculty of $6.8 million dollars was received in FY 2008. Under the direction of Dr. Lorna Role, who arrived as Chair in April 2008, the department looks forward to continued growth, expansion and innovation. If you consider yourself a Postdoc in training, regardless of your title, you are welcome to participate in our program.

Medical College of Georgia Tumor Bank
type: Resource
type: NamedIndividual
has db xref: nlx_35211
synonym: GHSU Cancer Center Tumor Bank
synonym: MCG Tumor Tissue and Serum Repository
abbrev: MCG Tumor Bank
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 31, 2016. The MCG Tumor Tissue and Serum Repository or tumor bank, located in the Department of Pathology, Murphey Pathology Building, was established with support from the Georgia Cancer Coalition (GCC). Its mission is to provide researchers access to high quality annotated specimens, an essential requirement for cancer research. The repository collection includes a variety of specimen types, such as tumor tissue and cells, blood and other biofluids as well as normal specimens used as controls. The quality of all specimens is reviewed by a pathologist, and the information is captured in the tumor bank''s database. An imaging system will be used in the future to capture this information. Human-derived specimens are a very precious resource, and therefore the operations of the tumor bank are overseen by an advisory board, representing GHSU and other stakeholders, to ensure that the specimens are properly utilized and the privacy of specimen donors is protected.

Xenopus Anatomy Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_35222
synonym: Xenopus anatomy and development ontology
abbrev: XAO
IAO_0000115: A structured, controlled vocabulary of the anatomy and development of the African clawed frogs (Xenopus laevis and tropicalis), organized in a graphical structure. Tissues are shown as being part of other tissues and the timing of their development is indicated by start and end stages. The lineage of tissues is represented by develops from relationships between different tissues at different developmental stages. Many items have been classified according to the Common Anatomy Reference Ontology. The Xenopus Anatomical Ontology will be used to annotate Xenopus gene expression patterns and mutant and morphant phenotypes. Its robust developmental map will enable powerful database searches and data analyses. They encourage community recommendations for updates and improvements to the ontology.

Duke Cancer Institute
type: Resource
type: NamedIndividual
has db xref: nlx_143695
synonym: Duke Cancer Institute: A National Cancer Institute-designated Comprehensive Cancer Center
abbrev: DCI
IAO_0000115: One of 40 centers in the country designated by the National Cancer Institute (NCI) as a comprehensive cancer center, it combines cutting-edge research with compassionate care. Its vision is to accelerate research advances related to cancer and improve Duke''s ability to translate these discoveries into the most advanced cancer care to patients by uniting hundreds of cancer physicians, researchers, educators, and staff across the medical center, medical school, and health system under a shared administrative structure.

BioVault
type: Resource
type: NamedIndividual
has db xref: nlx_35495
IAO_0000115: Private human tissue processing and storage bank in the UK based in Plymouth on the medical campus of Derriford Hospital, Europe''s 4th largest teaching hospital. The company was set up to serve the UK and private health sectors looking to outsource the processing and storage of human tissue to an accredited, trusted and experienced expert. Storing for human application, they now process and store human tissue for organizations all over the world, including the Plymouth Hospitals NHS Trust. They are also the only private tissue bank of any true scale in the UK with the ability to store well over 1 million human tissue samples on one site. BioVault has achieved a number of accreditations and forged relationships with numerous bodies since 2002, all designed to test the robustness of our internal procedures and reassure clients they are being given the highest levels of quality and service. Many of BioVault''s pioneering systems have been designed to exceed the criteria set out by the Human Tissue Authority (HTA) with whom we work closely. The HTA is the competent authority under the European Tissue and Cell Directive and sets the standards for regulating human tissue application establishments.

UCSF DataShare
type: Resource
type: NamedIndividual
has db xref: nlx_35596
synonym: UCSF Dataverse Network
IAO_0000115: Platform to facilitate sharing, discovery, and secure access to UCSF biomedical data. It''s powered by the Dataverse Network platform, which supports a variety of data types, as well as attribution and licensing needs. Researchers may share datasets, discover data from other labs, and reuse data. Links to tools and information that help scientists properly organize, manage, and document their datasets are also provided.

Schistosoma mansoni Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-03438
abbrev: SchistoDB
IAO_0000115: SchistoDB is a genomic database for the parasitic organism Schistosoma mansoni, one of the major causative agents of schistosomiasis worldwide. It currently incorporates sequences and annotation for S. mansoni in a single user-friendly database. Several genomic scale analyses are available as well as ESTs, oligonucleotides, metabolic pathways and drugs. Make your data available: If you''d like to have your updates and/or datasets integrated in SchistoDB, drop us an email.

HHS.gov/Open: Tools
type: Resource
type: NamedIndividual
has db xref: nlx_35661
synonym: HealthData.gov Tools
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Two types of tools are presently available, widgets and RSS. Widgets are code-bearing graphic elements that allow you add Department of Health and Human Services (HHS) content or functionality to your Web product. RSS are syndication feeds that allow you to automatically import HHS content into your Web product. You may search by keyword, HHS Agency and/or type. New tools are being added regularly. The links below will take you to Data.gov where you can access the data set, rate it, and view additional details.

WikiPatient
type: Resource
type: NamedIndividual
has db xref: nlx_35678
IAO_0000115: WikiPatient is the independent patient information & news source that anyone can edit. With 71,700 Textbook Chapters and News Articles in English, this wiki is all about Care, Community, and Co-Creation. Major sections include WikiPatient: Patient Resources, WikiPatient News: Today in Medicine, Diseases/Disease States and Care Centers. WikiPatient is available in other languages including Español, Français, Polski, Русский, Română, 中文, and Türkçe.

Best of the Web: Neuroscience
type: Resource
type: NamedIndividual
has db xref: nlx_36048
synonym: Best of the Web Neuroscience
synonym: BOTW Neuroscience Directory
abbrev: BOTW Neuroscience
IAO_0000115: Comprehensive neuroscience directory that places Neuroscience websites in a relevant category within the internet''s oldest directory. Search engines rely on these listings when evaluating where to place your website in their results. A listing in the BOTW Neuroscience Directory makes your website pop so be sure to take advantage of this opportunity and submit your site today! Currently major categories include: * Neuroanatomy (at) * Neurobiology * Neurochemistry * Blogs (at) * Education * Neuroscientists * News and Media * Organizations * Research See Also: * Kids and Teens: Science and Math: Science: Living Things: Human Body: Nervous System * Health: Conditions and Illness: Neurological Disorders * Health: Medicine: Medical Specialties: Neurology * Health: Medicine: Surgery: Neurosurgery

Cellular Technology Ltd Cryopreserved PBMC
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_36239
synonym: Cellular Technology Limited Cryopreserved PBMC
synonym: Cellular Technology Limited Cryopreserved Peripheral Blood Mononuclear Cells
synonym: CTL Cryopreserved PBMC
synonym: CTL Cryopreserved Peripheral Blood Mononuclear Cells
abbrev: CTL PBMC
IAO_0000115: A Commercial tissue bank

Columbia Biosciences Corporation
type: Organization
type: NamedIndividual
has db xref: nlx_152333
IAO_0000115: An Antibody supplier

onCore UK
type: Resource
type: NamedIndividual
has db xref: nlx_36545
IAO_0000115: No longer functioning as an independent charity, onCore UK is a national cancer biobanking organization. Our mission is to serve as an action team that informs, coordinates and develops cancer biobanking to enable research towards the discovery and development of new interventions against cancer. We also offer advice to researchers who need to collect and store samples for their own specific projects. Our main strategic objectives are: * To empower research using human biosamples to find new and effective means of preventing, detecting or treating cancer. * To improve access by researchers to the human biosamples they require for their work. * To facilitate an environment in which patients, the public, health professionals, researchers, funders of research, policy makers and regulators can work together to support cancer biobanking and the research it underpins. * To provide practical information, coordination and development for current and future people and organizations involved in cancer biobanking to ensure that they are not unnecessarily hindered in their work. * To provide an accurate and regularly updated picture of the cancer biobanking provision in the UK that will inform future decisions by funders supporting research using donated human biosamples. * To distribute the human biosamples that onCore UK has in its custody. onCore UK conducts its business within the overall scope of the National Cancer Research Institute (NCRI) and for the benefit of cancer research. In the past we have also worked with selected NHS hospitals in different parts of the country to collect biosamples and relevant clinical data donated by cancer patients. These biosamples are stored in a secure repository and researchers can apply to use them. We make anonymized biosamples and data available for scientifically and ethically approved research on a cost-recovery basis. onCore UK works with other cancer biobanks in the UK via the NCRI Confederation of Cancer Biobanks (CCB), and with…

BiblioSpec
type: Resource
type: NamedIndividual
has db xref: nlx_36841
IAO_0000115: BiblioSpec enables the identification of peptides from tandem mass spectra by searching against a database of previously identified spectra. This suite of software tools is for creating and searching MS/MS peptide spectrum libraries. BiblioSpec is available free of charge for noncommercial use through an interactive web-site at http://depts.washington.edu/ventures/UW_Technology/Express_Licenses/bibliospec.php The BiblioSpec package contains the following programs: * BlibBuild creates a library of peptide MS/MS spectra from MS2 files. * BlibFilter removes redundant spectra from a library. * BlibSearch searches a spectrum library for matches to query spectra, reporting the results in an SQT file. In addition to the primary programs, the following auxiliary programs are available: * BlibStats writes summary statistics describing a library. * BlibToMS2 writes a library in MS2 file format. * BlibUpdate adds, deletes, or annotates spectra. * BlibPpMS2 processes spectra (bins peaks, removes noise, normalizes intensity) as done in BlibSearch and prints the resulting spectra to a text file. Several reference libraries are available for download. These libraries are updated regularly and are for use under the Linux operating system. You will find libraries for * Escherichia coli * Saccharomyces cerevisiae * Caenorhabditis elegans

Doheny Eye and Tissue Transplant Bank
type: Resource
type: NamedIndividual
has db xref: nlx_36932
synonym: Doheny Eye & Tissue Transplant Bank
IAO_0000115: The community-based Doheny Eye & Tissue Transplant Bank has become a pioneer and leader in providing eye and tissue banking services to patients, surgeons and hospitals in southern California for more than 40 years. The mission of the Doheny Eye & Tissue Transplant Bank is to relieve human suffering by providing human tissue for transplant, research, and medical education in our community and around the world. The non-profit, non-governmental Doheny Eye & Tissue Bank is a member of the TBI/Tissue Banks International non-profit network of vision and certified by Eye Bank Association of America.

DRUT
type: Resource
type: NamedIndividual
has db xref: OMICS_01273
synonym: Discovery and Reconstruction of Unannotated Transcripts
IAO_0000115: Software for Discovery and Reconstruction of Unannotated Transcripts in Partially Annotated Genomes from High-Throughput RNA-Seq Data.

Dana Farber Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_37203
synonym: Dana-Farber/Harvard Cancer Center Pathology Specimen Locator
synonym: Dana-Farber/Harvard Cancer Center PSL
synonym: DF/HCC Pathology Specimen Locator
synonym: Pathology Specimen Locator
synonym: Pathology Specimen Locator: deidentified human specimens for translational cancer research
abbrev: DF/HCC PSL
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 31, 2016. The Dana-Farber/Harvard Cancer Center Pathology Specimen Locator (PSL) is a core developed to facilitate translational research requiring human specimens. The PSL is a distributed network of databases containing de-identified pathology reports and other specimen information from IRB-approved repositories within Dana-Farber/Harvard Cancer Center affiliated institutions. Using the PSL, researchers can work with the pathology departments to find appropriate specimens for their research. The Harvard VLS currently contains approximately two million de-identified pathology reports from the four main Harvard Teaching Hospitals.

Ancestrymap
type: Resource
type: NamedIndividual
has db xref: biotools:ancestrymap
has db xref: nlx_39116
has db xref: OMICS_02083
abbrev: ANCESTRYMAP
IAO_0000115: Software application that finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans. It can be downloaded for either UNIX or Linux.

Rocky Mountain MS Center
type: Organization
type: NamedIndividual
has db xref: grid.419238.5
has db xref: nlx_143690
synonym: Rocky Mountain Multiple Sclerosis Center
IAO_0000115: The Rocky Mountain MS Center is a patient-centered organization dedicated to changing the way we think about and treat MS in order to protect the futures of those living with the disease. Our mission is to improve the lives of people with Multiple Sclerosis (MS) and their families through care, support, education and research. * Medical Care and Support: We offer a comprehensive care approach that maximizes and enhances the brain''s ability to protect and repair itself and to promote quality of life for patients and their families. We incorporate wellness, exercise, diet and stress management, and supportive services in addition to the most progressive medical care. * Education: We empower patients, families and health care providers by sharing what we know. There are 10,000 peer reviewed articles published annually; we sort through that information and share the latest advances. * Research: We are pursuing new treatment approaches to save the brain. We are leading the way to assure that we prevent the silent but ongoing brain damage that results in disability. This means treating early and treating aggressively.

Karolisnka Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_37545
synonym: Karolinska Institutet Biobank
abbrev: KI Biobank
IAO_0000115: KI Biobank is an accredited core facility offering sample collection services. KI Biobank is located at the Department of Medical Epidemiology and Biostatistics. KI Biobank offer infrastructure for pre analytical sample handling and provide researchers guidance on how samples should be taken and labeled. The processes comprise registration, handling, storage and distribution of samples. KI Biobank also offers DNA-extraction from blood and saliva. In order to insure complete traceability on samples and belonging information all processes are controlled by a Laboratory Information Management System (LIMS). For every new study a contract is established describing the study and the disposition rights. We also help in writing Biobank agreements including multicenteravtal and Material Transfer Agreement. KI Biobank is, according to the Biobank law, responsible for all sample collections handled within the core facility and those that are stored on the departments on KI campus. Clinical sample collections are handled by the Biobank units at the respective hospitals within the Stockholm County Council. Besides the samples that are stored centrally at KI Biobank, KI Biobank is also the administrative biobank for research sample collections at Karolinska Institutet that are stored and administrated at the departments. All research sample collections must be reported to KI Biobank. The following types of sample collections are registered in the biobank; sample collections taken within the regular health care that has been transferred to Karolinska Institutet with an agreement of transfer, samples taken from healthy individuals or other persons out of the regular health care and samples that have been taken abroad.

WikiEcho
type: Resource
type: NamedIndividual
has db xref: nlx_37588
synonym: EACVI WikiEcho
IAO_0000115: Free, up-to-date and reliable encyclopaedia covering the rapidly advancing field of echocardiography. Anyone may contribute but articles will be reviewed by an European Association of Cardiovascular Imaging (EACVI) board of echocardiography experts. Watch out for the EACVI logo which indicates approved articles!

Emergency Medicine
type: Resource
type: NamedIndividual
has db xref: nlx_37822
synonym: Open-Content Textbook of Emergency Medicine
abbrev: OCTEM
IAO_0000115: Emergency Medicine is an Open-Content Textbook of Emergency Medicine. This wikibook is intended to be a collaborative communication between physicians, nurses, physician assistants, paramedics, EMTs and other healthcare providers. It is not intended for the general public. It is under development and inevitably contains many errors and omissions. As the information in this textbook can be edited by anyone, regardless of whether they are medically trained or not, it should not be used as a guide to treating yourself or anyone else! Contents * 1 SYMPTOMS AND PRESENTATIONS ** 1.1 GENERAL SYMPTOMS ** 1.2 HEAD AND NECK SYMPTOMS ** 1.3 CHEST SYMPTOMS ** 1.4 ABDOMINAL SYMPTOMS * 2 TOPICS ** 2.1 ABDOMINAL AND GASTROINTESTINAL DISORDERS ** 2.2 CARDIOVASCULAR DISORDERS ** 2.3 CUTANEOUS DISORDERS ** 2.4 DISASTER MEDICINE ** 2.5 ENDOCRINE, METABOLIC, AND NUTRITIONAL DISORDERS ** 2.6 ENVIRONMENTAL DISORDERS ** 2.7 HEAD, EAR, EYE, NOSE, THROAT DISORDERS ** 2.8 HEMATOLOGIC DISORDERS ** 2.9 IMMUNE SYSTEM DISORDERS ** 2.10 INFECTIOUS DISORDERS ** 2.11 MUSCULOSKELETAL DISORDERS (NONTRAUMATIC) ** 2.12 NERVOUS SYSTEM DISORDERS ** 2.13 OBSTETRICS AND GYNECOLOGY ** 2.14 RENAL AND UROGENITAL DISORDERS ** 2.15 THORACIC-RESPIRATORY DISORDERS ** 2.16 TOXICOLOGIC DISORDERS ** 2.17 TRAUMATIC DISORDERS * 3 TESTS ** 3.1 Imaging ** 3.2 Lab Investigations ** 3.3 Point of Care Testing * 4 TREATMENT ** 4.1 Procedures ** 4.2 Resuscitation ** 4.3 Other Treatment * 5 SPECIAL POPULATIONS * 6 PRACTICE AND ADMINISTRATION * 7 KNOWLEDGE AND COMMUNICATION

Functional Genomics Data Society
type: Resource
type: NamedIndividual
has db xref: nlx_37824
synonym: FGED Society
synonym: MGED Society
abbrev: FGED
abbrev: MGED
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 7, 2022. Functional Genomics Data Society - FGED Society, founded in 1999 as the MGED Society, advocates for open access to genomic data sets and works towards providing concrete solutions to achieve this. Our goal is to assure that investment in functional genomics data generates the maximum public benefit. Our work on defining minimum information specifications for reporting data in functional genomics papers have already enabled large data sets to be used and reused to their greater potential in biological and medical research. We work with other organizations to develop standards for biological research data quality, annotation and exchange. We facilitate the creation and use of software tools that build on these standards and allow researchers to annotate and share their data easily. We promote scientific discovery that is driven by genome wide and other biological research data integration and meta-analysis.

John Theurer Cancer Center
type: Resource
type: NamedIndividual
has db xref: nlx_143712
abbrev: JTCC
IAO_0000115: Throughout the past 25 years, John Theurer Cancer Center at Hackensack University Medical Center has become one of the largest and most comprehensive cancer centers in the United States. Today, we are a top 50 U.S. News and World Report Best Hospitals for cancer the only cancer center in New Jersey with this prestigious designation. Its mission is to deliver extraordinary care that is multidisciplinary, personalized, innovative, and at the appropriate cost with superior outcomes to the most satisfied patients. Year after year, we have harnessed the newest technologies and retained world-class physicians, nurses and scientists to help service the needs of our patients within our 14 specialized cancer divisions.

National Autonomous University of Mexico; Mexico City; Mexico
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100005739
has db xref: grid.9486.3
has db xref: ISNI:0000 0001 2159 0001
has db xref: nlx_151584
has db xref: Wikidata:Q222738
synonym: National Autonomous University of Mexico
synonym: Universidad Nacional Autonoma de Mexico
synonym: Universidad Nacional Aut�noma de M�xico
abbrev: UNAM
IAO_0000115: Founded in 1551, this research university features murals by Diego Rivera and other famous artists.

Rocky Mountain MS Center Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_143691
synonym: Rocky Mountain Multiple Sclerosis Center Tissue Bank
synonym: Tissue Bank: Rocky Mountain MS Center
IAO_0000115: Scientists throughout the world depend on the Rocky Mountain MS Center Tissue Bank to supply high quality human brain tissue and cerebral spinal fluid to support their research. Funded in part by the National MS Society, the Tissue Bank is one of only four MS-related tissue banks in the nation. The Tissue Bank has distributed specimens to more than 160 investigators worldwide and over 1,600 people have consented to be donors after death. Tissue banks provide a unique bridge between those who live with MS and the scientific community. Studies conducted with samples from the Center have led to several important discoveries and 130 publications. While deeply personal, the decision to donate has far-reaching effects as scientists unlock the mysteries of multiple sclerosis. If you would like to donate, arrangements must be made in advance because it is important that tissue is taken within a few hours of death. For more information on making a donation, visit the How To Donate section of this website and contact the Rocky Mountain MS Center Tissue Bank at 303.788.4030 x111.

VIROME
type: Resource
type: NamedIndividual
has db xref: OMICS_01506
synonym: Viral Informatics Resource for Metagenome Exploration
synonym: Viral Informatics Resource for Metagenome Exploration - VIROME
IAO_0000115: A web-application designed for scientific exploration of metagenome sequence data collected from viral assemblages occurring within a number of different environmental contexts. The VIROME informatics pipeline focuses on the classification of predicted open-reading frames (ORFs) from viral metagenomes. The portal allows you to submit your viral metagenome to be processed through the VIROME analysis pipeline, and enable you to investigate your data via the VIROME user interface., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

MultiFun
type: Resource
type: NamedIndividual
has db xref: nlx_38338
synonym: MultiFun: a cell function assignment schema
synonym: MultiFun: a cellfunction assignment schema
IAO_0000115: MultiFun is a multifunctional classification scheme for Escherichia coli K-12 gene products. In the classification scheme, cellular functions are divided into 10 major categories: Metabolism, Information Transfer, Regulation, Transport, Cell Processes, Cell Structure, Location, Extra-chromosomal Origin, DNA Site, and Cryptic Gene. These major categories are further sub-divided into a hierarchical scheme. Two thousand nine hundred twenty-two gene products of E. coli K-12 were assigned to one or more functions depending on the role they play in the cell. Functional assignments were made to 66% of E. coli gene products, ranging from 1 to 16 assignments per gene product. The expansion of cellular function categories and the assignment to more than one category (multifunction) provides a more complete description of the gene products and their roles and hence better reflects the functional complexity of organisms. We believe this classification system will be useful in the field of genome analysis, both for annotation purposes and for comparative studies. The functional classification scheme and the cellular function assignments made to E. coli gene products can be accessed from the web at the databases GenProtEC (http://genprotec.mbl.edu) and EcoCyc (http://www.ecocyc.org).

WiCell Research Institute
type: Organization
type: NamedIndividual
has db xref: grid.439113.d
has db xref: ISNI: 0000 0004 0387 4731
has db xref: nlx_38454
has db xref: Wikidata: Q7997962
abbrev: WiCell
IAO_0000115: A nonprofit organization offering research and clinical grade pluripotent stem cell lines, cytogenetic testing, quality control testing and cell banking services to researchers worldwide. The organization is focused on enhancing and expanding the study of human pluripotent stem cells by supporting basic research; establishing research protocols; creating and distributing cell lines; providing training to scientists worldwide; and supporting efforts to unlock the therapeutic potential of stem cell technologies. As home to the Wisconsin International Stem Cell (WISC) Bank, and previously the first US National Stem Cell Bank, WiCell serves the worldwide scientific stem cell community through banking, characterization, and distribution of stem cell lines as well as providing technical support. WiCell also offers cytogenetic services, quality control testing services and clinical grade cell lines to researchers across the globe.

SourceForge
type: Resource
type: NamedIndividual
has db xref: nlx_38463
IAO_0000115: Web based service that offers software developers centralized online location to control and manage free and open source software projects. Open source software tool and business public software platform.

Office of Naval Research
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100000006
has db xref: grid.482851.2
has db xref: ISNI: 0000 0001 0257 7469
has db xref: nlx_144142
has db xref: Wikidata: Q1063818
abbrev: ONR
IAO_0000115: Organization within the United States Department of the Navy responsible for the science and technology programs of the U.S. Navy and Marine Corps.

Sterol and Isoprenoid Research Consortium
type: Resource
type: NamedIndividual
has db xref: nlx_143697
synonym: STAIR Consortium
abbrev: STAIR
IAO_0000115: A consortium which represents a collaborative group of investigators along with their academic medical centers and the National Institutes of Health, patient advocacy groups, and clinical research programs. Members of the STAIR Consortium are dedicated to participating in clinical research regarding disorders related to cholesterol and other sterol and isoprenoid metabolism. The overall objective of the Sterol and Isoprenoid Research Consortium (STAIR) is to study a group of diseases bound by common biochemistry, impact on health, and rarity. STAIR will conduct several clinical studies, support a full-scale training program in the field of sterol and isoprenoid diseases, and engage several patient advocacy groups in consortium activities. Researchers interested in partnering with STAIR may contact its Administrative Director.

Marshfield Clinic Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_38684
synonym: Marshfield Clinic Personalized Medicine Research Project bio-bank
synonym: Marshfield Clinic PMRP bio-bank
synonym: Personalized Medicine Research Project bio-bank
abbrev: PMRP bio-bank
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. A large collection of biological samples and health information collected for the Personalized Medicine Research Project (PMRP) for use in biological research. Genetic information from 20,000 participants forms a database enabling scientists to study which genes cause disease, which genes predict reactions to drugs, and how environment and genes work together to cause disease. The goal of this project is to learn how to apply genetic science to human health. This knowledge will help researchers develop new medications and diagnostic tests, and will enable physicians to prescribe medications that work best for a particular person. Marshfield Clinic Personalized Medicine Research Project (PMRP) resources currently available: DNA, plasma, serum, questionnaire, electronic medical records to construct phenotypes; ability to recontact subjects for additional information (where they have given consent for recontact); stored pathology specimens collected for clinical purposes; 51 clinically relevant polymorphisms; Illumina 660 quad for ~4200 subjects aged 50+.

RDCRN Patient Contact Registry
type: Resource
type: NamedIndividual
has db xref: nlx_143699
synonym: Rare Diseases Clinical Research Network Patient Contact Registry
synonym: STAIR Contact Registry
IAO_0000115: A portal specifically for patients (and their families) with sterol and other related disorders where they can register themselves with STAIR in order to be contacted in the future about clinical research opportunities and updated on the progress of the STAIR research projects. An online Registry form exists for all the BVMC disorders currently being studied.

Vanator
type: Resource
type: NamedIndividual
has db xref: OMICS_01505
synonym: Vanator-CVR
synonym: Vanator-CVR - A metagenomics & virus discovery pipeline
synonym: Vanator-CVR: A metagenomics and virus discovery pipeline
synonym: Virus Alignment de Novo Assembly and Taxonomy On Reads
IAO_0000115: A Perl pipeline utilising a large variety of common alignment, assembly and analysis tools to assess the metagenomic profiles of Illumina deep sequencing samples. The emphasis is on the discovery of novel viruses in clinical and environmental samples.

RETICULUM - Neuroscience History Resources
type: Resource
type: NamedIndividual
has db xref: nlx_38747
abbrev: RETICULUM
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016. RETICULUM is a gateway to Internet resources for history and historians of basic, clinical, and behavioral neuroscience. Links to existing sites are reviewed for salience and accuracy, organized by topic for convenient access, and regularly tested for availability. Comments, questions, and additional resource suggestions and submissions are welcomed. Major categories include: Calendar/Announcements, Professional societies and associations, Internet forums, Placement opportunities, Funding opportunities, Education opportunities, Repositories and collections, Catalogs and indexes, Texts on the Internet, Images on the Internet, Exhibits on the Internet, Periodicals, Commercial resources, Subject guides, Internet introductions, tutorials and tools, Questions-Comments-Suggestions-Submissions, Credits

Rare Diseases Clinical Research Network
type: Resource
type: NamedIndividual
has db xref: nlx_143707
abbrev: RDCRN
IAO_0000115: The Rare Diseases Clinical Research Network (RDCRN) was created to facilitate collaboration among experts in many different types of rare diseases. Our goal is to contribute to the research and treatment of rare diseases by working together to identify biomarkers for disease risk, disease severity and activity, and clinical outcome, while also encouraging development of new approaches to diagnosis, prevention, and treatment. The Rare Diseases Clinical Research Network (RDCRN) is made up of 19 distinctive consortia that are working in concert to improve availability of rare disease information, treatment, clinical studies, and general awareness for both patients and the medical community. The RDCRN also aims to provide up-to-date information for patients and to assist in connecting patients with advocacy groups, expert doctors, and clinical research opportunities.

UniProtKB Subcellular Locations
type: Resource
type: NamedIndividual
has db xref: nlx_38886
synonym: UniProt Subcellular Locations
abbrev: SP SL
IAO_0000115: The subcellular locations in which a protein is found are described in UniProtKB entries with a controlled vocabulary, which includes also membrane topology and orientation terms. You may search in subcellular locations or list them all along with their definitions (490). By default, searching the subcellular locations will look for matches in both name and definition.

SO
type: Resource
type: NamedIndividual
has db xref: nlx_38918
synonym: Sequence Ontology
synonym: Sequence Ontology Project
synonym: Sequence Types and Features Ontology
IAO_0000115: A collaborative ontology for the definition of sequence features used in biological sequence annotation. SO was initially developed by the Gene Ontology Consortium. Contributors to SO include the GMOD community, model organism database groups such as WormBase, FlyBase, Mouse Genome Informatics group, and institutes such as the Sanger Institute and the EBI. Input to SO is welcomed from the sequence annotation community. The OBO revision is available here: http://sourceforge.net/p/song/svn/HEAD/tree/ SO includes different kinds of features which can be located on the sequence. Biological features are those which are defined by their disposition to be involved in a biological process. Biomaterial features are those which are intended for use in an experiment such as aptamer and PCR_product. There are also experimental features which are the result of an experiment. SO also provides a rich set of attributes to describe these features such as polycistronic and maternally imprinted. The Sequence Ontologies use the OBO flat file format specification version 1.2, developed by the Gene Ontology Consortium. The ontology is also available in OWL from Open Biomedical Ontologies. This is updated nightly and may be slightly out of sync with the current obo file. An OWL version of the ontology is also available. The resolvable URI for the current version of SO is http://purl.obolibrary.org/obo/so.owl.

FACIL
type: Resource
type: NamedIndividual
has db xref: OMICS_00299
synonym: FACIL genetic code prediction tool
synonym: Genetic code prediction tool FACIL: Fast and Accurate genetic Code Inference and Logo
IAO_0000115: Genetic code prediction tool that infers the genetic code directly from any set of nucleic acid sequences and assigns a Random Forest-based reliability score to its predictions.

FishBase
type: Resource
type: NamedIndividual
has db xref: nlx_39009
has db xref: r3d100010912
synonym: FishBase: A Global Information System on Fishes
IAO_0000115: A global species database and encyclopedia of over 32,800 species and subspecies of fishes that is searchable by common name, genus, species, geography, family, ecosystem, references literature, tools, etc. It links to other, related databases such as the Catalog of Fishes, GenBack, and LarvalBase. It is associated with a partner journal, Acta Ichthyologica et Piscatoria. It is available in English, Greek, Spanish, Portuguese, French, Dutch, Italian, and German. Photo and video submissions are welcome. FishBase 2004 is also available on DVD or CD-ROMs with full information on 28,500 species. It comes together with the FishBase 2000 book and can be ordered for 95 US$ including air-mail.

Velvet-SC
type: Resource
type: NamedIndividual
has db xref: OMICS_01504
synonym: Velvet Single Cell
abbrev: Velvet SC
IAO_0000115: Software package for short read data from single cells that improves assembly through use of progressively increasing coverage cutoff. Used for single cell Illumina sequences, allows variable coverage datasets to be utilized with assembly of E. coli and S. aureus single cell reads. Assembles single cell genome of uncultivated SAR324 clade of Deltaproteobacteria.

Ontology of Pneumology
type: Resource
type: NamedIndividual
has db xref: nlx_157537
abbrev: ONTOPNEUMO
IAO_0000115: Ontology of pneumology (french version) developped by Audrey Baneyx, under the direction of Jean Charlet about knowledge engineering expertise and by Francois-Xavier Blanc in collaboration with Bruno Housset about medical expertise.

Mantle Cell Lymphoma Cell Bank
type: Resource
type: NamedIndividual
has db xref: nlx_39167
synonym: Mantle Cell Lymphoma (MCL) Cell Bank
abbrev: MCL Cell Bank
IAO_0000115: The Lymphoma Research Foundation (LRF), in collaboration with American Type Culture Collection (ATCC), has created a Mantle Cell Lymphoma (MCL) Cell Bank. The Cell Bank is a collection of various MCL lines created by scientists from all over the world. The idea for the Cell Bank was generated by the scientists that make up the MCL Consortium (MCLC). It was created to provide a single, centralized location where scientists can easily acquire high-quality, well-characterized MCL cell lines in an effort to accelerate discoveries in MCL. LRF has acquired 8 different MCL cell lines (July 2010): Mino, Z-138, JVM-2, JVM-13, REC-1, NCEB-1, JeKo-1, and Maver-1. The Cell Bank is chaired by Dr. Owen O''Connor of New York University Langone Medical Center and is housed at ATCC, the world''s largest biological resource center and the most comprehensive source of reference cultures and reagents used by researchers in the academic and industry laboratories. The Cell Bank was made possible by the scientists who generously agreed to share their resources, including, Dr. Elias Campo, Dr. Zeev Estrov, Dr. Richard Ford, Dr. Junia Melo and Dr. Alberto Zamo.

Neuroendocrine Tumors Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_39248
abbrev: NET BioBank
IAO_0000115: Aims to carry out an integrated (epi)genomic analysis of the NET BioBank established at the Royal Free and UCL Hospitals to identify new biomarkers for translation into diagnostics and therapeutics. The Neuroendocrine Tumour (NET) Unit at the Royal Free Campus of UCL Hospitals has an international reputation for the management of neuroendocrine tumor patients. It currently receives around 10 new referrals per month and has an active patient cohort of over 800 patients. We receive referrals from across the UK as well as from abroad. It is the designated center for NETs within the North London Cancer Network. In order to improve both treatment and outcome in Neuroendocrine Tumors (NETs), better understanding of their biology and the biological pathways involved is imperative (reviewed in (Modlin et al., 2008)). Currently, the use of targeted treatments is limited and management challenging due to the lack of knowledge of the molecular pathogenesis and mechanistic regulation of these tumors (Barakat et al., 2004). Due to the rarity of NETs and difficulty in obtaining fresh tissue and archival samples, very little is known about the (epi)genetic and germline mutations associated with neuroendocrine tumors ����?? which encompass a clinically and genetically heterogeneous group. To date, studies have been small and under-powered. Clinical trials have included small patient numbers and are often non-randomized phase II trials comparing a new therapy against a non-standardized first line treatment. Initially we will undertake genome-wide methylation analysis on our entire cohort of neuroendocrine tumors in order to determine the methylation profiles of differing NET types. This will improve diagnostic accuracy and potentially identify new therapeutic targets and biomarkers. These studies will be performed on high-throughput analysis platforms based on micoarrays and next-generation sequencing. In parallel, we will analyze the mRNA expression profiles of these tumors to enab…

WikiHealth
type: Resource
type: NamedIndividual
has db xref: nlx_39377
IAO_0000115: WikiHealth is a collaborative online health and wellness community where your participation makes a difference! WikiHealth''s goal is to offer the most comprehensive, current and insightful information to help anyone and everyone achieve optimal health. Our belief is that your knowledge matters--- and you can help others by sharing what you know. WikiHealth is a collaborative writing project aiming to build an extensive and valueable repository on a variety of health and wellness topics. Our mission is to bring free, accesible and thorough information on health and wellness into the homes of every individual worldwide. The goal is for new articles on any health and wellness topic to be added regularly and for existing articles to be improved by volunteer contributors. In time, we envision WikiHealth to be the best health resource to come to for unbiased information as well as prescriptive advice on any health or wellness topic. Please join us by writing a new article or editing an existing one.

Case Comprehensive Cancer Center Biorepository and Tissue Processing Core Facility
type: Resource
type: NamedIndividual
has db xref: nlx_39515
synonym: Biorepository and Tissue Processing Core Facility of the Case Comprehensive Cancer Center
synonym: Biorepository Tissue Processing Core Facility
synonym: Case BTPC
synonym: Case CCC Biorepository Tissue Processing Core Facility
synonym: Case CCC BTPC
synonym: Case Comprehensive Cancer Center Biorepository Tissue Processing Core Facility
synonym: Case Western Biorepository
synonym: Case Western Biorepository and Tissue Processing Core Facility
synonym: Case Western Reserve University: Biorepository and Tissue Processing Core Facility
synonym: CWRU BTPC
synonym: CWRU CCC Biorepository Tissue Processing Core Facility
abbrev: BTPC
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. The Case Comprehensive Cancer Center''s Biorepository and Tissue Processing Core Facility (BTPC) serves two primary functions: 1. To build an inventory of remnant human tissues, blood and other body fluids (collectively termed biospecimens) targeted towards cancer and other medical research, for later assignment to investigators; and 2. To provide long term, controlled storage of biospecimens for specific researchers. These samples are for research purposes only and may not be used for clinical diagnosis or implantation into humans. Clinical information relating to the samples and donors are collected and maintained in a secure database. Samples and data are de-identified or de-linked before release to the researcher unless he/she has specific IRB approval to gain access to this information. Remnant biospecimens are prospectively collected from surgical procedures, autopsies and clinical laboratories for the BTPC by the Human Tissue Procurement Facility (HTPF), which operates under UH-IRB Protocol 01-02-45. Blood and bone marrow specimens are collected for the BTPC by the Hematopoietic Stem Cell Core Facility (HSCC), which operates under UH-IRB Protocol 09-90-195. The Division of Surgical Pathology at University Hospitals Case Medical Center (UHCMC) has clinical archives of paraffin blocks that can be made available through the BTPC for retrospective research studies under the approval of the Vice Chair for Clinical Affairs at UHCMC. Surgical Pathologists associated with the BTPC are responsible for determining which blocks can be made available and how much material can be removed from the blocks. Types of Tissue Available * Malignant, benign, diseased, normal and normal human tissues * Normal adjacent tissues available paired with tumor specimens in many cases * Tissues are collected from over 50 anatomic sites * Frozen specimens, OCT-embedded and paraffin-embedded tissues * Large array of para…

SNiPer-HD
type: Resource
type: NamedIndividual
has db xref: OMICS_00735
synonym: SNiPer-HD: Improved genotype calling accuracy
IAO_0000115: Improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays.

Maryland Brain Collection
type: Resource
type: NamedIndividual
has db xref: nlx_39828
abbrev: MBC
IAO_0000115: The Maryland Brain Collection (MBC), a resource of the Maryland Psychiatric Research Center (MPRC), is dedicated to promoting research with brain tissue obtained post-mortem from individuals with schizophrenia or related disorders. The primary goal of the MBC is to provide high-quality tissue, along with comprehensive clinical information, for hypothesis-driven research. The MBC is not conceptualized as a Brain Bank with open access but is maintained and funded through collaborative research. The Maryland Brain Collection is managed by researchers at the Maryland Psychiatric Research Center (MPRC). MPRC scientists are dedicated to understanding the causes and improving the treatment of mental illness. The Maryland Brain Collection is associated with the Office of the Chief Medical Examiner for the State of Maryland and other donor sources. MPRC scientists collaborate with scientists from around the world to understand how abnormalities in brain tissue relate to mental illness. The purpose of the MBC is to study the following: Schizophrenia, Bipolar Disorder, Depression, Suicide/Teen suicide, Substance Abuse.

Squeezambler
type: Resource
type: NamedIndividual
has db xref: OMICS_01503
IAO_0000115: Software to sequence and de novo assemble all distinct genomes present in a microbial sample with a sequencing cost and computational complexity proportional to the number of genome types, rather than the number of cells.

Health.Data.gov
type: Resource
type: NamedIndividual
has db xref: nlx_143714
has db xref: r3d100010593
synonym: Health Data and Tools
synonym: Health Data and Tools Available on Data.gov
synonym: Health.Data.gov Data Tools
synonym: US HealthData Gov
IAO_0000115: Public, high-value federal datasets, tools, and applications using data about health and health care gathered from agencies across the U.S. government.

Case Western Reserve University Case Comprehensive Cancer Center
type: Resource
type: NamedIndividual
has db xref: nlx_40003
abbrev: Case CCC
abbrev: CWRU Case CCC
IAO_0000115: Core is a partnership organization supporting all cancer-related research efforts at CWRU, University Hospitals Case Medical Center, and the Cleveland Clinic. The Case CCC is organized into 9 interdisciplinary scientific programs plus one program initiative. Research programs of the Case CCC are extending into CWRU affiliated hospitals including MetroHealth Medical Center (the region's county hospital), Louis Stokes Veterans Affairs Hospital, and 13 community medical centers operated by University Hospitals and Cleveland Clinic. The Center operates an NCI-supported Cancer Information Service (CIS) serving the northern half of Ohio as part of the Midwest consortium and has an active outreach program for clinical practice-based prevention and screening initiatives, educational programs, minority recruitment, and facilitation of patient referrals. Case CCC is a member of NCI's CaBIG initiative and is actively pursuing electronic databases for clinical trials, tissue repositories, and related bioinformatics.

Biointeractive
type: Resource
type: NamedIndividual
has db xref: nlx_40070
synonym: HHMI BioInteractive
synonym: Howard Hughes Medical Institute BioInteractive
abbrev: BioInteractive
IAO_0000115: Collection of biology-focused teaching materials created and administered by the Howard Hughes Medical Institute including free lectures, videos and animations for science education. Many of the resources are also available on DVD and CD-ROM. In addition to the resources on the website, BioInteractive offers DVDs of HHMI''s annual Holiday Lectures on Science and CD-ROMs of the Virtual Lab series. These materials are available to educators for free and can be ordered from the catalog at http://catalog.hhmi.org. Each Holiday Lectures on Science is a set of four one-hour lectures presented each December at the headquarters of the Howard Hughes Medical Institute in Chevy Chase, Maryland . The lectures give students and teachers the opportunity to learn about cutting-edge biomedical research directly from some of the world''s leading scientists. Intended to inspire young students to pursue careers in science, the lectures bring the latest developments in a rapidly moving field of research into the classroom. The lectures are primarily geared to high school students in honors and Advanced Placement biology classes. Other high school students and undergraduates can certainly benefit from the content of the lectures. Some of the related materials on the biointeractive website (http://www.biointeractive.org/) are aimed at a broader audience. With a teacher''s guidance, middle school students can also enjoy learning about the topic. Holiday Lectures are webcast live at http://www.hhmi.org/biointeractive/hl/. Following the live event, they are available as on-demand streaming video at the same Web address. Webcasts of all past Holiday Lectures are available as on-demand streaming video at http://www.hhmi.org/biointeractive/lectures/index.html. Holiday Lectures are also available as podcasts from http://www.hhmi.org/biointeractive/podcast_popup.html

ORION Software
type: Resource
type: NamedIndividual
has db xref: nlx_40212
IAO_0000115: ORION is our neuron reconstruction software package developed for the morphological reconstruction of neurons from confocal and multiphoton microscopy data. It accepts raw neuron stack data as input and it is capable of reconstructing the neuron structure, visualizing the output, and exporting the reconstruction in a variety of formats. We are developing tools that will enable Neuroscientists to explore single neuron function via sophisticated image analysis. Advanced optical imaging can produce both structural and functional data and is at the forefront of experimentally exploring the fast, small-scale dynamics of living neurons. Further, compartmental modeling of neuronal function enables rapid testing of hypotheses and estimating experimentally inaccessible parameters. Combining these two techniques will afford unprecedented capabilities in the study of single neuron function. Our software utility bridges the two Neuroscience techniques by rapidly, accurately, and robustly generating, from structural image data, a cylindrical morphology model suitable for simulating neuronal function.

Angioma Alliance DNA/Tissue Bank and Patient Registry
type: Resource
type: NamedIndividual
has db xref: nlx_143719
synonym: Angioma Alliance BioBank
synonym: CCM DNA & Tissue Bank
synonym: CCM DNA and Tissue Bank
synonym: Cerebral Cavernous Malformations (CCM) DNA & Tissue Bank
synonym: Cerebral Cavernous Malformations (CCM) DNA and Tissue Bank
synonym: Cerebral Cavernous Malformations DNA and Tissue Bank
IAO_0000115: Angioma Alliance has established a DNA/Tissue Bank and matching clinical database for cerebral cavernous malformations (CCM, cavernous angioma, cavernoma). Our goal is to create the world''s largest collection of CCM genetic samples with matching clinical data to be used as a resource to drive research. We are recruiting individuals with a history of cerebral cavernous malformations to participate in the study. Qualified participants donate a blood sample and complete a comprehensive questionnaire or interview. Blood donation kits will be sent in the mail for participants to take to their doctor, clinic or blood draw center to have their blood drawn. The kit is then mailed to a private lab where the sample is processed. If a surgery is scheduled, the Angioma Alliance DNA/Tissue Bank will work with the participant, the surgeon, and the hospital to coordinate tissue donation. If surgery scheduling allows, dry ice will be shipped to the hospital facility along with a tissue collection kit for use and return to the private lab. The Angioma Alliance DNA/Tissue Bank will attempt to acquire Institutional Review Board approvals at facilities where this is required. The Angioma Alliance BioBank will follow up with participants on a yearly basis to update their clinical information. If the participant has not already had documented genetic testing, we will test their DNA sample for possible CCM1, CCM2, or CCM3 mutation or CCM2 exon 2-10 deletion. If additional causative genes are identified for the illness, we will also test for mutations on these. Participants will not be informed of the results of testing, but if a mutation or deletion is found, they will be informed that results can be released to a diagnostic laboratory in order to obtain follow-up confirmatory clinical diagnostic testing. This could mean a substantial cost savings to the patient whose insurance does not cover genetic testing or who is uninsured. All researchers requesting the use of DNA and/or Tissue sam…

Office of the NCI Director
type: NamedIndividual
has db xref: nlx_inv_1005137
synonym: National Cancer Institute Office of the Director
abbrev: CO

CAMO - Cell Adhesion Molecule Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_40219
synonym: Cell Adhesion Molecule Ontology
abbrev: CAMO
IAO_0000115: CAMO (Cell Adhesion Molecule Ontology) is a set of standard vocabulary that provide a hierarchical description of cell adhesion molecules and their functions. We compiled a list for cell adhesion molecules by integrating Gene Ontology annotations, domain structure information, and keywords query against NCBI Entrez Gene annotations. Totally 496 unique human genes were identified to function as cell adhesion molecules, which is by far the most comprehensive dataset including cadherin, immunoglobulin/FNIII, integrin, neurexin, neuroligan, and catenin families. CAMO was constructed as a directed acyclic graph (DAG) using DAG-Edit to input, manage and update data. We annotated each term with name, definition and source references, as well as the relationship to other terms, based on manual reviews of domain architecture and functional annotations. If vertices represent terms and the relationships between terms are represented by edges, the terms in a DAG can be connected via a directed graph without cycles. CAMO thus provides a hierarchical description of functions of CAMs with five top-level categories: CAM gene families, CAM genetics, CAM regulation, CAM expression and CAM diseases. Each top-level term is further divided into several categories to describe the functions in detail.

EBI Dbfetch
type: Resource
type: NamedIndividual
has db xref: nlx_40225
synonym: Database fetch
synonym: Dbfetch
synonym: EMBL fetch
synonym: emblfetch
IAO_0000115: Dbfetch is an acronym for database fetch. Dbfetch provides an easy way to retrieve entries from various databases at the EBI in a consistent manner and allows you to retrieve up to 50 entries at a time from various up-to-date biological databases. It can be used from any browser as well as well as within a web-aware scripting tool that uses wget, lynx or similar. From the browser, follow these instructions... * Select a database: If you are using the first form to paste your search items: choose a database name from this form. If you are using the second form to upload your search items: the database name is included at the beginning of each line line of the upload file followed by a colon. * Enter search terms: These MUST BE in the appropriate database format, up to 200 search items can be queried in one run. If you are using the first form: separate search items with a comma or space. If you are using the second form: separate search items with a new line. * Choose an output format: Here you can choose the simpler fasta format, or the databases' ''' default format for the chosen database. * Style: You can get your results as text or html. * Retrieve! - You are now ready to fetch your results, by pressing the Retrieve button.

Segtools
type: Resource
type: NamedIndividual
has db xref: nlx_40271
IAO_0000115: Segtools is a Python package designed to put genomic segmentations back in the context of the genome! Using R for graphics, Segtools provides a number of modules to analyze a segmentation in various ways and help you interpret its biological relevance. Segmentations should be in BED4+ or GFF format, with the ''name'' field of each line used specifying the segment label of that line. The Segtools commands allow you to compare the properties of the segment labels with one another.

Biomedical Research Program UCA
type: Resource
type: NamedIndividual
has db xref: nlx_143715
synonym: Biomedical Research Institute
synonym: Biomedical Research Institute UCA
synonym: Biomedical Research Institute UCA - CONICET
synonym: Programa de Investigaciones Biom��dicas
synonym: UCA Biomedical Research Program
synonym: UCA PIB
abbrev: PIB
IAO_0000115: The Biomedical Research Program (PIB) of the School of Medical Sciences was created in 2007, after a Collaboration Protocol was established between UCA and the National Council of Scientific and Technical Research (CONICET). Research at PIB aims at unraveling the molecular, biochemical and genetic aspects of human diseases, therefore contributing to understanding complex pathologies. Research Groups include: * Molecular and Cell Biology Lab (LBCM) - Group leader: Tom��s A. Santa Coloma, Ph.D. * Nanotechnology Lab - Group leader: Tom��s A. Santa Coloma, Ph.D. * Molecular Neurobiology Lab - Group leader: Francisco J. Barrantes, Ph.D.

Sulfolobus Database
type: Resource
type: NamedIndividual
has db xref: nif-0000-03508
IAO_0000115: This database contains the three sequenced Sulfolobus genomes and the sequenced extrachromosomal elements belonging to Sulfolobales. Users can browse, export, and compare sequences in addition to utilizing BLAST searching.

MPI Research
type: Organization
type: NamedIndividual
has db xref: grid.421937.a
has db xref: ISNI: 0000 0004 0445 7016
has db xref: nlx_143716
abbrev: MPI
IAO_0000115: MPI Research exists to provide comprehensive discovery, safety evaluation, bioanalytical, and analytical services that meet the requirements of biopharmaceutical, medical device, animal health, and chemical companies as we partner globally to bring safer and more effective products to the world. Our goal is to exceed the expectations of our Sponsors and maintain the highest respect in our industry by providing customized, responsive, and on-time services that add value to our Sponsors'' efforts to discover, develop, and enhance products in regulated international environments. We excel as a high performance, high quality organization because of our scientific knowledge and experience, integrity, trust, teamwork, and dedication to strong and enduring Sponsor relationships. MPI Research has conducted thousands of drug safety, discovery, bioanalytical, and analytical studies. We offer extensive support and resources including, but not limited to * A wide and diverse range of classes of compounds * All routes of administration except inhalation * Studies with numerous species and models * Comprehensive reporting capabilities Flexibility and ample capacity enable us to * Accommodate multiple requirements simultaneously * Adjust schedules readily * Produce results quickly Responding to a broad spectrum of research needs: Working in partnership with pharmaceutical, biotech, medical device, and chemical companies, we conduct customized preclinical research throughout the discovery and development process, from early proof of concept testing to regulatory submissions, including IND, EPA/OPPTS, NDA, PMA, and 510K.

Wisconsin International Stem Cell Bank
type: Resource
type: NamedIndividual
has db xref: nlx_40896
abbrev: WISC Bank
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. High quality, well characterized pluripotent stem cell lines for distribution to researchers worldwide. Offerings include human embryonic and induced pluripotent stem cell lines, as well as modified cell lines tailored to specific research needs. *Human Embryonic Stem Cell Lines *Modified Cell Lines *Induced Pluripotent Stem Cells (iPS) *Clinical Grade (cGMP) Human ES Cell Banks

MAGNet - Multiscale Analysis of Genomic and Cellular Networks
type: Resource
type: NamedIndividual
has db xref: nlx_40968
synonym: Center for the Multiscale Analysis of Genomic and Cellular Networks
abbrev: MAGNet
IAO_0000115: The mission of the Center for the Multiscale Analysis of Genomic and Cellular Networks (MAGNet) is to develop novel Structural and Systems Biology methods and tools for the dissection of molecular interactions in the cell and for the interaction-based elucidation of cellular phenotypes. These tools are made freely available to the the members of the research community. They are also validated in the context of the Center' '''s own research program through collaborative projects with experimental biologists. MAGNet is one of 7 National Centers for Biomedical Computing (NCBC). These Centers, in conjunction with individual investigator awards, are creating a networked effort to build the computational infrastructure for biomedical computing in the nation. The NCBC program is devoted to all facets of biomedical computing, from basic research in computational science to providing the tools and resources that biomedical and behavioral researchers need to do their work. In addition to carrying out fundamental research the NCBCs play a major role in educating and training researchers to engage in biomedical computing. MAGNet is also one of 12 inter-disciplinary Centers for Cancer Systems Biology (CCSBs), a component of the National Cancer Institute' '''s Integrative Cancer Biology Program. The CCSBs provide a core framework for applying systems biology approaches to cancer research through the development and implementation of computational models of processes relevant to cancer prevention, diagnostics and therapeutics. The CCSBs seek to integrate experimental biology with mathematical modeling to foster new insights in the biology and new approaches to the management of cancer. MAGNet' '''s Training Core ensures that the methods developed by the Center are integrated into the educational offerings of Columbia University' '''s Medical School.

Mid-America Transplant Services
type: Resource
type: NamedIndividual
has db xref: nlx_41044
abbrev: MTS
IAO_0000115: For 35 years, Mid-America Transplant Services (MTS) has served as the regional organ and tissue procurement organization for eastern Missouri, southern Illinois, and northeast Arkansas, serving 4.3 million people in 84 counties. From our founding goal to assist in the coordination of kidney donations, we have grown to become a multi-faceted organization dedicated to saving lives and enhancing the quality of all donated organs and tissues currently available for transplant. MTS''s primary service offering is to facilitate and coordinate the organ and tissue donation process. With a mission to save lives through excellence in organ and tissue donation, we have been at the forefront of enhancing the quality of organs and tissue for transplant. Throughout our history, we have relentlessly pursued our core values of compassion, quality, teamwork, and honesty to create a positive donation experience for Donor Families, which is at the heart of what matters most to MTS. Located in Saint Louis, Missouri, MTS is one of 58 federally designated organizations of its kind in the United States. Incorporated in the State of Missouri, MTS is a private, not-for-profit 501(c)(3). To fulfill our mission, we work closely with the four transplant centers and over 110 donor hospitals located within our service area.

neurodebian
type: Resource
type: NamedIndividual
has db xref: nlx_143723
synonym: Debian Neuroscience Repository
synonym: neuro debian
abbrev: NeuroDebian
IAO_0000115: Collection based on a collaborative effort of popular neuroscience research software for the Debian operating system as well as Ubuntu and other derivatives. Popular packages include AFNI, FSL, PyMVPA and many others. It contains both unofficial or prospective packages which are not (yet) available from the main Debian archive, as well as backported or simply rebuilt packages also available elsewhere. A listing of current and planned projects is available if you want to get involved. The main goal of the project is to provide a versatile and convenient environment for neuroscientific research that is based on open-source software. To this end, the project offers a package repository that complements the main Debian (and Ubuntu) archive. NeuroDebian is not yet another Linux distribution, but rather an effort inside the Debian project itself. Software packages are fully integrated into the Debian system and from there will eventually migrate into Ubuntu as well. With NeuroDebian, installing and updating neuroscience software is no different from any other part of the operating system. Maintaining a research software environment becomes as easy as installing an editor. There is also virtual machine to test NeuroDebian on Windows or Mac OS. If you want to see your software packaged for Debian, please drop them a note.

Anopheles gambiae (African malaria mosquito) genome view
type: Resource
type: NamedIndividual
has db xref: nlx_41106
synonym: African malaria mosquito genome view
synonym: Anopheles gambiae genome view
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A database for the Anopheles gambiae str. PEST genome that was sequenced using a whole genome shotgun approach. The database aims to contribute to the understanding of mosquito genome structure and organization and will assist the development of malaria control strategies and improved anti-malarial drugs and vaccines. Sequences were generated and assembled into contigs for submission to GenBank.

Autism Genetic Resource Exchange
type: Resource
type: NamedIndividual
has db xref: nif-0000-00226
abbrev: AGRE
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A private repository of clinical and genetic information on families with autism. Genetic and clinical data are obtained from families that have more than one family member diagnosed with an Autism Spectrum Disorder. The biological samples, along with the accompanying clinical data, are made available to AGRE-approved researchers worldwide. As they become available, additional family pedigrees will be posted in the online catalog. Cell lines have been established for the majority of families in this collection and serum/plasma is available on a subset of the subjects until stocks are depleted. The diagnosis of autism has been made using the standard Autism Diagnostic Interview-Revised (ADI-R) algorithm and the Autism Diagnostic Observation Scale (ADOS-G). Detailed birth and medical histories (including basic dysmorphology assessments) on children as well as family and medical information for parents and unaffected siblings, are available for nearly all families. DNA, cell lines, serum, plasma and clinical information are made available to AGRE-approved researchers for analysis.

Neuroscience News: Neuroscience Lab Equipment
type: Resource
type: NamedIndividual
has db xref: nlx_143834
abbrev: Neuroscience Lab Equipment
IAO_0000115: Neuroscience Lab Equipment offers a few neuroscience lab products available for purchase including lab coats, oscilloscopes, neuroscience research software, electrophysiology equipment, micromanipulators, centrifuges, lab glassware, pipettes, neuroscience charts and much more. Take a look around and if you don''t find what you need, let us know and we will try to update our Neuroscience Lab Equipment area to sell it.

UniGene
type: Resource
type: NamedIndividual
has db xref: nlx_41571
has db xref: OMICS_01663
has db xref: r3d100010774
synonym: NCBI UniGene
synonym: Organized View of the Transcriptome
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Web tool for an organized view of the transcriptome. Collection of the computationally identified transcripts from the same locus. Information on protein similarities, gene expression, cDNA clones, and genomic location. System for automatically partitioning GenBank sequences into a non redundant set of gene oriented clusters.

Moffitt Cancer Center Tissue Core
type: Resource
type: NamedIndividual
has db xref: nlx_143721
abbrev: MCC TC
IAO_0000115: A central tissue repository at Moffitt specializing in protocol-driven human tissue collection, storage, processing and dissemination. Tissue Core provides investigators with access to high quality, well-annotated human specimens obtained from representative of the patient populations. The advent of powerful molecular technologies has opened the door to developing more effective treatments of patients with cancer. Access to high quality specimens with associated clinical, treatment, recurrence outcome data will be critical to developing and validating the tests needed for diagnosis and prediction of response to therapy. Since its commencement in 1993, the Tissue Core has collected more than 8,000 cases of human liquid cancers and solid primary and metastatic tumors both malignant and benign with adjacent normal, from variety of sites and diagnoses. Collected samples are mostly remnant tissues obtained from patients undergoing therapeutic surgical procedures at the Center. The core also ensures tissue release compliance with USF-IRB and Privacy Board recommendations. * Protocol driven sample collection, processing and distribution * Collection of sample and patient demographic information. * Nucleic acid extractions from tissue sections, FNA, core biopsies blood and bone marrow. * Histology services: H&E slides, staining, sectioning, paraffin blocks, OCT blocks, sample microdissection * WBC, plasma and serum isolation. * Project development and support: Facility staff provides advice and guidance to researchers.

National Drug Abuse Treatment Clinical Trials Network
type: Resource
type: NamedIndividual
has db xref: nif-0000-00227
synonym: NIDA CTN
abbrev: CTN
IAO_0000115: A collaboration in which the National Institute on Drug Abuse, treatment researchers, and community-based service providers cooperatively develop, validate, refine, and deliver new treatment options to patients in Community Treatment Programs (CTPs). The partnership between CTPs and academic research leaders aims to achieve the following objectives: * Conducting studies of behavioral, pharmacological, and integrated behavioral and pharmacological treatment interventions of therapeutic effect in rigorous, multisite clinical trials to determine effectiveness across a broad range of community-based treatment settings and diversified patient populations; and * Ensuring the transfer of research results to physicians, clinicians, providers, and patients. The CTN, with its core of CTPs engaging diverse populations, is also designed to provide a platform for other studies, which would be funded under separate research grants. Three important ways to use the CTN are: to conduct ancillary studies in connection with CTN protocols; to utilize CTN Node facilities as a platform for investigations; and for Nodes to serve as home bases for NIH Training Centers and individual researchers who have NIH fellowships or career development awards.

Catalog of Fishes
type: Resource
type: NamedIndividual
has db xref: nlx_41737
synonym: Catalog of Fishes database
abbrev: CASGEN
abbrev: CASREF
abbrev: CASSPC
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. The Catalog of Fishes is the authoritative reference for taxonomic fish names, featuring a searchable on-line database. The Catalog of Fishes covers more than 53,000 species and subspecies, over 10,000 genera and subgenera, and includes in excess of 16,000 bibliographic references. The Catalog of Fishes consists of three hardbound volumes of 900-1000 pages each, along with a CD-ROM. The online database is updated about every 8 weeks and is now about twice the size of the published version. It is one of the oldest and most complete databases for any large animal group. References are over 30,000. Valid species are over 30,000. This work is an essential reference for taxonomists, scientific historians, and for any specialist dealing with fishes. Entries for species, for example, consist of species/subspecies name, genus, author, date, publication, pages, figures, type locality, location of type specimen(s), current status (with references), family/subfamily, and important publication, taxonomic, or nomenclatural notes. Nearly all original descriptions have been examined, and much effort has gone into determining the location of type specimens. The Genera are updated from Eschmeyer''s 1990 Genera of Recent Fishes. Both genera and species are listed in a classification using recent taxonomic schemes. Also included are a lengthy list of museum acronyms, an interpretation of the International Code of Zoological Nomenclature, and Opinions of the International Commission involving fishes.

Open Biological and Biomedical Ontologies Relationship Types
type: Resource
type: NamedIndividual
has db xref: nlx_157539
abbrev: OBOREL
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Ontology that defines core relations used in all OBO ontologies. Obsolete. Replaced with RO.

Lymphoma Research Foundation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100001219
has db xref: grid.429292.6
has db xref: ISNI: 0000 0004 0441 7356
has db xref: nlx_41811
abbrev: LRF
IAO_0000115: The Lymphoma Research Foundation (LRF) is the nation''s largest non-profit organization devoted exclusively to funding innovative lymphoma research and providing people with lymphoma and healthcare professionals with up-to-date information about this type of cancer. LRF''s mission is to eradicate lymphoma and serve those touched by this disease. LRF was formed in November 2001 by the merger of the Cure for Lymphoma Foundation (CLF) and the Lymphoma Research Foundation of America (LRFA). Both organizations were founded by lymphoma advocates who sought to use their personal experiences with lymphoma to benefit others with the disease. CLF was founded in 1994 in New York City by Jerry Freundlich, a non-Hodgkin lymphoma survivor, and his wife Barbara Freundlich. LRFA was founded in 1991 by Ellen Glesby Cohen, who lost her own battle with non-Hodgkin lymphoma in August 2000. Our goal is to change the future for everyone whose life has been affected by a lymphoma diagnosis. We are dedicated to funding biomedical research focused on the origins, treatment and identification of a cure for lymphoma; to raising public awareness of the disease; and providing support and services to people with lymphoma, their families and caregivers.

PROCURE Quebec Prostate Cancer Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_41815
abbrev: PROCURE Qu��������bec Prostate Cancer Biobank
IAO_0000115: PROCURE proposes to enable the collection and storage of standardized high volumes of prostatic tissues, blood, urine, clinical information and socio-demographic data from men undergoing prostate cancer screening and surgery across the province of Quebec and facilitate access to these resources. PROCURE will make the Biobank materials and information available to the global scientific community to facilitate the implementation of studies at an accelerated pace. Informed consent, upholding full confidentiality, will be sought from the thousands of men already undergoing prostate biopsies and radical prostatectomies in Quebec each year. Quebec is an ideal location to conduct this initiative with its diverse ethnic groups and low migration. The low migration will allow for repeated follow-up with individuals. This large collection of biospecimen and information will be used for biochemical and genetic analysis with great statistical power and will facilitate learning about the manifestation and progression of prostate cancer over time. Additional benefits include the acceleration of clinical trials, better prevention, earlier detection and diagnosis, the development of personalized medicine, more efficacious treatment, and follow-up care. The Biobank is a collaborative organization with long term partnerships established between PROCURE, the four Qu��������bec universities (McGill University, Universit�������� de Sherbrooke, Universit�������� Laval, Universit�������� de Montr��������al), with the Fonds de recherche en sant�������� du Qu��������bec and other key groups to be confirmed over time.

SCPD - Saccharomyces cerevisiae promoter database
type: Resource
type: NamedIndividual
has db xref: nif-0000-03445
has db xref: OMICS_01867
synonym: SCPD - The Promoter Database of Saccharomyces cerevisiae
abbrev: SCPD
IAO_0000115: A promoter database of Saccharomyces cerevisiae. Users can explore the promoter regions of ~6000 genes and ORFs in yeast genome, annotate putative regulatory sites of all genes and ORFs, locate intergenic regions, and retrieve sequence of the promoter region. In regards to regulatory elements and transcription factors, users can provide information on transcriptionally related genes, browse matrix and consensus sequences, view the correlation between elements, observe binding affinity and expression, and look at genomewise distribution. SCPD also provides some simple but useful tools for promoter sequence analysis. Gene, consensus and matrix records may be submitted.

GASSST
type: Resource
type: NamedIndividual
has db xref: biotools:gassst
has db xref: OMICS_00663
synonym: GASSST : Global Alignment Short Sequence Search Tool
synonym: Global Alignment Short Sequence Search Tool
IAO_0000115: Software that finds global alignments of short DNA sequences against large DNA banks. It is able to perform fast gapped alignments and works well for both short and longer reads. It has been tested for reads up to 500bp.

AcaWiki
type: Resource
type: NamedIndividual
has db xref: nlx_42053
IAO_0000115: AcaWiki enables graduate students and researchers to share summaries of academic papers online. There are currently over 600 Creative Commons licensed summaries of academic papers on AcaWiki. Browse summaries in economics, psychology, sociology, business, or computer science among other fields. AcaWiki enables you to easily post summaries and literature reviews of peer-reviewed research. Many summaries on AcaWiki come up high on Google results. If you want to find summaries or literature reviews of peer-reviewed research, you can either browse summaries or search.

Stem Cell Commons
type: Resource
type: NamedIndividual
has db xref: nlx_42085
synonym: Harvard Stem Cell Institute Blood Genomics
synonym: Harvard Stem Cell Institute Blood Program
synonym: HSCI Blood Genomics
synonym: HSCI Blood Program
IAO_0000115: Open source environment for sharing, processing and analyzing stem cell data bringing together stem cell data sets with tools for curation, dissemination and analysis. Standardization of the analytical approaches will enable researchers to directly compare and integrate their results with experiments and disease models in the Commons. Key features of the Stem Cell Commons * Contains stem cell related experiments * Includes microarray and Next-Generation Sequencing (NGS) data from human, mouse, rat and zebrafish * Data from multiple cell types and disease models * Carefully curated experimental metadata using controlled vocabularies * Export in the Investigation-Study-Assay tabular format (ISA-Tab) that is used by over 30 organizations worldwide * A community oriented resource with public data sets and freely available code in public code repositories such as GitHub Currently in development * Development of Refinery, a novel analysis platform that links Commons data to the Galaxy analytical engine * ChIP-seq analysis pipeline (additional pipelines in development) * Integration of experimental metadata and data files with Galaxy to guide users to choose workflows, parameters, and data sources Stem Cell Commons is based on open source software and is available for download and development.

DigiMorph
type: Resource
type: NamedIndividual
has db xref: nlx_143746
has db xref: r3d100011511
synonym: Digital Morphology
synonym: Digital Morphology library
IAO_0000115: A dynamic archive of information on digital morphology and high-resolution X-ray computed tomography of biological specimens serving imagery for more than 750 specimens contributed by almost 150 collaborating researchers from the world''s premiere natural history museums and universities. Browse through the site and see spectacular imagery and animations and details on the morphology of many representatives of the Earth''s biota. Digital Morphology, part of the National Science Foundation Digital Libraries Initiative, develops and serves unique 2D and 3D visualizations of the internal and external structure of living and extinct vertebrates, and a growing number of ''invertebrates.'' The Digital Morphology library contains nearly a terabyte of imagery of natural history specimens that are important to education and central to ongoing cutting-edge research efforts. Digital Morphology visualizations are now in use in classrooms and research labs around the world and can be seen in a growing number of museum exhibition halls. The Digital Morphology site currently presents: * QuickTime animations of complete stacks of serial CT sections * Animated 3D volumetric movies of complete specimens * Stereolithography (STL) files of 3D objects that can be viewed interactively and rapidly prototyped into scalable physical 3D objects that can be handled and studied as if they were the original specimens * Informative introductions to the scanned organisms, often written by world authorities * Pertinent bibliographic information on each specimen * Useful links * A course resource for our ''Digital Methods for Paleontology'' course, in which students learn how to generate all of the types of imagery displayed on the Digital Morphology site

AIDS Malignancy Bank
type: Resource
type: NamedIndividual
has db xref: nlx_143727
abbrev: AMB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 27, 2012. The National Cancer Institute established centers in the United States and its territories for the collection and distribution of tissues, blood and secretions from patients with clinically-characterized AIDS related malignancies in 1994. The AIDS Malignancy Bank makes these tissues available to qualified investigators in the United States for research on AIDS malignancies. It is hoped that by providing access to these high-quality specimens, research in AIDS-related malignancies will be encouraged and expanded. The AMB contains formalin-fixed paraffin-embedded tissues, fresh-frozen tissues, malignant-cell suspensions, fine-needle aspirates, and cell lines from AIDS-related malignancies. The bank also contains serum, plasma, urine, bone marrow, cervical secretions, anal swabs, saliva semen and multi-site autopsy tissues from patients with AIDS-related malignancies who have participated in clinical trials. The bank has an associated database that contains prognostic, staging, outcome and treatment data on patients from whom tissues were obtained. Researchers pay for preparation and shipping of specimens.

University of Chicago Human Tissue Resource Center Biospecimen Banking
type: Resource
type: NamedIndividual
has db xref: nlx_42397
synonym: Biospecimen banking
abbrev: BSB
IAO_0000115: Biospecimen banking (BSB) involves collecting, processing, storing and distributing of human or animal tissues and body fluids of molecular grade. Human tissues and body fluids are banked in compliance with IRB approved protocols without compromising the diagnostic process and maintaining donor confidentiality (HIPAA compliant). Investigator-driven biobanking initiatives are of paramount importance at the University. The BSB provides investigators with the infrastructure to establish organ-specific biobanks in a centralized location. This arrangement allows for minimal duplication of costs, as well as establishing a working template for all tissue collections. The BSB has grown exponentially, and has a strong team of experienced personnel banking tissues for clinical trials, investigator-driven projects, and future biospecimen-based research. In addition, the BSB now collects and stores saliva, urine, blood, plasma, serum, and derivatives. The BSB is a complex process, requiring multiple interacting systems to ensure the scientific quality of procured tissue, and body fluids, patient confidentiality, adherence to good clinical practices, and regulated disbursement of biospecimens to approved investigators. They are also aware that policies, HIPAA guidelines, and federal and state tissue procurement regulations may change, and will be fully compliant with all new regulations.

UAB SPORE Biorepository Banks
type: Resource
type: NamedIndividual
has db xref: nlx_143728
synonym: UAB SPORE Breast Cancer Tissue Bank
IAO_0000115: A biomaterial supply resource which stores and provides ovarian, breast, pancreatic, and cervical tissue samples and fluids to cancer researchers. The UAB Tissue Collection and Banking Facility collects tissue samples for the UAB Ovarian, Breast, Pancreatic, and Cervix SPORE banks. Samples from the former Ovarian SPORE bank are available to UAB Cancer Center members via the Tissue Procurement Shared Facility, and to other researchers via the Cooperative Human Tissue Network.

SnoopCGH
type: Resource
type: NamedIndividual
has db xref: biotools:snoopcgh
has db xref: OMICS_00736
IAO_0000115: A java desktop application for visualising and exploring comparative genomic hybridization (CGH) data.

Childhood Brain Tumor Foundation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100002725
has db xref: grid.478649.0
has db xref: ISNI: 0000 0004 5902 3100
has db xref: nlx_143731
abbrev: CBTF
IAO_0000115: The Childhood Brain Tumor Foundation (CBTF), an all-volunteer organization, was founded in 1994 by families, friends and physicians of children with brain tumors. Our mission is to raise funds for scientific research and heighten public awareness of this most devastating disease and to improve prognosis and quality of life for those that are affected. Founded and incorporated in Virginia, relocated to Maryland in 1998, the Foundation (a 501(c) (3), strives to meet the goals of our mission. Friends, families, and physicians brought CBTF together and are dedicated to serving the needs of families and children with brain tumors, in hopes of improving the quality of life and find cures for pediatric brain tumors. Annually, CBTF funds basic science or clinical research for pediatric brain tumors; conferences and other programs. We provide informational materials on our website and mail other information (nationally and internationally) upon request. The Childhood Brain Tumor Foundation (CBTF) has funded state-of-the-art research and supported conferences for pediatric brain tumors over the past 17 years. Grants submissions are reviewed thoroughly by our dedicated renown team of scientific advisors to ensure that CBTF selects the highest quality research for pediatric brain tumors. Each year, we receive so many outstanding applications and it is through the support of private and public donations that this is all possible. With your support, together, we will strive to find a cure for children''s brain tumors.

Childrens Brain Tumor Foundation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100002017
has db xref: grid.428138.4
has db xref: nlx_143732
synonym: Children's Brain Tumor Foundation
abbrev: CBTF
IAO_0000115: Children''s Brain Tumor Foundation, a non-profit organization, was founded in 1988 by dedicated parents, physicians and friends. Our mission is to improve the treatment, quality of life and the long term outlook for children with brain and spinal cord tumors through research, support, education, and advocacy to families and survivors. Knowledge is critical for families to access expert care and ensure quality of life. Our free publication A Resource Guide for Parents of Children with Brain and Spinal Cord Tumors is now in its fourth edition, and is full of practical information to sort out the complexities of medical procedures, interruptions in school and social life, and uncertainty about the future. CBTF co-sponsors conferences for families, survivors and health care professionals, offering the latest information about research, treatments and strategies for living. Only scientific research will identify the causes and lead to effective treatments for brain tumors in children. CBTF funds cutting-edge research by scientists at top academic medical centers. Their discoveries hold the promise of improving the lives of affected children today and discovering the means of prevention for future generations. CBTF has awarded over $5 million in grants for basic and clinical research related to pediatric brain and spinal cord tumors. Also, over $625,000 has been given out in Quality of Life Grants.

Clontech
type: Organization
type: NamedIndividual
has db xref: nlx_152332
IAO_0000115: An Antibody supplier

Danish Multiple Sclerosis Center
type: Organization
type: NamedIndividual
has db xref: grid.488278.9
has db xref: nlx_143734
abbrev: DMSC
IAO_0000115: The Danish Multiple Sclerosis Center (DMSC) comprises the MS Clinic and the MS Research Unit including the Neuroimmunology Laboratory. The main research areas are: clinical research including investigator driven trials of new therapies in MS, neuroimaging, neuropsychology and rehabilitation; pathogenesis of MS with focus on immunology, biomarkers and treatment response; as well as studies in the pathology and genetics of MS. DMSC is part of the Department of Neurology, Rigshospitalet, and the Faculty of Medicine, University of Copenhagen. The research facilities are located in sections 6311 and 9392 at the hospital site. DMSC constitutes one of the European MS Centers of Excellence and has extensive collaboration with institutions in Denmark, in other European countries, as well as overseas. DMSC is supported by both national and international grants.

UniProtKB
type: Resource
type: NamedIndividual
has db xref: nlx_53981
has db xref: r3d100011521
synonym: UniProt Knowledgebase
synonym: UniProtKB/Swiss-Prot
synonym: UniProtKB/TrEMBL
IAO_0000115: Central repository for collection of functional information on proteins, with accurate and consistent annotation. In addition to capturing core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and experimental and computational data. The UniProt Knowledgebase consists of two sections, UniProtKB/Swiss-Prot and UniProtKB/TrEMBL. UniProtKB/Swiss-Prot (reviewed) is a high quality manually annotated and non-redundant protein sequence database which brings together experimental results, computed features, and scientific conclusions. UniProtKB/TrEMBL (unreviewed) contains protein sequences associated with computationally generated annotation and large-scale functional characterization that await full manual annotation. Users may browse by taxonomy, keyword, gene ontology, enzyme class or pathway.

Diagnostic Radiology
type: Resource
type: NamedIndividual
has db xref: nlx_42895
IAO_0000115: This is a wiki on diagnostic radiology. Major topics include General Types of Radiology, Imaging Modalities, Radiography, CT scanning, Sonography, MRI Magnetic Resonance Imaging, Nuclear medicine, Normal Radiological Anatomy, Imaging of Specific Anatomic Regions, Diagnosis of Specific Anatomic Regions, Imaging in Pediatric Radiology, and External resources. Radiology is the branch of medical science dealing with medical imaging. It may use x-ray machines or other such radiation devices. It also uses techniques that do not involve radiation, such as MRI and ultrasound. The medical information provided on Wikibooks is, at best, of a general nature and cannot substitute for the advice of a medical professional (for instance, a qualified doctor/physician, nurse, pharmacist/chemist, and so on). Wikibooks is not a doctor.

Biostor Ireland
type: Resource
type: NamedIndividual
has db xref: nlx_42920
IAO_0000115: To meet the strategic objectives of ongoing and future scientific and medical research, Biostor Ireland designed and constructed a technologically advanced repository for storage and distribution of biological materials. It offers secure, certified realtime biostorage of valuable biological materials for medical / scientific research, healthcare, medical device, pharmaceutical and biopharmaceutical sectors. This facility has been inspected by the Irish Medicines Board (IMB) and complies with the requirements of the EU Directive 2004/23/EU for storage and distribution of Human Tissues and Cells. Biostor also complies with the principals of current Good Manufacturing Practice (GMP), FDA requirements 21 CFR Part 1271 and ISBER (International Society of Biological and Environmental Repositories) Best Practices for Repositories. Outsourcing biostorage makes sense * Increase Workspace * Reduce Storage Costs * Peace of Mind * Expand your Business * Reduce Labor Costs * Uniform Maintenance * Improve Productivity * Tailored Storage * Delegate

Open HHS Blog
type: Resource
type: NamedIndividual
has db xref: nlx_42950
synonym: HealthData.gov: Open HHS Blog
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. In the Open HHS Blog, Chief Technology Officer, Todd Park, writes about harnessing the power of data, technology and innovation to improve the health and welfare of the nation.

CiTO - the Citation Typing Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_43122
synonym: Citation Typing Ontology
synonym: CiTO the Citation Typing Ontology
abbrev: CiTO
IAO_0000115: An ontology for describing the nature of reference citations in scientific research articles and other scholarly works, both to other such publications and to Web information resources, and for publishing these descriptions on the Semantic Web. Citation are described in terms of the factual and rhetorical relationships between citing publication and cited publication, the in-text and global citation frequencies of each cited work, and the nature of the cited work itself, including its publication and peer review status. CiTO is useful both for the annotation of bibliographic reference lists and for the visualization of citation networks. CiTO is written in the Web Ontology Language OWL, uses the namespace http://purl.org/net/cito/, and is available from http://purl.org/net/cito/. This site uses content negotiation to deliver to the user an OWLDoc Web version of the ontology if accessed via a Web browser, or the OWL ontology itself if accessed from an ontology management tool such as Protege 4 (http://protege.stanford.edu/). Collaborative work is under way to harmonize CiTO with other ontologies describing bibliographies and the rhetorical structure of scientific discourse.

Cell Signaling Technology
type: Organization
type: NamedIndividual
has db xref: grid.420530.0
has db xref: ISNI: 0000 0004 0580 0138
has db xref: nif-0000-20826
has db xref: nlx_152330
has db xref: Wikidata: Q3392342
abbrev: CST
IAO_0000115: Privately held company that develops and produces antibodies, ELISA kits, ChIP kits, proteomic kits, and other related reagents used to study cell signaling pathways that impact human health., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Bone Bank Allografts
type: Resource
type: NamedIndividual
has db xref: nlx_43262
IAO_0000115: Bone Bank Allografts is the distributor of the SteriGraft line of high quality bone and soft tissue allografts to medical professionals. The company has been in existence for over 13 years and has helped doctors and their patients with over one hundred thousand successful transplantations. Bone and soft tissue allografts in the SteriGraft line are validated to a sterility assurance level (SAL) of 10(-6) in accordance with ISO 11137-2 Method 1. Bone Bank Allografts was founded in 1993 in response to a growing need for allograft tissue in South Texas. Since 1993, Bone Bank Allografts'' distribution network has grown to cover Texas, the country and the globe, fulfilling surgical needs for allograft tissue in more than 175,000 successful transplantations. Located in San Antonio, Texas, Bone Bank Allografts is dedicated to a just, equitable and fair distribution of cadaveric tissue to surgeons, hospitals, surgicenters and dental offices. Over the years, our customers have come to rely on the superior quality of our tissue products as well as the unmatched service of our well trained, certified Tissue Bank Specialists (CTBS) and our knowledgeable distribution staff. With accreditation from the American Association of Tissue Banks (AATB), registration with the U.S. Food and Drug Administration (FDA) and compliance with the FDA''s Good Tissue Practices, Bone Bank Allografts continues to pursue our mission: To enhance the quality of patient care by providing safe, high quality allograft tissues to health care professionals for transplant and research. Most recently, Bone Bank Allografts has taken the next important step in tissue banking by developing a powerful partnership with Texas Human Biologics (THB) in order to process donated human tissue.

Gray Matters
type: Resource
type: NamedIndividual
has db xref: nlx_54435
synonym: Gray Matters Radio Series
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 06, 2013. Gray Matters is a radio series on brain topics that has been produced since 1994 by Public Radio International in association with the Dana Alliance. More than 25 programs have been created on topics ranging from stress, neuroethics, learning throughout life and sports, fitness and the Brain. Dana Alliance members serve as advisers to Gray Matters programming and are interviewed during the programs. The transcripts are also available.

NIMH Data Archive
type: Resource
type: NamedIndividual
has db xref: nlx_143735
has db xref: r3d100010717
has db xref: r3d100012653
synonym: National Database for Autism Research
synonym: National Database for Autism Research (NDAR)
synonym: National Institute of Mental Health Data Archive
synonym: NDAR
abbrev: NDA
IAO_0000115: The National Institute of Mental Health Data Archive (NDA) makes available human subjects data collected from hundreds of research projects across many scientific domains. Research data repository for data sharing and collaboration among investigators. Used to accelerate scientific discovery through data sharing across all of mental health and other research communities, data harmonization and reporting of research results. Infrastructure created by National Database for Autism Research (NDAR), Research Domain Criteria Database (RDoCdb), National Database for Clinical Trials related to Mental Illness (NDCT), and NIH Pediatric MRI Repository (PedsMRI).

Allograft Innovations, LLC
type: Resource
type: NamedIndividual
has db xref: nlx_43376
abbrev: Allograft Innovations
IAO_0000115: Allograft Innovations was formed in 2006 to facilitate quality biologic grafts for surgery. We are committed to providing quality tissue to enhance patients'' health, mobility and quality of life nationwide and across the globe. Our goal is to provide the safest, most clinically effective allografts available. The health of tissue recipients is top priority to us, and we take every possible step to ensure safety and integrity during all processes. Allograft Innovations partners with federally designated OPO''s (Organ Procurement Organization), as well as Tissue recovery agencies that comply with all 21 CFR 1270 and 1271 FDA Standards, and have achieved AATB accreditation.

Origene China
type: Organization
type: NamedIndividual
has db xref: nlx_43459
abbrev: OriGene China
IAO_0000115: A commercial antibody vendor.

Taverna
type: Resource
type: NamedIndividual
has db xref: nlx_43462
has db xref: OMICS_01146
IAO_0000115: An open source and domain independent Workflow Management System ����?? a suite of tools used to design and execute scientific workflows and aid in silico experimentation. Taverna Workbench now has support for service sets, offline workflow editing, workflow validation, improved workflow run monitoring, and the pausing and canceling of workflow runs. The command line tool allows you to run workflows outside of the workbench and is available as a stand-alone download or bundled with the Taverna Workbench 2.2.0 download. The Taverna suite is written in Java and includes the Taverna Engine (used for enacting workflows) that powers both the Taverna Workbench (the desktop client application) and the Taverna Server (which allows remote execution of workflows). Taverna is also available as a Command Line Tool for a quick execution of workflows from a terminal. Taverna 2.2.0 includes * Copy/paste, shortcuts, undo/redo, drag and drop * Animated workflow diagram * Remembers added/removed services * Secure Web services support * Secure access to resources on the web * Up-to-date R support * Intermediate values during workflow runs * myExperiment integration * Excel and csv spreadsheet support * Command line tool

dkCOIN
type: Resource
type: NamedIndividual
has db xref: nlx_44256
synonym: NIDDKConsortium Interconnectivity Network
abbrev: dkCOIN
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented October 13, 2014. The resource has moved to the NIDDKInformation Network (dkNET) project. Contact them at info_at_dknet.org with any questions. Database of large pools of data relevant to the mission of NIDDKwith the goal of developing a community-based network for integration across disciplines to include the larger DKuniverse of diseases, investigators, and potential users. The focus is on greater use of this data with the objective of adding value by breaking down barriers between sites to facilitate linking of different datasets. To date (2013/06/10), a total of 1,195 resources have been associated with one or more genes. Of 11,580 total genes associated with resources, the ten most represented are associated with 359 distinct resources. The main method by which they currently interconnect resources between the providers is via EntrezGene identifiers. A total of 780 unique genes provide the connectivity between 3,159 resource pairs across consortia. To further increase interconnectivity, the groups have been further annotating their data with additional gene identifiers, publications, and ontology terms from selected Open Biological and Biomedical Ontologies (OBO).

MindSpec: Informatics for Neurodevelopmental Conditions
type: Resource
type: NamedIndividual
has db xref: nlx_43490
synonym: MindSpec - Informatics for Neurodevelopmental Disorders
abbrev: MindSpec
IAO_0000115: MindSpec is a nonprofit organization that utilizes innovative bioinformatics strategies to accelerate research on common neurodevelopmental disorders. With our research we hope to foster discovery and development of treatments that alleviate the symptoms of affected individuals. Our core mission at MindSpec is to advance research on neurodevelopmental conditions. Founded in 2006, MindSpec is an independent, non-profit research organization established to facilitate the discovery of a cure for autism. Although the initial focus was autism, we have gradually expanded our scope to other neurological disorders. We develop bioinformatics strategies using current information technology platforms to build disease specific databases. At MindSpec we place a strong emphasis on translational research, that is, closing the gap between basic science discoveries and practical treatments with the potential of benefiting people who have autism. Goals: * Build an integrated, up-to-date, relevant, searchable resource on autism, AutDB. * Build a community of scientists, practitioners, educators, policymakers and people affected by autism to share and disseminate knowledge of autism. * Identify gaps in autism research around the world. * Identify priority areas in autism research based on real-world needs. * Build an autism dictionary and digital information library. * Address cultural differences in treatments for autism, a social disease. * Build knowledge about autism for immediate use.

qiqqa
type: Resource
type: NamedIndividual
has db xref: nlx_43805
abbrev: Qiqqa
IAO_0000115: Qiqqa is a free reference management tool that provides all the tools you need to manage your documents and notes effectively, visualize your ideas, and find insights you would have missed otherwise. Engineered by academics, its mission is to make your research life easier. Qiqqa allows users to annotate PDF''s, assign tags, share documents and offers cloud storage for a nominal fee. We help academics, researchers, and professionals manage all their PDFs and get more out of them, with our award winning Qiqqa software. * PDF management, OCR, reading, annotation * Unique tools to understand and discover * Cloud sync, cite, and much much more * Free. Trusted by academia and industry for all five stages of the knowledge lifecycle. Add all your papers, and it helps you do all the rest, quicker. # Organize # Discover # Review and Understand # Collaborate # Create

Guthy-Jackson Charitable Foundation
type: Resource
type: NamedIndividual
has db xref: nlx_43879
IAO_0000115: The Guthy-Jackson Charitable Foundation is dedicated to funding basic science research to find answers that will lead to the prevention, clinical treatment programs and a potential cure for Neuromyelitis Optica (NMO) Spectrum Disease. The decision to create our Foundation came from a personal family crisis. Our daughter was officially diagnosed with NMO in June 2008. Since that time, we have met with many clinicians and researchers in order to understand what this means for our beautiful daughter and our family. Additionally, we have gathered and read every piece of information and NMO research article that is available on the Web. We are now beginning to understand that NMO is not only considered an orphan disease, but that very little research is available. We met with the All Greater Good Foundation in early July 2008 when it became clear that there is little-to-no funding available to research this rare and often misunderstood disease. We joined hands with the All Greater Good Foundation to immediately begin our work, and thus, The Guthy-Jackson Charitable Foundation was born. The Guthy-Jackson Charitable Foundation is dedicated to funding biomedical research in the search to understand the pathophysiology and biochemistry of NMO Spectrum Disease. It is our greatest hope that together we will reverse the effects of NMO and eventually cure this disease.

Louisiana Organ Procurement Agency - LOPA
type: Resource
type: NamedIndividual
has db xref: nlx_43907
synonym: Louisiana Organ Procurement Agency
abbrev: LOPA
IAO_0000115: The Louisiana Organ Procurement Agency (LOPA) is the federally-designated organ procurement organization for the State of Louisiana. The agency focuses on educating the medical community and the general public about organ and tissue donation issues, working with families through the donation process, recovering donated organs and tissue, and placing the organs and tissue for transplant. Our mission is to save and enhance lives through organ and tissue donation. We envision a world in which no one suffers due to a lack of donor organs or tissues. LOPA has its main office in Metairie, with regional offices in Lafayette, and Shreveport. Additionally, LOPA has representatives in Baton Rouge, Alexandria, Lake Charles, and Monroe.

Biomedical Resource Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_143813
abbrev: BRO
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 27,2023. A controlled terminology of resources, which is used to improve the sensitivity and specificity of web searches. It includes ''resource_type'', ''area of research'', and ''activity''. It is under development by a number of NIH-funded researchers who have a combined interest in classification of biomedical resources. The biositemaps site is no longer available but the biomedical resource ontology is still available via bioportal Biomedical Resource Ontology (BRO).

Penn Alzheimer's Disease Center
type: Resource
type: NamedIndividual
has db xref: nlx_144494
synonym: Penn ADC
synonym: University of Pennsylvania Alzheimer's Disease Center
IAO_0000115: A national Alzhiemer's disease research center funded by the National Institute on Aging, and the research arm of the Penn Memory Center.

EDAR study: biomarkers for Alzheimer's disease
type: Resource
type: NamedIndividual
has db xref: nlx_143737
synonym: Early Diagnosis of AD and as marker of treatment response
synonym: Early Diagnosis of AD and as marker of treatment response (EDAR study)
synonym: EDAR study
abbrev: EDAR
IAO_0000115: A European collaborative study to develop and validate new biomarkers for Alzheimer's disease. Central in the project is the development of an assay for the measurement of beta amyloid oligomers in cerebrospinal fluid and plasma. In order to validate the assay for beta amyloid oligomers, cerebrospinal fluid and plasma will be repeatedly collected in subjects with Alzheimer's disease, other types of dementia, mild cognitive impairment, and control subjects.

Cooperative Human Tissue Network
type: Resource
type: NamedIndividual
has db xref: nlx_44126
abbrev: CHTN
IAO_0000115: The Cancer Diagnosis Program of the National Cancer Institute (NCI) initiated the Cooperative Human Tissue Network (CHTN) in 1987 to provide increased access to human tissue for basic and applied scientists from academia and industry to accelerate the advancement of discoveries in cancer diagnosis and treatment. This unique resource provides remnant human tissues and fluids from routine procedures to investigators who utilize human biospecimens in their research. Unlike tissue banks, the CHTN works prospectively with each investigator to tailor specimen acquisition and processing to meet their specific project requirements. Because the CHTN is funded by the NCI, the CHTN is able to maintain nominal processing fees for its services. The CHTN is comprised of five adult divisions and one pediatric division. Each of the adult divisions coordinates investigator applications/requests based upon the investigator's geographic location within North America. The Pediatric Division manages all investigators who request pediatric specimens only. The CHTN divisions share coordination for requests from outside North America. The CHTN divisions work both independently with individual investigators and together as a seamless unit to fulfill requests that are difficult to serve by any single division. The CHTN's unique informatics system allows each division to effectively communicate and network the needs of its investigators to all CHTN divisions. The Network as a whole can then help fulfill an investigator's request. Biospecimens from surgeries, autopsies and other routine procedures: Malignant, Benign, Diseased, Normal, Biofluids (urine, serum, plasma, buffy coat) High quality specimens at LOW processing fees: Fresh, Frozen, Floating in fixative, RNAlater, Paraffin embedded or and/or unstained slides, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

UMass Cancer Center Tissue and Tumor Bank
type: Resource
type: NamedIndividual
has db xref: nlx_44171
synonym: Cancer Center Tissue and Tumor Bank
synonym: Cancer Center Tissue Tumor Bank
synonym: UMass Cancer Center Tissue Tumor Bank
IAO_0000115: The UMass Cancer Center Tissue and Tumor Bank is a dynamic tissue procurement service: Collection, Storage, Annotation, and Distribution of Human Biologic Specimens. Our goal is to facilitate basic science, clinical research and translational studies by providing researchers with the ability to obtain and study human tissues using a dynamic collection, storage, annotation, and distribution service. * Fresh, diseased tissue is collected and processed immediately after surgery. ** When possible, surrounding healthy tissue is collected as a matched normal control. ** Anonymous, de-identified clinical and pathologic data are linked to the specimens in a secure database. * Bone marrow and blood specimens are collected and available as fresh cell isolates, frozen cell isolates or unprocessed. * A variety of services are available including routine histology, fresh tissue for cell culture, frozen sections, as well as DNA and RNA extraction. * Specific study needs can be met. * Consultation during study design is available and recommended. Contact Us * Assistance in the IRB approval process is offered. ** New: IRB approval is required only if you need identifiable private clinical information and/or patient follow-up for your study. The UMass Cancer Center Tissue and Tumor Bank is an open access biorepository. Specimens are available to investigators both internal and external to UMass. The Tumor Bank ships specimens to researchers worldwide. Please contact us to determine if we have specimens that meet your research needs.

Epilepsy Research Ireland
type: Resource
type: NamedIndividual
has db xref: nlx_143739
abbrev: ERI
IAO_0000115: Epilepsy Research Ireland is a non-profit organization (Charity CHY17527), run by a group of volunteers, who are dedicated to find cure for epilepsy by raising awareness and money for research. We can say cure now with much more confidence than we could even 10 years ago because recent advances in genetics, brain imaging and drug therapy, all hold out the promise of that holy grail the cure. We can also say with confidence that you can be part of that push by participating in this new foundation since we have collaborations with doctors and scientists all over Europe, the US and Australia, all of whom share the same goal. Epilepsy research, conducted by Epilepsy Research Ireland, is essential and will deliver benefits across the board. Research planned and already underway by Epilepsy Research Ireland will help develop and improve clinical skills; it will provide a knowledge base to develop new ways to manage and treat epilepsy; it will help in the evaluation of new medical advances. Ultimately we can improve the quality of care and provide greater understanding, better and more accurate diagnosis and more tailored treatments. Ireland is uniquely well-positioned, given its relatively homogenous population to make the goal, of making real discoveries in epilepsy research that will directly improve the lives of people with epilepsy, a realistic one.

Cell Marque
type: Organization
type: NamedIndividual
has db xref: nlx_152327
synonym: Cell Marque Corp.
IAO_0000115: An Antibody supplier

ProFunc
type: Resource
type: NamedIndividual
has db xref: nlx_44430
synonym: ProFunc - prediction of protein function from 3D structure
synonym: ProFunc: Analysis of a protein''''s 3D structure to help identify its likely biochemical function
IAO_0000115: The ProFunc server had been developed to help identify the likely biochemical function of a protein from its three-dimensional structure. It uses both sequence- and structure-based methods including fold matching, residue conservation, surface cleft analysis, and functional 3D templates, to identify both the protein' '''s likely active site and possible homologues in the PDB. Often, where one method fails to provide any functional insight another may be more helpful. You can submit your own structure, analyze an existing PDB entry, or retrieve the results of a previously submitted run. The files are usually stored for about 6 months before being deleted. However, they are stored on a partition that is not backed up; so, in principle, they could disappear at any time.

Crimson Biospecimen Core
type: Resource
type: NamedIndividual
has db xref: nlx_44583
IAO_0000115: The Crimson Biospecimen Core prospectively collects discarded clinical materials matching investigator-defined criteria. Queries are run against real-time data on recently received clinical samples, including ICD.9 codes and results of clinical laboratory testing. Studies using the core must either (1) have an IRB-approved protocol for discarded clinical materials and anonymized information or (2) a protocol to allow collection of discarded samples from patients consented for their study. Collected samples may be additionally processed, aliquotted, or tested per the menu of tests available within the BWH and MGH Clinical Laboratories and Partners Genomics Center. Services: * Collection of discarded clinical specimens including serum, plasma, CSF, urine and microbiological isolates for IRB-approved studies. * Processing or additional clinical testing of collected materials. * Ability to receive consented patient samples for processing and clinical testing. * Online interface to manage collected sample inventories, associated test results, and study users/workgroup per IRB-approval.

Northern Ireland Virtual Tissue Archive
type: Resource
type: NamedIndividual
has db xref: nlx_44619
abbrev: NIVTA
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. A pan European network for virtual tissue archiving aimed at supporting clinical trials, biomarker research, tissue microarray analysis and virtual slide based education. NIVTA has state-of-the-art digital scanning systems including an Aperio CS system, Aperio OS system (one of only two currently available in Europe) and a Hamamatsu system with fluorescent scanning capability.

Stem Cell Discovery Engine
type: Resource
type: NamedIndividual
has db xref: biotools:scde_discovery
has db xref: nlx_44656
synonym: Harvard Stem Cell Discovery Engine
synonym: SCDE - Stem Cell Discovery Engine
abbrev: SCDE
IAO_0000115: An online database of curated cancer stem cell (CSC) experiments coupled to the Galaxy analytical framework. Driven by a need to improve our understanding of molecular processes that are common and unique across cancer stem cells (CSCs), the SCDE allows users to consistently describe, share and compare CSC data at the gene and pathway level. The initial focus has been on carefully curating tissue and cancer stem cell-related experiments from blood, intestine and brain to create a high quality resource containing 53 public studies and 1098 assays. The experimental information is captured and stored in the multi-omics Investigation/Study/Assay (ISA-Tab) format and can be queried in the data repository. A linked Galaxy framework provides a comprehensive, flexible environment populated with novel tools for gene list comparisons against molecular signatures in GeneSigDB and MSigDB, curated experiments in the SCDE and pathways in WikiPathways. Investigation/Study/Assay (ISA) infrastructure is the first general-purpose format and freely available desktop software suite targeted to experimentalists, curators and developers and that: * assists in the reporting and local management of experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships) from studies employing one or a combination of technologies; * empowers users to uptake community-defined minimum information checklists and ontologies, where required; * formats studies for submission to a growing number of international public repositories endorsing the tools, currently ENA (genomics), PRIDE (proteomics) and ArrayExpress (transcriptomics). Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples and much much more. Best of all, Galaxy' '''s history system provides a complete analyses record that can be shared. Every h…

National Psoriasis Foundation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100003185
has db xref: grid.453839.0
has db xref: ISNI: 0000 0004 4904 0118
has db xref: nlx_44871
has db xref: Wikidata: Q6975105
synonym: Psoriasis Foundation
abbrev: NPF
IAO_0000115: The National Psoriasis Foundation (NPF) is a non-profit, voluntary health agency dedicated to finding a cure for psoriasis and psoriatic arthritis and eliminating their devastating effects through research, advocacy and education. Founded in 1966, the Psoriasis Foundation has evolved to become the leading patient advocacy group for the 7.5 million Americans living with psoriasis and psoriatic arthritis. As emerging research continues to demonstrate the serious, systemic effects of these chronic autoimmune diseases, our highest priority is to find a cure. Guided by our five year-strategic plan, we are moving towards this goal with an integrated approach that leverages the work of members, health care providers, advocates and scientists in four critical areas: * Research: ** Directly supporting the most promising early-stage research and emerging researchers. ** Hosting the world''s largest bank of psoriasis DNA samples. * Advocacy: ** Advancing a public policy agenda to secure more federal funding for psoriasis research. ** Improving access to care for patients. * Education: ** Providing extensive patient education. ** Keeping health care professionals up to date on psoriasis treatment. * Connection: ** Online communities, support networks, mentorship programs. ** Building a grassroots network of volunteers and advocates. * Leadership: ** A volunteer Board of Trustees steers the strategic direction of the National Psoriasis Foundation. ** Our Medical Board, made up of leading national psoriasis experts, provides medical guidance, leadership and advocacy. ** An executive staff of seasoned non-profit leaders drives the organization to achieve its strategic plan goals.

PASHA
type: Resource
type: NamedIndividual
has db xref: OMICS_00024
IAO_0000115: A parallel short read assembler for large genomes using de Bruijn graphs.

miRDeepFinder
type: Resource
type: NamedIndividual
has db xref: OMICS_00362
IAO_0000115: Provides an comprehensive workflow of analyzing data from plant microRNA (miRNA) deep sequencing.

ScienceCare
type: Resource
type: NamedIndividual
has db xref: nlx_44986
synonym: ScienceCare of Colorado
abbrev: Science Care
IAO_0000115: Science Care''s whole body donation program supports medical research, training and professional education, which provides enormous benefits to humankind. Given the increasing advancements in medical technologies, donation is of greater importance than ever. A life-affirming choice, donation is also a highly individual decision. In every way possible, Science Care honors that decision by adhering to the strictest guidelines and providing the most compassionate care. Science Care was founded in 2000 with the vision to become the world''s leading whole body donor program. Under the leadership of James Rogers, Founder and CEO, Science Care has accelerated research on many fronts leading to the development of new medical devices and safer, more effective treatments for patients. At Science Care, we provide the opportunity to make a final choice with control and dignity. Our donors know that their last act was donating to the welfare of humankind, and their gift provides a lasting legacy.

St. James Hospital Cryobiology Laboratory Stem Cell Facility
type: Resource
type: NamedIndividual
has db xref: nlx_143743
synonym: St. James''s Hospital Cryobiology Laboratory Stem Cell Facility
synonym: St. James''s Hospital Stem Cell Facility
synonym: St. James''s Stem Cell Facility
abbrev: St. James Stem Cell Facility
IAO_0000115: The Cryobiology laboratory is a stem cell processing laboratory, preparing clinical grade haemopoietic (bone marrow or peripheral blood) stem cells for transplant. The Laboratory supports the National Adult Stem Cell Transplant Programme based in St James Hospital treating Leukemia and related disorders. Approximately 100 Transplants are carried out annually. The Tissue Establishment is part of a network of hospitals carrying out stem cell transplant. Stem cells are imported from abroad and exported world wide for stem cell transplantation. The Laboratory is a GMP Tissue Establishment and is licensed by the Irish Medicines Board to process cells under the EU tissue directive.

Network Science
type: Resource
type: NamedIndividual
has db xref: nlx_45289
synonym: Network Science - NetSci
abbrev: NetSci
IAO_0000115: Scientific focus articles and general resources for scientists within the pharmaceutical and biotechnology industries that take a comprehensive look at the industry and the tools that are in use to speed drug discovery and development. Resources include a forum, courseware, and a listing of professional societies, associations and companies/organizations. In addition to features on classical drug discovery, NetSci will address biotechnology, genomic research, and materials design as well as subjects suggested by readers. Network Science has collected an extensive list of professional societies and associations and companies/organizations that are a part of the world-wide efforts in drug discovery and development. These organizations were selected based upon the fact that they contribute to pharmaceutical research and development and healthcare throughout the world. The forum for experts to explore and discuss current applications of science and technology with their colleagues world-wide, permits publication of scientific data without the delays inherent in traditional printed media and encourages immediate dialog using hypertext (a contextual linkage of related information sources), multimedia, interactive electronic feedback forms, and automatic electronic mail connections which are not available within any other media. CourseWare provides a collection of materials which examine the pharmaceutical industry and the use of technology in drug discovery. Topics range from an introduction to the drug development process to an in-depth examination of the tools and techniques used in pharmaceutical research and development. If your would like to see a topic added to this collection, or know about companies and products that you feel would be of interest to the readers, would like to add your organization to the list or correct the listing that is on-line, please contact us.

National Alliance for Medical Image Computing
type: Resource
type: NamedIndividual
has db xref: nlx_45301
abbrev: NA-MIC
abbrev: NAMIC
IAO_0000115: The National Alliance for Medical Image Computing (NA-MIC) is a multi-institutional, interdisciplinary team of computer scientists, software engineers, and medical investigators who develop computational tools for the analysis and visualization of medical image data. The purpose of the Center is to provide the infrastructure and environment for the development of computational algorithms and open-source technologies, and then oversee the training and dissemination of these tools to the medical research community. Electronic resources provided by NA-MIC include software, data, tutorials, presentations, and more.

BrainNet Europe
type: Resource
type: NamedIndividual
has db xref: nlx_45326
synonym: BrainNet Europe Consortium
abbrev: BNE
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 7, 2022. Consortium of 19 brain banks across Europe with an aim to harmonize neuropathological diagnostic criteria and develop gold standards for quality, safety and ethics standards for brain banking. BrainNet Europe also contributes to research on rare diseases, such as: Pick''s disease or other rare forms of dementia, as well as to questions after the events in the aging brain. Anyone can be a donor - irrespective of disease of the central nervous system or not, because for research purposes, one does not only need tissue samples from ill donors, but also from healthy ones for comparison.

CEDARLANE Laboratories Limited
type: Organization
type: NamedIndividual
has db xref: nlx_152326
synonym: CEDARLANE
IAO_0000115: An Antibody supplier

STAR
type: Resource
type: NamedIndividual
has db xref: biotools:star
has db xref: OMICS_01254
has db xref: SCR_015899
synonym: rna-star
synonym: Spliced Transcripts Alignment to a Reference (STAR)
synonym: Spliced Transcripts Alignment to Reference
synonym: ultrafast universal RNA-seq aligner
IAO_0000115: Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays.

Essential Tremor Centralized Brain Repository
type: Resource
type: NamedIndividual
has db xref: nlx_143745
abbrev: ETCBR
IAO_0000115: Finding a cure for any neurological disorder begins with the scientific study of the disorder''s causes, processes, and development in the brain. For essential tremor (ET), rigorous study of this kind had not been undertaken until 2003, when the Essential Tremor Centralized Brain Repository (ETCBR) was established at Columbia University. For the past five years, brain tissue from ET donors has been collected, processed and compared alongside age-matched control brains at the ETCBR, and already several significant findings have been made. However, there is still much to learn and a severe shortage of ET brains for scientific study. If you have been diagnosed with essential tremor, donating your brain tissue in the hours immediately after your death is of utmost importance in providing crucial information about what causes ET. Direct analysis of the shape and number of nerve cells and their content will provide medical researchers with the information they need in order to understand this complex illness. By advancing our medical knowledge of ET, the gift of brain tissue is a central piece of the puzzle in the search to develop better treatments and find a cure.

South Dakota Lions Eye Bank
type: Resource
type: NamedIndividual
has db xref: nlx_45501
synonym: SD Lions Eye Bank
abbrev: SDLEB
IAO_0000115: Through the South Dakota Lions Eye Bank, donors can provide the gift of sight and health through the donation of bone, connective tissue, heart valves, veins, skin, and corneas. The option of donation is available to both men and women, up to the age of 95. Since 1990, the South Dakota Lions Eye Bank has restored sight to over 5500 people world wide. In recent statistics the South Dakota Lions Eye Bank has transplanted 2217 corneas since 2001; 1237 transplanted in the United States and 980 transplanted overseas. It is the fondest hope of the South Dakota Lions Eye Bank that you will become an eye, tissue and organ donor and pass along to someone the greatest gift of all, Life.

Iowa State University Neuroscience Program
type: Organization
type: NamedIndividual
has db xref: nlx_45726
synonym: Iowa State University Neuroscience
abbrev: ISU Neuroscience
IAO_0000115: The Neuroscience Program at Iowa State University has a philosophy based on the balanced combination of mentoring, general curriculum and frontier collaborative research to teach graduate students essential theoretical, research, teaching, writing and presentation skills and to prepare students for the competitive environment in academia and industry. The program reflects the structure of contemporary neuroscience which has become a diverse and inter-disciplinary field. Students of diverse educational, ethnic and national backgrounds are encouraged to apply to the program. Participating Departments in Neuroscience * Animal Science * Biochemistry, Biophysics and Molecular Biology * Biomedical Sciences * Chemical and Biological Engineering * Chemistry * Computer Science * Genetics, Development and Cell Biology * Kinesiology * Psychology

Estonian Genome Center
type: Resource
type: NamedIndividual
has db xref: nlx_45748
synonym: Estonian Biobank
synonym: Estonian Genome Center University of Tartu
abbrev: EGC
abbrev: EGCUT
IAO_0000115: The Estonian Biobank is the population-based biobank of the EGCUT. The project is conducted in accordance with the Estonian Genes Research Act and all participants have signed a broad informed consent form (www.biobank.ee <http://www.biobank.ee/> and Metspalu 2004, Drug Dev. Res.). As of December 2011, the biobank contains 51,515 participants (gene donors). The database of genotypic, phenotypic, health and genealogical information represents about 5% of Estonia''s adult population, and is the largest cohort ever gathered in Estonia. The age, sex and geographical distribution of this cohort reflect the structure of the adult population in Estonia. The database enables to conduct research in order to find links between genes, environmental factors, lifestyles and complex diseases or other traits. Active use of the biobank has started and although the first users are researchers all over the world with hundreds of different projects currently underway, industry is also interested. At the international level, the EGCUT will join the BBMRI follow-up program (ERIC) and through this channel provide service (biobanking, genotyping, sequencing and data analysis) for the centers in Europe who need it. Currently, the first follow-up study is underway and the molecular information of the cohort will be increased. For example, we have over 12 000 DNA samples analyzed by high density genotyping arrays and over 10 000 plasma samples analyzed by NMR scans, over 1000 individuals with RNA expression arrays, 2000 individuals with clinical laboratory analysis (over 40 tests) and over 60 full genomes are under deep sequencing. The infrastructure of the EGCUT includes a laboratory for DNA genotyping and next generation sequencing all based on Illumina platforms (HiScanSQ, HiSeq2000 and robotics), an IT unit (databases) with required computing power and storage space (1.2PB), data analysis team (bioinformatics and statistical genetics) and last but not least, a patient recruitment unit (h…

Cureline Biopathology
type: Resource
type: NamedIndividual
has db xref: nlx_45810
synonym: Cureline BioPathology: Research Histology Laboratory
abbrev: Cureline BioPathology
IAO_0000115: Cureline BioPathology is a research histology laboratory providing high-quality human and animal tissue processing, preparation and analysis. In collaboration with Cureline, Cureline BioPathology offers a complete portfolio of services in human tissue research, including human tissue acquisition, biospecimen storage, tissue processing and comprehensive tissue analysis using special stains and immunohistochemical methods. The laboratory was founded in San Francisco Bay area by Cureline, Inc., to leverage already established relationships with clinical sites and biotechnology companies. Cureline has extensive experience in human tissue procurement, preservation and biospecimen management, and has been providing effective human tissue research services to pharmaceutical and biotechnology clients since 2003. Our experienced and motivated team is dedicated to providing support to academia and industry clients in all aspects of human and animal tissue processing, target profiling, antibody cross-reactivity studies, and toxicology.

Spanki
type: Resource
type: NamedIndividual
has db xref: OMICS_01414
synonym: Splicing Analysis Kit
IAO_0000115: A set of tools to facilitate analysis of alternative splicing from RNA-SEQ data.

Feinstein Institute for Medical Research
type: Organization
type: NamedIndividual
has db xref: grid.250903.d
has db xref: ISNI: 0000 0000 9566 0634
has db xref: nlx_143748
has db xref: Wikidata: Q7733638
synonym: Feinstein Institute
IAO_0000115: The Feinstein Institute for Medical Research is the research branch of the North Shore-Long Island Jewish Health System. Biomedical research has been a vital aspect of its two academic medical centers North Shore University Hospital and Long Island Jewish Medical Center since their establishment in the early 1950''s. Through its connection to the hospital system, the Institute bridges the gap between biomedical research and patient care, accessing hundreds of thousands of patients in the health system''s 15 hospitals, four long-term care facilities, three trauma centers, six home health agencies and dozens of outpatient facilities. Institute scientists collaborate with clinicians throughout the system to shed light on basic biological processes underlying disease. This knowledge is used to develop new therapies and diagnostics. Currently, more than 800 scientists and investigators are conducting research in oncology, immunology and inflammation, genetics, psychiatry, neurology, pediatrics, surgery, urology, obstetrics/gynecology and many other specialties. In 2008, the Feinstein received funding from the National Institutes of Health in excess of $28 million, and an additional $10 million from other federal sources. Total annual research funding from all sources exceeded $44 million in 2008. We stand at the threshold of an extraordinary time in medicine. Over the last 100 years, biomedical science has progressed very rapidly. Advances coming from the integration of genomics, proteomics and bioinformatics into the biomedical toolkit hold the promise that this transformation will continue well into the 21st century. The Feinstein Institute for Medical Research is a growing force in research innovation, education and progress.

Roswell Park Comprehensive Cancer Center
type: Organization
type: NamedIndividual
has db xref: Crossref Funder ID 100001320
has db xref: GRID grid.240614.5
has db xref: ISNI 0000 0001 2181 8635
has db xref: nlx_143749
has db xref: Wikidata Q7370121
synonym: Roswell Park Cancer Institute
abbrev: RPCI
IAO_0000115: Cancer research and treatment center located in Buffalo, New York. Founded by surgeon Roswell Park in 1898, the center was the first in the United States to specifically focus on cancer research. The center is usually called Roswell Park in short.

CardioVascular Research Grid (CVRG)
type: Resource
type: NamedIndividual
has db xref: nlx_143758
has db xref: r3d100012849
synonym: Cardio Research Grid
synonym: The Cardiovascular Research Grid
abbrev: CVRG
IAO_0000115: Infrastructure for sharing cardiovascular data and data analysis tools. Human ExVivo heart data set and canine ExVivo normal and failing heart data sets are available. Canine hearts atlas and human InVivo atlases are available.

European Molecular Biology Laboratory
type: Organization
type: NamedIndividual
has db xref: nlx_46173
synonym: EMBL
IAO_0000115: Intergovernmental organisation funded by public research money from its member states in Europe. Groups and laboratories perform basic research in molecular biology and molecular medicine, training for scientists, students and visitors. Provides development of services, new instruments and methods, data and technology in its member states.

WikiHealthCare
type: Resource
type: NamedIndividual
has db xref: nlx_54565
IAO_0000115: WikiHealthCare is The Joint Commission''s interactive forum for health care professionals. It is designed to enable and encourage discussion and collaboration among all users for the purpose of improving health care quality. While The Joint Commission provides the forum, users of the site control its content. The WikiHealthCare Quality Improvement forum is a collaborative network for health care professionals, researchers, and other health care stakeholders. Within this forum, you can freely exchange information, describe your implementation experiences and create and share performance improvement solutions. Registered members of the WikiHealthCare community are free to use this forum to create new web pages, initiate blogs, and dialogue with other members of the community.

WHO International Clinical Trials Registry Platform
type: Resource
type: NamedIndividual
has db xref: nlx_143764
has db xref: r3d100012586
synonym: International Clinical Trials Registry Platform
synonym: International Clinical Trials Registry Platform (ICTRP)
synonym: WHO ICTRP
abbrev: ICTRP
IAO_0000115: Public database of information about all clinical trials involving humans, this global initiative provides a single point of access to information about ongoing and completed clinical trials. It contains the trial registration data sets made available by data providers around the world meeting criteria for content and quality control. It also aims to: * To improve the comprehensiveness, completeness and accuracy of registered clinical trial data * To communicate and raise awareness of the need to register clinical trials * To ensure the accessibility of registered data * To build capacity for clinical trial registration * To encourage the utilization of registered data * To ensure the sustainability of the ICTRP The mission of the WHO International Clinical Trials Registry Platform is to ensure that a complete view of research is accessible to all those involved in health care decision making. This will improve research transparency and will ultimately strengthen the validity and value of the scientific evidence base. The registration of all interventional trials is a scientific, ethical and moral responsibility. The ICTRP: * Publishes the ICTRP Search Portal * Supports the WHO Registry Network * Supports countries and regions wanting to establish WHO-compliant clinical trial registries or policies on trial registration.

Stem-Health Hellas Stem Cell Bank
type: Resource
type: NamedIndividual
has db xref: nlx_46178
synonym: Stem Health
synonym: Stem Health Hellas
synonym: Stem-Health Hellas
IAO_0000115: An accredited cord blood bank and stem cell bank in Europe. Services offered include family cord blood banking, public banking, directed allogeneic transplantation, umbilical cord tissue banking and HLA typing.

NEWT
type: Resource
type: NamedIndividual
has db xref: biotools:newt
has db xref: nlx_46189
synonym: UniProt Taxonomy
synonym: UniProt Taxonomy Database
synonym: UniProtKB taxonomy database
IAO_0000115: NEWT is the taxonomy database maintained by the UniProt group. It integrates taxonomy data compiled in the NCBI database and data specific to the UniProt Knowledgebase. Browse by hierarchy, List all, or Complete proteomes. Organisms are classified in a hierarchical tree structure. Our taxonomy database contains every node (taxon) of the tree. UniProtKB taxonomy data is manually curated: next to manually verified organism names, we provide a selection of external links, organism strains and viral host information. Species with protein sequences stored in the UniProt Knowledgebase are named according to UniProt nomenclature. We endeavour to maintain a list of manually curated species names for which protein sequence data is available. In particular, we have adopted a systematic convention for naming viral and bacterial strains and isolates. Links to external sites are chosen by the UniProt taxonomy team and show pictures and various scientific data of interest (taxonomy, biology, physiology,...).

CFC International INTERNATIONAL REGISTRY
type: Resource
type: NamedIndividual
has db xref: nlx_143759
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016.

SysMO-DB
type: Resource
type: NamedIndividual
has db xref: nlx_46298
synonym: SysMO Database
synonym: SysMO DB
synonym: Systems Biology for Micro-Organisms Database
synonym: Systems Biology for Micro-Organisms DB
synonym: Systems Biology of Micro-Organisms Database
synonym: Systems Biology of Micro-Organisms DB
IAO_0000115: SysMO-DB is a project that is creating a web-based platform, and tooling, for finding, sharing and exchanging Data, Models and Processes in Systems Biology. It was designed to support the SysMO Consortium (Systems Biology for Micro-Organisms), but the principles and methods employed are equally applicable to other multi-site Systems Biology projects. All code is open source and available for download. SEEK, a component of SysMO-DB, is a private community collaboration and asset sharing platform for Systems Biology models, data and protocols serving 120 research institutions throughout Europe. SEEK is the main web-based access point to the system and provides an access control layer to enable researchers to restrict access to collaborators, colleagues or other individuals until they are ready to share with the whole consortium or the wider community. The main objectives of SysMO-DB are to: facilitate the web-based exchange of data between research groups within- and inter- consortia, and to provide an integrated platform for the dissemination of the results of the SysMO projects to the scientific community. We aim to devise a progressive and scalable solution to the data management needs of the SysMO initiative, that: * facilitates and maximizes the potential for data exchange between SysMO research groups; * maximizes the ''shelf life'' and utility of data generated by SysMO; * provides an integrated platform for the dissemination of the results of the SysMO projects to the scientific community; and * facilitates standardization of practices in Systems Biology for the interfacing of modeling and experimentation. We follow several key principles: * exploit what is already available, both within the consortium and outside it, and do not reinvent; * identify the least we can do to make a benefit and do this incrementally. SysMO-DB will soon be opening it up to the wider scientific community, but for now it is currently only available for those within the SysMO consorti…

NEXTDB
type: Resource
type: NamedIndividual
has db xref: nlx_46406
synonym: Nematode Expression Pattern DataBase
abbrev: NextDB
IAO_0000115: Expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans through EST analysis and systematic whole mount in situ hybridization. NEXTDB is the database to integrate all information from their expression pattern project and to make the data available to the scientific community. Information available in the current version is as follows: * Map: Visual expression of the relationships among the cosmids, predicted genes and the cDNA clones. * Image: In situ hybridization images that are arranged by their developmental stages. * Sequence: Tag sequences of the cDNA clones are available. * Homology: Results of BLASTX search are available. Users of the data presented on our web pages should not publish the information without our permission and appropriate acknowledgment. Methods are available for: * In situ hybridization on whole mount embryos of C.elegans * Protocols for large scale in situ hybridization on C.elegans larvae

Scientific Data Sharing Project
type: Resource
type: NamedIndividual
has db xref: nlx_46687
synonym: Data Sharing Project
IAO_0000115: While many data sharing programs exist worldwide, widespread sharing of raw data has not yet won across-the-board acceptance in the scientific community, and the very existence of all these databases makes the approach fractured at best. The Data Sharing Project, launched last year by University of California-San Francisco Professor Michael Weiner, has two goals: One is to make widespread raw data sharing a reality initially in the realm of medicine through creation of a repository system accessible to all researchers; the second goal is to foster broad scientific support for this move and its adoption in other fields of research. With major projects such as the Human Genome Project demonstrating the tremendous scientific breakthroughs made possible by data sharing and with the decline of technological barriers impeding such efforts, the time has come to work to achieve widespread sharing of raw data worldwide. The Data Sharing Project proposes to further this goal initially in the field of medicine by working to create a raw data sharing program that will serve as a model to other disciplines attempting to make their own way in this arena. The Northern California Institute for Research and Education (NCIRE) together with the University of California-San Francisco and support from the Michael J. Fox Foundation is now in the process of canvassing the scientific community to analyze the best possible data sharing program and practices to establish in the field of medicine.

Zebrafish Neurophenome Project Database
type: Resource
type: NamedIndividual
has db xref: nlx_143762
synonym: Zebrafish Neurophenome Database
synonym: Zebrafish Neurophenome Project
synonym: ZNP Database
synonym: ZNPdb
abbrev: ZNP
IAO_0000115: Database of neurobehavioral and physiological data of adult zebrafish models, complementing the available repositories for zebrafish genetic information, by providing a dynamic, open-access data repository of comprehensive, curated collection of results from zebrafish neurobehavioral experiments. As of May 2012, it contains over 4,500 experimental results, from over 75 unique physiological and behavioral tests and 330 different drug treatments. ZNP incorporates validated and curated data from work published in this field, to improve the accessibility of current knowledge to researchers interested in using adult zebrafish models. Overall, this program will allow investigators to rapidly review data, to direct their research using these models. Data and protocol submissions are now being accepted.

VAMPS
type: Resource
type: NamedIndividual
has db xref: OMICS_01501
synonym: VAMPS Project
synonym: Visualization and Analysis of Microbial Population Structure
IAO_0000115: A publicly-accessible website to measure and visualize similarities and differences between molecular profiles of complex microbial communities. The project includes visualization tools such as heat maps that simultaneously compare the taxonomic distributions of multiple datasets and 3-D charts of the frequency distributions of 16S rRNA tags. Analytical tools include Chao diversity estimates and rarefaction curves. As a service to the community, researchers have the opportunity to upload their own data to the site for private viewing with the full range of data and analysis tools. Public data can be downloaded for further analysis locally.

MGED Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_47223
synonym: Microarray and Gene Expression Data Ontology
abbrev: MO
IAO_0000115: An ontology including concepts, definitions, terms, and resources for a standardized description of a microarray experiment in support of MAGE v.1. The MGED ontology is divided into the MGED Core ontology which is intended to be stable and in synch with MAGE v.1; and the MGED Extended ontology which adds further associations and classes not found in MAGE v.1. These terms will enable structure queries of elements of the experiments. Furthermore, the terms will also enable unambiguous descriptions of how the experiment was performed.

Arnold Arboretum of Harvard University: Weld Hill Microscopy Lab
type: Resource
type: NamedIndividual
has db xref: nlx_156117
IAO_0000115: Microscopists at Weld Hill will find a range of tools from the simple hand lens to the confocal microscope for 3-D reconstructions.

ECGpedia
type: Resource
type: NamedIndividual
has db xref: nlx_47270
synonym: ECGpedia.org
IAO_0000115: Free online electrocardiography (ECG) course and textbook via a wiki where anyone can contribute and changes are supervised by physicians. Learn from cases and examples. It designed for medical professionals such as cardiac care nurses and physicians. All content is freely accessible. The information on this site should NOT be used as a substitute for the advice of an appropriately qualified and licensed physician or other health care provider. For questions like these we advise you to contact your physician.

ResearchInformatics.org
type: Resource
type: NamedIndividual
has db xref: nlx_47438
synonym: Clinical Research Informatics Wiki
synonym: CRI Wiki
synonym: Research Informatics.org
IAO_0000115: An open-access portal for discussion, information sharing, and collaboration among those working to advance the rapidly developing field of clinical research informatics (CRI). We hope that you find the content useful and that you use our interactive features to contribute your knowledge and experience for the benefit of our community. Research Informatics.org Contents include: * CRI Initiatives * CRI News * CRI Events * CRI Resources * CRI Wiki * CRI Forum * CRI Blog

LifeTek OrthoBiologics
type: Organization
type: NamedIndividual
has db xref: nlx_47539
synonym: LifeTek OrthoBiologics LLC
abbrev: LifeTek
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. LifeTek is a full service International Tissue Bank, with recovery and processing partners in the United States, Spain and Mexico. Our goal is to provide safe, quality allograft implants, therefore serving donor families, physicians and recipients. Following regulations established by state and federal agencies, including the United States Food and Drug Administration, specific steps are taken to ensure donor suitability, including serologic testing performed by CLIA certified laboratories. LifeTek aseptically process tissues in Class 100 Cleanrooms, significantly reducing the risk of airborne contaminants. Equipment and reagents used are sterilized in steam autoclaves. Grafts are further processed and sterilized using Clearant Technology. LifeTek allografts are provided either freeze-dried or frozen. Freeze-dried allografts are stored at ambient temperatures, while frozen allografts are stored at -40 degrees C or colder. Freeze-dried allografts are provided with a maximum of two years expiration, frozen allografts are provided with a maximum of five years expiration.

TissueNet
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_47663
abbrev: tn
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 17,2021. Manufacturer of allograft tissue grafts in the United States in the ortho-biologics field of medicine. They develop new products for the patients they serve, including the UltraGraft non-irradiated & sterile line of allograft tissue implants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Transporter Classification Database
type: Resource
type: NamedIndividual
has db xref: biotools:tcdb
has db xref: nlx_47724
abbrev: TC
abbrev: TCDB
IAO_0000115: Curated, relational database containing sequence, classification, structural, functional and evolutionary information about transport systems from variety of living organisms based on IUBMB-approved transporter classification (TC) system. Descriptions, TC numbers, and examples of over 600 families of transport proteins are provided. TC system is analogous to Enzyme Commission (EC) system for classification of enzymes, except that it incorporates both functional and phylogenetic information. TCDB users may submit their own sequenced proteins and descriptions for inclusion into database. The software tools used are all freely available for download. These programs are used for analysis of Protein and DNA sequences. Programs require UNIX server to run.

Brain Science Podcast
type: Resource
type: NamedIndividual
has db xref: nlx_47745
abbrev: BSP
IAO_0000115: Podcast, hosted by Dr. Ginger Campbell, featuring the latest books about neuroscience as well as interviews with leading scientists from around the world. In this podcast, she shares recent discoveries from the world of neuroscience in a way that people of all backgrounds can enjoy. Dr. Campbell is an experienced emergency physician with a long-standing interest in mind-body medicine, the brain, and consciousness. She believes that understanding how the brain works gives us insight into what makes us human. She is also committed to showing how the scientific method has unraveled many long-standing mysteries. Brain Science Transcripts are also available.

Basic OligoNucleotide Design
type: Resource
type: NamedIndividual
has db xref: OMICS_00827
synonym: BOND: Basic OligoNucleotide Design
abbrev: BOND
IAO_0000115: Software program to compute highly specific DNA oligonucleotides, for all the genes that admit unique probes, while running orders of magnitude faster than the existing programs.

Foundation for the National Institutes of Health
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100000009
has db xref: grid.428807.1
has db xref: ISNI: 0000 0000 9836 9834
has db xref: nlx_143768
has db xref: Wikidata: Q16837497
synonym: Foundation for NIH
abbrev: FNIH
IAO_0000115: A public charity whose mission is to support the NIH in its mission to improve health, by forming and facilitating public-private partnerships for biomedical research and training. Its vision is Building Partnerships for Discovery and Innovation to Improve Health. The FNIH draws together the world''s foremost researchers and resources, pressing the frontier to advance critical discoveries. They are recognized as the number-one medical research charity in the countryleveraging support, and convening high level partnerships, for the greatest impact on the most urgent medical challenges we face today. Grants are awarded as part of a public-private partnership with the National Heart, Lung, and Blood Institute (NHLBI) on behalf of The Heart Truth in support of women''s heart health education and research. Funding for the Community Action Program is provided by the FNIH through donations from individuals and corporations including The Heart Truth partners Belk Department Stores, Diet Coke, and Swarovski. Successful biomedical research relies upon the knowledge, training and dedication of those who conduct it. Bringing multiple disciplines to bear on health challenges requires innovation and collaboration on the part of scientists. Foundation for NIH partnerships operate in a variety of ways and formats to recruit, train, empower and retain their next generation of researchers. From lectures and multi-week courses, to scholarships and awards through fellowships and residential training programs, their programs respond to the needs of scientists at every level and stage in their careers.

HelioScan
type: Resource
type: NamedIndividual
has db xref: nlx_143787
synonym: Helio Scan
IAO_0000115: HelioScan is a versatile control software for microscopes written in the intuitive graphical programming language LabVIEW. It solves a number of problems observed with custom-built image acquisition systems by providing the following features: * Extendability: both hardware components and software functionality are encapsulated in exchangeable, software components. Additional components can be implemented easily and plugged in at run-time. Components can be independently developed, allowing multiple developers to work in parallel. * Flexibility: Components are independently configurable; each component can have an unlimited number of configurations. * Understandability: The LabVIEW code is well-structured, commented and documented. * High speed: The software supports FPGA-based hardware that enables intelligent and extremely fast signal acquisition and generation. FPGA logic can be easily programmed using LabVIEW. * Tailored to in vivo brain imaging: The software is especially suited for 2-photon Calcium imaging, but can in principle be used for any kind of microscopy. The out-of-the-box software supports different imaging modalities (camera, galvanometric scan mirrors, acusto-optic deflectors) and imaging modes (camera video acquisition, intrinsic optical imaging, two-photon frame scan and tilted frame scan, 2D line scan, 3D spiral scan) and can easily be extended to other imaging modalities (e.g., resonance scanners), imaging modes (e.g., 2D and 3D arbitrary line scans) and associated hardware (e.g., stimulation devices). * Open file-format with extensible meta-data schema: HelioScan saves data in the OME-TIFF file format, which contains image data as multipage TIFF and meta-data as human-readable XML in the TIFF description tag according to the OME schema.

Psychiatric Genomics Consortium
type: Resource
type: NamedIndividual
has db xref: nlx_143769
synonym: PGC
synonym: Psychiatric GWAS Consortium
IAO_0000115: Consortium conducting meta-analyses of genome-wide genetic data for psychiatric disease. Focused on autism, attention-deficit hyperactivity disorder, bipolar disorder, major depressive disorder, schizophrenia, anorexia nervosa (AN), Tourette syndrome (TS), and obsessive-compulsive disorder (OCD). Used to investigate common single nucleotide polymorphisms (SNPs) genotyped on commercial arrays, structural variation (copy number variation) and uncommon or rare genetic variation. To participate you are asked to upload data from your study to central computer used by this consortium. Genetic Cluster Computer serves as data warehouse and analytical platform for this study . When data from your study have been incorporated, account will be provided on central server and access to all GWAS genotypes, phenotypes, and meta-analytic results relevant to deposited data and participation aims. NHGRI GWAS Catalog contains updated information about all GWAS in biomedicine, and is usually excellent starting point to find comprehensive list of studies. Files can be obtained by any PGC member for any disease to which they contributed data. These files can also be obtained by application to NIMH Genetics Repository. Individual-level genotype and phenotype data requires application, material transfer agreement, and informed consent consideration. Some datasets are also in controlled-access dbGaP and Wellcome Trust Case-Control Consortium repositories. PGC members can also receive back cleaned and imputed data and results for samples they contributed to PGC analyses.

Ricopili
type: Resource
type: NamedIndividual
has db xref: nlx_143770
IAO_0000115: Ricopili is a tool for visualizing regions of interest in select GWAS data sets. How it works Choose a data set and enter a genomic location or a gene name in the form below. A .pdf plot will be generated, as well as a text file with single SNP results. You can also specify the following options: * Clumping: Independent regions will be colored differently, to highlight LD. If you request more than one clump, be sure to have at least one SNP passing the specified p-value-threshold (for performance reasons.) * SNP: SNPs in the region are colored by LD to this index SNP. * Anonymity: Frequency information is from HapMap to protect anonymity. * NHGRI results: Results from the NHGRI GWAS catalog will be included in the plot. Finally, please note that this tool is in development (it was released on September 19th, 2011) and should be considered beta. In particular, our development server is not equipped for high traffic. If the server fails to respond to your request, please try again at a later time.

Tree and reticulogram REConstruction
type: Resource
type: NamedIndividual
has db xref: biotools:t-rex
has db xref: OMICS_04264
synonym: Trex-online
abbrev: T-REX
IAO_0000115: A web server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer (HGT) events.

University of Ljubljana; Ljubljana; Slovenia
type: NamedIndividual
has db xref: nlx_97788

Pharmacovigilance Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157547
abbrev: PVONTO
IAO_0000115: A pharmacovigilance ontology to connect known facts on drugs, disease, ADEs, and their molecular mechanisms.

King-Devick Test
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_143775
synonym: King Devick Test
IAO_0000115: An accurate and reliable method for identifying athletes with head trauma, and a strong candidate rapid sideline screening test for concussion. The test is able to capture impairments of eye movement, attention, language and other symptoms of impaired brain function. It is a physical method of evaluating visual tracking and saccadic eye movements is based on the time to perform rapid number naming. It involves reading aloud a series of single digit numbers from left to right on three test cards. Participants are asked to read the numbers on each card from left to right as quickly as possible but without making any errors. The sum of the three test card time scores constitutes the summary score for the entire test. The test is a proven indicator of oculomotor inefficiencies regarding eye movements during reading. Published medical studies have determined that deficiencies in saccadic eye movements can be an indicator of mild Traumatic Brain Injury (mTBI) or concussions. Studies have shown that there is a significant relationship between poor oculomotor functions and learning disabilities (including dyslexia detection). Saccadic eye movement deficiencies can be improved with training and correspondingly reading performance also can be improved. Simply put, subjects who don''t perform well on this test are not efficient readers, although because there are many reasons for poor reading unrelated to eye movements, some poor readers do fine on the test. They believe that the test should be in the hands of teachers in order to help them determine if a student''s poor reading performance is related to deficiencies in their ability to move their eyes efficiently.

Institute of Computational Linguistics
type: Resource
type: NamedIndividual
has db xref: nlx_48409
synonym: ILC-CNR
synonym: Istituto di Linguistica Computazionale
synonym: Istituto di Linguistica Computazionale Antonio Zampolli
abbrev: ILC
IAO_0000115: ILC-CNR has been one of the major promoters of the notion of language resources as the central component of the linguistic infrastructure (aware also of its cultural, economical and political implications), has coordinated the major initiatives relating to language resources and standardization and has often been the promoter of new paradigms in the field. ILC-CNR has coordinated numerous international, European and national strategic initiatives and projects. ILC-CNR has designed and built several types of corpora and lexicons and the respective ontologies, has developed a complete chain of tools for a robust processing of the Italian language, for the acquisition of information from corpora and for word-sense disambiguation and has developed technologies for several application domains (question answering, information retrieval, text mining, monolingual and multilingual terminology extraction, ontology acquisition and structuring, summarisation, filtering of Web documents, preservation of the cultural heritage through digital image processing and digital libraries techniques etc.). The research fields of the Institute are: Models and methods for natural language processing, and mono- and multilingual application prototypes. Design of international standards and development of computational language resources. Design and implementation of architectures and infrastructures for language resources and language technologies. Computational methods and tools for humanistic research, particularly in linguistic, literary, and philological disciplines, and in lexicography.

Cell Sciences
type: Organization
type: NamedIndividual
has db xref: nlx_152329
IAO_0000115: An Antibody supplier

Swedish Regional Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_48758
synonym: RBC Southern Health Care Region
synonym: Regional Biobank Centre Southern Health Care Region
synonym: Swedish Regional Biobank Center
synonym: Swedish Regional Biobank Center Southern Health Care Region
abbrev: Swedish RBC
IAO_0000115: To meet the law requirements and regulations of the National Board of the Southern Health Care Region, Region Skane and Lund University agreed to establish a common biobanking center for Southern healthcare region. Regional biobanksrcentrum will develop and maintain systems for quality assurance and integrity protected using biobanks. The Regional Biobank center is responsible for matters relating to the collection, storage and use of samples stored in biobanks in the Southern healthcare region. Regional Biobank center operations consist of: * to promote the use of biobank material is in accordance with legal requirements biobank * to promote integrity protected and safe storage of repository material * to provide information about the biobank law and biobank materials used for individual sample donors, health professionals, researchers and the public * to handle requests for modified consent and desire to destroy or de test * maintaining a current and privacy protected records of repository material in the region * work to the individual''s integrity will be strengthened in relation to research on biobank material. Tissue samples available to other parties, by surrendering, or by sending tissue samples for analysis, requiring the return or destruction, after completion of the analysis. Regional Biobank Centre (RBC) for the southern healthcare region was established in 2004 and was until 2010 in the Oncology Centre. As of January 1, 2011 it is under the management of RBC Labmedicin Skane.

Cryo-Save
type: Resource
type: NamedIndividual
has db xref: nlx_48843
synonym: Cells Limited
synonym: Cryo-Save: Save for Life
synonym: Cryo-Save: The Family Stem Cell Bank
IAO_0000115: Stem cell banking is a unique opportunity to store the precious building blocks of the human body; cord blood, cord tissue and fat tissue are just some sources of stem cells ready to provide the foundation for more than 70 treatments of blood, blood related diseases and future applications in regenerative medicine. To not consider the storage or donation of these precious stem cells could be a missed opportunity! Cryo-Save is officially recognized as the largest family stem cell bank in Europe. With more than 180,000 samples stored and four fully-owned storage facilities throughout the world, Cryo-Save has over ten years'' experience and state-of-the-art technical know-how, providing the basis for a strong and reliable organization. An ethical approach, scientific professionalism and customer-focused care are the core elements of our daily activities, as we strive to be an active player in life-science development in over 40 countries. Our company was established in 2000, is headquartered in the Netherlands and successfully active in 40 countries across four continents. We are officially accredited by the regulatory authorities and set the highest quality standards in everything we do. We follow a dual storage system, meaning that the stem cells are stored independently in two separate storage tanks within our state-of-the-art facility. Our dedication to research in collaboration with universities, physicians and stem cell scientists has put us at the forefront of technological developments.

Defense and Veterans Brain Injury Center
type: Resource
type: NamedIndividual
has db xref: nlx_143817
synonym: Defense and Veterans Head Injury Program
synonym: DVHIP
abbrev: DVBIC
IAO_0000115: The Defense and Veterans Brain Injury Center (DVBIC) is a congressionally mandated collaboration of the Department of Defense (DoD) and Veterans Affairs (VA) health centers serving patients with traumatic brain injury (TBI). Its mission is to serve active duty military, their beneficiaries, and veterans with traumatic brain injuries (TBIs) through state-of-the-art clinical care, innovative clinical research initiatives and educational programs. DVBIC fulfills this mission through ongoing collaboration with military, VA and civilian health partners, local communities, families and individuals with TBI. In 2008, DVBIC''s mission expanded to include Force Health Protection and Management. This encompasses the following Department of Defense (DoD) programs: * TBI Surveillance * TBI Registry * Pre-deployment neurocognitive testing * Family Caregiver Curriculum * 15 year longitudinal study of TBI * Independent study of automated neurocognitive tests DVBIC has been named the Office of Responsibility or Executive Agency for these programs. The DVBIC multi-site network includes a growing number of DoD and VA hospitals as well as civilian TBI rehabilitation programs. Each DVBIC site works collaboratively to provide and improve TBI care for active duty military, veterans and their eligible beneficiaries. DVBIC''s multi-center network design and collaborations with forward medical commands allows for clinical innovation along the entire continuum of care: from initial injury in the war zone through to medical evacuation, acute care, rehabilitation and ultimately a return to community, family, and work or continued duty when possible. WHAT WE DO * Develop and provide advanced TBI-specific evaluation, treatment and follow-up care for military personnel, their beneficiaries, and veterans with mild to severe TBIs * Conduct clinical research that defines optimal care and treatment for individuals with TBI * Develop and deliver effective educational materials and programming for the …

National Surgical Adjuvant Breast and Bowel Project Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_48875
synonym: National Surgical Adjuvant Breast Bowel Project Tissue Bank
abbrev: NSABP Tissue Bank
IAO_0000115: The NSABP (National Surgical Adjuvant Breast and Bowel Project) Tissue Bank is the central repository of tissue samples (stained and unstained slides, tissue blocks, and frozen tissue specimens) collected from clinical trials conducted by the NSABP. The main scientific aim of the NSABP Division of Pathology is to develop clinical context-specific prognostic markers and predictive markers that predict response to or benefit from specific therapeutic modality. To achieve this aim, the laboratory collects the tumor and adjacent normal tissues from cancer patients enrolled into the NSABP trials through its membership institutions, and maintain these valuable materials with clinical follow-up information and distribute them to qualified approved investigators. Currently, specimens from more than 90,000 cases of breast and colon cancer are stored and maintained at the bank. Paraffin embedded tumor specimens are available from NSABP trials. We currently do not bank frozen tissues. All blocks are from patients enrolled in prospective NSABP treatment protocols and complete clinical follow up information as well as demographic information is available. Depending on the project, unstained tissue sections of 4-micrometer thickness, tissue microarrays, or stained slides are provided to the investigators in a blinded study format. Any investigators with novel projects that conform to the research goals of NSABP may apply for the tissue. Please refer to the NSABP Tissue Bank Policy to determine if your project conforms to these goals. Priority is given to NSABP membership institutions who regularly submit tissue blocks.

ACT: Artemis Comparison Tool
type: Resource
type: NamedIndividual
has db xref: nlx_48986
has db xref: OMICS_00928
synonym: Artemis Comparison Tool
abbrev: ACT
IAO_0000115: A free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyze regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It is based on the software for Artemis, the genome viewer and annotation tool. ACT runs on UNIX, GNU/Linux, Macintosh and MS Windows systems. It can read complete EMBL and GENBANK entries or sequences in FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format.

University of Virginia Tissue Culture Facility
type: Resource
type: NamedIndividual
has db xref: nlx_49028
synonym: University of Virginia School of Medicine Tissue Culture Facility
synonym: UVa Tissue Culture Facility
abbrev: UVa TCF
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 11,2024. Tissue Culture Facility provides mycoplasma testing, baculovirus titer measurements, growing of cultured cells and cell storage, to University of Virginia researchers. The Facility also supplies cell culture reagents and supplies. Training and access to facilities is also available. Products and services are only available to users at the University of Virginia.

SPInDel
type: Resource
type: NamedIndividual
has db xref: OMICS_01496
synonym: SPecies Identification by Insertions/Deletions
synonym: SPInDel - Species identification by insertions/deletions
IAO_0000115: A multifunctional workbench for species identification using insertion/deletion variants. The SPInDel workbench provides a step-by-step environment for the alignment of target sequences, selection of informative hypervariable regions, design of PCR primers and the statistical validation of the species-identification process. It includes a large dataset comprising nearly 1,800 numeric profiles for the identification of eukaryotic, prokaryotic and viral species.

KORA-gen
type: Resource
type: NamedIndividual
has db xref: nlx_49266
synonym: Cooperative Health Research in the Region of Augsburg-gen
IAO_0000115: KORA-gen is infrastructure to provide phenotypes, genotypes and biosamples for collaborative genetic epidemiological research. From all four surveys that have been conducted so far, the following biological material is on hand: genomic DNA, blood serum, blood plasma and EBV immortalized cell lines (form KORA S4 only). These have been extracted from blood samples and are stored in nitrogen tanks and -80 degrees C refrigerators. Genomic DNA from more than 18.000 adult subjects from Augsburg and the surrounding counties is available at present. So far, EBV immortalized cell lines from 1.600 participants are cultivated. To meet the manifold demands of researchers with genetic and molecular questions KORA-gen fulfills the following prerequisites for successful genetic-epidemiological research: * representative samples from the general population, * well characterized disease phenotypes and intermediate phenotypes, * information on environmental factors, * availability of genomic DNA, serum, plasma and urine, as well as EBV immortalized cell lines. In total, four population based health surveys have been conducted between 1984 and 2000 with 18000 participants in the age range of 25 to 74 years, and a biological specimen bank was established in order to enable scientists to perform epidemiologic research with respect to molecular and genetic questions. The KORA study center conducts regular follow-up investigations and has collected a wealth of information on sociodemography, general medical history, environmental factors, smoking, nutrition, alcohol consumption, and various laboratory parameters. This unique resource will be increased further by follow-up studies of the cohort. The assessment of statistical questions covers the definition of the study design and the calculation of statistical power. Furthermore, we offer assistance in data analysis. Kora-gen can be used by external partners. Interested parties can inform themselves interactively via internet about the ava…

WHO World Health Mental Health Surveys
type: Resource
type: NamedIndividual
has db xref: nlx_143796
synonym: The WHO World Mental Health Surveys: Global Perspectives on the Epidemiology of Mental Disorders
synonym: World Health Mental Health Surveys
abbrev: WMH Survey
IAO_0000115: The WMH Survey Initiative is a project of the Assessment, Classification, and Epidemiology (ACE) Group at the World Health Organization coordinating the implementation and analysis of general population epidemiologic surveys of mental, substance use, and behavioral disorders in countries in all WHO Regions. Reported are the first results of the WHO World Mental Health (WMH) Survey Initiative, a highly ambitious series of cross-national psychiatric epidemiological surveys. The general population surveys in the WMH series span 17 countries in all parts of the world. In many of these countries the WMH surveys provide the first community epidemiological data ever available on mental disorders in the population. The detailed information on lifetime prevalence, age of onset, course, correlates, and treatment of mental disorders in this volume provides mental health professionals and healthcare policy planners with an unprecedented reference on the cross-national descriptive epidemiology of mental disorders. The WHO Global Burden of Disease Study estimates that mental and addictive disorders are among the most burdensome in the world and their burden will increase over next decades. However, these estimates and projections are based largely on literature reviews and limited and isolated studies rather than on cross-national epidemiologic surveys. In order to move forward with public health initiatives aimed at addressing the global burden of mental disorders the WMH Survey Initiative carried out rigorously implemented general population surveys that estimate the prevalences of mental disorders, evaluate risk factors for purposes of targeting interventions, study patterns of and barriers to service use, and validate estimates of disease burden world-wide. The WMH Survey Initiative aims to obtain accurate cross-national information about the prevalences and correlates of mental, substance, and behavioral disorders. Included in studies of correlates will be analyses of impair…

Eukaryotic Pathogen Database Resources
type: Resource
type: NamedIndividual
has db xref: nlx_49652
has db xref: r3d100011557
synonym: Apicomplexan Database
synonym: Apicomplexan Database Resources
synonym: ApiDB
synonym: Eukaryotic Pathogen Genome Database
synonym: EuPath
synonym: EuPathDB
IAO_0000115: EuPathDB integrates numerous database resources and multiple data types. The phylum Apicomplexa comprises veterinary and medically important parasitic protozoa including human pathogenic species of genera Cryptosporidium, Plasmodium and Toxoplasma. ApiDB serves not only as database but unifies access to three major existing individual organism databases, PlasmoDB.org, ToxoDB.org and CryptoDB.org, and integrates these databases with data available from additional sources. Through ApiDB site, users may pose queries and search all available apicomplexan data and tools, or they may visit individual component organism databases. EuPathDB Bioinformatics Resource Center for Biodefense and Emerging/Re-emerging Infectious Diseases is a portal for accessing genomic-scale datasets associated with eukaryotic pathogens.

Nu-OSCAR
type: Resource
type: NamedIndividual
has db xref: nlx_49691
has db xref: OMICS_00507
has db xref: SCR_010892
synonym: Nucleosome-Occupancy Study for Cis-elments Accurate Recognition
synonym: One-class SVM for Cis-elements Accurate Recognition
abbrev: OSCAR
IAO_0000115: Software tool to identify binding sites of known transcription factors on promoter regions. The algorithm is based on one-class support vector machine (One-class SVM). OSCAR uses the sequential composition of known binding sites, and further incorporates the locational preferences of binding events. Nu-OSCAR (Nucleosome-Occupancy Study for Cis-elments Accurate Recognition) is a program that can be used to identify binding sites of known transcription factors, which further incorporates nucleosome occupancy around sites on promoter regions, thereby improving the accuracy of prediction. The derivation of the the algorithm is based on a biophysical view of interactions between protein factors and nucleosome DNA.

Soybean Ontologies
type: Resource
type: NamedIndividual
has db xref: nlx_49793
synonym: SoyBase Ontologies
synonym: SoyBase Soybean Ontologies
IAO_0000115: Controlled vocabulary for soybean field growth stages (Soybean Whole Plant Growth Ontology), plant structure names (Soybean Structure Ontology), development (Soybean Development Ontology) and plant traits (Soybean Trait Ontology). These are only a suggestion. Input from the community will be necessary to update and extend the ontologies. Because of this, these ontologies should also be considered a work in progress. Where applicable, soybean specific terms have been associated with their Plant Ontology (PO) and Gramene Plant Trait Ontology (TO) synonyms to facilitate cross species comparisons. Please feel free to contact them for corrections, additions, and questions.

Banyan Biomarkers
type: Resource
type: NamedIndividual
has db xref: nlx_143797
IAO_0000115: Banyan Biomarkers was founded in 2002 by Ron Hayes, PhD , Kevin Wang, PhD, and Nancy Denslow, PhD to create the first Point of Care (POC) Blood Test to diagnose traumatic brain injury (TBI) and to diagnose neurological diseases. Initially inspired by research conducted at the University of Florida and The Evelyn F. and William McKnight Brain Institute, Banyan Biomarkers has made significant progress in developing and clinically validating novel enzyme linked immunosorbent assays (ELISAs) for traumatic brain injury (TBI). Banyan scientists have created an extensive pipeline of potential biomarkers and the company has a robust intellectual property portfolio. Jackson Streeter, Banyan''s CEO, has extensive experience in development of medical devices for acute brain injury. Currently no blood test exists for use by physicians to detect the presence and severity of brain trauma. Banyan Biomarkers'' research has identified unique and proprietary biomarkers present in the patient''s blood following injury to the brain. The detection and quantification of these biomarkers may provide early indications of brain trauma essential for earlier intervention and management. Banyan Biomarkers, Inc. offers preclinical and clinical sample analyses with a proven panel of neurological, psychiatric, neurodegenerative disease, and organ toxicity biomarker assays. The company provides analytical services to a wide range of customers including pharmaceutical companies, biotechnology companies and investigators at academic research institutes.

Swiss Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_50970
synonym: swissbiobank.com
IAO_0000115: With expertise in the preservation of biological specimens, Swiss Biobank is a biobank of cell therapy products (stem cells, progenitor). Strategically located in Suisse Romande, the center is accessible 7J/7J, 365 days / year. The laboratories and technology platforms are tailored to international standards. Service is prompt, courteous, and responsive to your needs. The first opportunity to harvest adult stem cells, which is the only type at Swiss Biobank, occurs just after the birth of a baby. The umbilical cord blood and placenta are rich in hematopoietic stem cells and can regenerate all cells in the bloodstream. The cord and placenta tissues themselves contain mesenchymal cells that can be used for the regeneration of connective tissue. The standardized procedures for collecting cord blood units are made ����??����??by the medical staff of the hospital / clinic according to international standards. The sample is transported by a courier Swiss Medical Biobank in which it is prepared and cryo-preserved by qualified personnel within 24 hours. In the case of public biobanking, cells, tissues, organs are donated and can be used with consent of the donor, a third person for transplantation, or as part of clinical research. The HLA (Human Leukocyte Antigen) is a group of proteins on the cell surface, and specific to each individual. This allows the immune system to distinguish our own cells for foreign elements (pathogens) that are likely to be attacked. Histocompatibility between the donor and recipient is of primary importance in organ transplantation, tissues and / or cells, to minimize the chances of rejection. There is one chance in four that two siblings have the same HLA code.

NIGMS Human Genetic Cell Repository
type: Resource
type: NamedIndividual
has db xref: nlx_143798
synonym: Human Genetic Cell Repository
abbrev: NIGMS Repository
IAO_0000115: Highly characterized cell lines and high quality DNA for cell and genetic research representing a variety of disease states, chromosomal abnormalities, apparently healthy individuals and many distinct human populations. The NIGMS Repository contains more than 10,600 cell lines, primarily fibroblasts and transformed lymphoblasts, and over 5,500 DNA samples. The NIGMS Repository has a major emphasis on heritable diseases and chromosomally aberrant cell lines. In addition, it contains a large collection dedicated to understanding human variation that includes samples from populations around the world, the CEPH collection, the Polymorphism Discovery Resource, and many apparently healthy controls. Human induced pluripotent stem cell lines, many of which were derived from NIGMS Repository fibroblasts, have recently become available through the NIGMS Repository. Sample donation facilitates all areas of research by making available well-characterized materials to any qualified researcher who might have otherwise been unable to invest the time and resources to collect needed samples independently. Donations to the Repository have created a resource of unparalleled scope. Samples from the collection have been used in more than 5,500 publications and are distributed to scientists in more than 50 countries. This resource is continuously expanding to support new directions in human genetics.

PhenX Phenotypic Terms
type: Resource
type: NamedIndividual
has db xref: nlx_157548
abbrev: PHENX
IAO_0000115: Ontology for standard measures related to complex diseases, phenotypic traits and environmental exposures

Eye mutant resource - The Jackson Laboratory
type: Resource
type: NamedIndividual
has db xref: nif-0000-00228
abbrev: Eye mutant resource
IAO_0000115: The Eye mutant resource lists and describes mouse models for ocular research available from The Jackson Laboratory and provides continuing results from a Jackson Laboratory screening program to identify genes and new mutations that affect vision. It also provides a list of known mouse mutations that affect vision and presents updated information on the cloning of vision-related genes. The primary focus is on the mouse as a model of human inherited vision disorders. The number of known serious or disabling eye diseases in humans is large and affects millions of people each year. Yet research on these diseases frequently is limited by the obvious restrictions on studying pathophysiologic processes in the human eye. Likewise, many human ocular diseases are genetic in origin, but appropriate or available families often are not easy for genetic studies. Mouse models of inherited ocular disease provide powerful tools for quick genetic analysis and characterization. The mouse eye is remarkably similar in structure to the human eye, and many developmental or invasive experiments can be done in mice that are impossible in human beings. Comparative mapping and sequencing between human and mouse genomes shows that knowing the gene location in either man or mouse allows for the same gene to be found more quickly in the other. Finally, the use of inbred strains, where all mice in the strain are alike genetically except for the mutation being studied, is a powerful tool for linkage analysis, and assures phenotypic reproducibility of any model found in a strain. The virutal identity of mice in an inbred strain also allows for fewer numbers of mice to be studied clinically. Mouse models of retinal degeneration have been investigated for many years in the hope of understanding the causes of photoreceptor cell death. 16 naturally occurring mouse mutants that manifest degeneration of photoreceptors in the retina with preservation of all other retinal cell types have been found: retina…

NINDS Repository
type: Resource
type: NamedIndividual
has db xref: nlx_143800
synonym: NINDS Human Genetics DNA and Cell Line Repository
synonym: NINDS Human Genetics DNA Cell Line Repository
synonym: The NINDS Human Genetics DNA and Cell Line Repository
synonym: The NINDS Human Genetics Resource Center
synonym: The NINDS Repository
IAO_0000115: Open resource of biological samples (DNA, cell lines, and other biospecimens) and corresponding phenotypic data to promote neurological research. Samples from more than 34,000 unique individuals with cerebrovascular disease, dystonia, epilepsy, Huntington's Disease, motor neuron disease, Parkinsonism, and Tourette Syndrome, as well as controls (population control and unaffected relatives) have been collected. The mission of the NINDS Repository is to provide 1) genetics support for scientists investigating pathogenesis in the central and peripheral nervous systems through submissions and distribution; 2) information support for patients, families, and advocates concerned with the living-side of neurological disease and stroke.

DOAJ - Directory of Open Access Journals
type: Resource
type: NamedIndividual
has db xref: nlx_51167
synonym: Directory of Open Access Journals
abbrev: DOAJ
IAO_0000115: Database providing access to quality controlled Open Access Journals. For a journal to be included it should exercise quality control on submitted papers through an editor, editorial board and/or a peer-review system. It is not be limited to particular languages or subject areas. Offering free online access to high quality full text content, plus excellent search tools, the portal enables researchers to find, use and re-use a vast range of materials with ease. The content of DOAJ will be even more visible and disseminated through this portal. The aim of the Directory is to increase the visibility and ease of use of open access scientific and scholarly journals thereby promoting their increased usage and impact. As of April 2014, DOAJ has 9,709 journals, 5,624 journals searchable at article level, 133 Countries and 1,600,991 articles. The database may be browsed by title or subject, or searched through the interface to for journals or articles.

Kdetrees
type: Resource
type: NamedIndividual
has db xref: biotools:kdetrees
has db xref: OMICS_04172
synonym: kdetrees: Nonparametric method for identifying discordant phylogenetic trees
IAO_0000115: R package using a non-parametric method for estimating distributions of phylogenetic trees, with the goal of identifying trees that are significantly different from the rest of the trees in the sample.

eyeGENE
type: Resource
type: NamedIndividual
has db xref: nif-0000-00229
synonym: National Ophthalmic Disease Genotyping Network
synonym: National Ophthalmic Disease Genotyping Network (eyeGENE)
synonym: National Ophthalmic Disease Genotyping Network (eyeGENETM)
IAO_0000115: National network of research laboratories for genetic testing of eye disease. They offer testing for affected individuals coupled to registry of clinical information available through patient registry. Large data set for investigators to identify additional genetic risk factors and to explore relationship between genetic disease (genotype) and its clinical manifestation (phenotype).

Ask Dr Wiki
type: Resource
type: NamedIndividual
has db xref: nlx_51425
synonym: AskDrWiki
synonym: AskDrWiki.com
IAO_0000115: A medical, nonprofit, educational wiki created to support a collective online memory for physicians, nurses, and medical students. Users can publish review articles, clinical notes, pearls, and medical images on the site. Anyone with a medical background can contribute to or edit medical articles. Images include: EKG, x-ray, coronary angiograms, peripheral angiograms, structural angiograms, searchable angiograms, echocardiograms, and radiology. Tutorials include: EKG tutorials, coronary angiography tutorials, and ventriculography tutorials.

Pathology Informatics Curriculum Wiki
type: Resource
type: NamedIndividual
has db xref: nlx_51469
synonym: Path.Informatics
synonym: Pathology Informatics Wiki
IAO_0000115: The Pathology Informatics Curriculum Wiki is a public wiki based on community-based, continually updated online resources. It is about computers and information technology as tools within the field of pathology. Its content includes information management and communication (e.g. meetings on quality, electronic medical records, electronic order entry, reporting critical values, etc.) The goals of the Pathology Informatics Curriculum Wiki are four-fold: 1. To increase interest among pathology residents in pathology informatics; 2. To become a shared educational resource for pathology training programs to supplement or develop their own local curriculum in pathology informatics; 3. To increase research activities in the field; and 4. To connect pathology residents to experts in pathology informatics. We encourage contributors to (1) use the the wiki format to improve and extend this curriculum; (2) help edit and maintain the pathology informatics related pages in Wikipedia that are linked to this curriculum, and (3) create new pathology informatics pages in Wikipedia and link them to this website. In each of the lessons of the curriculum, we highlight areas where we feel that there is need for new or updated articles in Wikipedia relating to that topic.

American Diabetes Association
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100000041
has db xref: grid.427608.f
has db xref: ISNI: 0000 0001 1033 6008
has db xref: nlx_143804
has db xref: Wikidata: Q4743610
abbrev: ADA
IAO_0000115: The mission of the American Diabetes Association (ADA) is to prevent and cure diabetes and to improve the lives of all people affected by diabetes. We lead the fight against the deadly consequences of diabetes and fight for those affectedby diabetes. * We fund research to prevent, cure and manage diabetes. * We deliver services to hundreds of communities. * We provide objective and credible information. * We give voice to those denied their rights because of diabetes.

Immunology
type: Resource
type: NamedIndividual
has db xref: nlx_52404
IAO_0000115: Immunology is a wikibook with the following contents: * Introduction * Organs of the Immune System * Cells of the Immune System * Antigens * Antibodies * Immune System Genetics * Antibody/Antigen Interactions * Major Histocompatibility Complex * Antigen Processing and Presentation * T Cells * B Cells * Cell-Mediated Immune Response * Cytokines * The Complement System * Inflammation * Hypersensitivity * Infectious Disease * Immunodeficiency * Autoimmunity * Transplants * Cancer * Vaccines * Experimental Methods in Immunology You may download as a PDF or print it.

NHGRI Sample Repository for Human Genetic Research
type: Resource
type: NamedIndividual
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synonym: Sample Repository for Human Genetic Research
abbrev: NHGRI Repository
IAO_0000115: DNA samples and cell lines from fifteen populations, including the samples used for the International HapMap Project, the HapMap 3 Project and the 1000 Genomes Project (except for the CEPH samples). All of the samples were contributed with consent to broad data release and to their use in many future studies, including for extensive genotyping and sequencing, gene expression and proteomics studies, and all other types of genetic variation research. NHGRI led the contribution of the NIH to the International HapMap Project, which developed a haplotype map of the human genome. This haplotype map, called the HapMap is a publicly available tool that allows researchers to find genes and genetic variations that affect health and disease. The samples from four populations used to develop the HapMap were initially housed in the Human Genetic Cell Repository of the National Institute of General Medical Sciences (NIGMS). Except for the Utah CEPH samples that were in the NIGMS Repository before the initiation of the HapMap Project and remain there, the NHGRI Repository now houses all of the HapMap samples. The NHGRI repository also houses the extended set of HapMap samples, which includes additional samples from the HapMap populations and samples from seven additional populations. All of the samples were collected with extensive community engagement, including discussions with members of the donor communities about the ethical and social implications of human genetic variation research. These samples were studied as part of the HapMap 3 Project. The NHGRI repository also houses the samples for the International 1000 Genomes Project. This Project is lightly sequencing genome-wide 2500 samples from 27 populations. This project aims to provide a detailed map of human genetic variation, including common and rare SNPs and structural variants. This map will allow more precise localization of genomic regions that contribute to health and disease. The 1000 Genomes Project includes many…

Bioinformatics Web Service Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_157332
abbrev: OBIWS
IAO_0000115: Ontology that extends the Ontology for Biomedical Investigations (OBI) to support consistent annotation of Bioinformatics Web services.

Biobank of Hospital Clinic - IDIBAPS
type: Resource
type: NamedIndividual
has db xref: nlx_51631
synonym: Biobank of Hospital Clinic Barcelona IDIBAPS
synonym: Hospital Clinic Barcelona - IDIBAPS biobank
IAO_0000115: A biobank of repositories which works to obtain, store, manage and distribute large collections of human biological samples of phenotypes and diseases of marked interest for researchers. The biobank sample collection is made up of three extensive repositories. The Neurological Tissue Biobank is a nervous tissue repository (brain and spinal cord) created from donations from cadavers with or without neurological conditions. It helps facilitate research in neurological illnesses. The Tumour Biobank and Anatomical Pathologies Collections is a repository of tumorous tissue and samples from cancer patients. The Blood and Fluid Biobank is a repository which contains samples of metabolic, inflammatory bowel, hepatic, digestive and maternal and foetal diseases, among others. It houses a large range of samples of scientific interest, primarily DNA, serum and plasma.

ProTECT
type: Resource
type: NamedIndividual
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synonym: ProTECT III - Progesterone for Traumatic Brain Injury: Experimental Clinical Treatment: Phase III Clinical Trial
IAO_0000115: Recently, our team completed an NINDS-funded, Phase IIa double-blinded, placebo-controlled pilot clinical trial that examined the pharmacokinetics, safety, and activity of progesterone, a steroid found to have powerful neuroprotective effects in multiple animal models of brain injury. Our pilot study demonstrated a 50% reduction in death among severe TBI patients and less disability among moderate TBI patients treated with progesterone. Based on these promising results and supportive preclinical data, we are conducting a large, phase III clinical trial (ProTECT III) to definitively assess the safety and efficacy of this treatment for adults with moderate to severe acute TBI. The study is slated to begin August 2008. WHY Progesterone: Although progresterone is widely considered a sex steroid, it is also a potent neurosteroid. Progesterone is naturally synthesized in the CNS. A large and growing body of animal studies indicate that early administration of progesterone after TBI reduces cerebral edema, neuronal loss, and behavioral deficits in laboratory animals. Certain properties of progesterone make it an ideal therapeutic candidate. First, in contrast to most drugs tested to date, progesterone rapidly enters the brain and reaches equilibrium with the plasma within an hour of administration. Second, unlike other experimental agents, progesterone has a long history of safe use in humans. Finally, the findings of our pilot clinical trial (presented in the Preliminary Data Section, below) indicate that progesterone has consistent and predictable pharmacokinetic properties, is unlikely to produce harm, and may be efficacious for treating acute TBI in humans.

Standards-based Infrastructure with Distributed Resources
type: Resource
type: NamedIndividual
has db xref: nlx_52124
abbrev: SIDR
IAO_0000115: A searchable public data repository for multi-assay studies in the field of high-throughput biology. Studies are annotated and curated using ontologies and controlled vocabularies according to the recommendations of the OBO foundry (Open Biological and Biomedical Ontologies) and the NCBO bioportal. Each data set is assigned a digital object identifier (DOI) provided by DataCite. In addition, the SIDR team has developed an ISA-XML (ISA-ML) version of the ISA-TAB format and the mapping to the FuGE object model (ISA-TABtoFuGE); these improvements should facilitate further tool integration, including web services. SIDR contributes to the proof-of-concept addressing the critical success factor for data integration. The SIDR team will continue to put in place the building blocks for giving access to interoperable data through a world-wide network of national hubs in the context of the community-based ISA infrastructure.

tree editor
type: Resource
type: NamedIndividual
has db xref: OMICS_04262
synonym: tred: web-based visualization and editing of phylogenetic trees
abbrev: tred
IAO_0000115: Software tool to visualize and edit phylogenetic trees. It combines a browser-based Javascript client with a Python (web2py) server. Trees are rendered in SVG using Raphael.

Regional Biobank of Central Norway
type: Resource
type: NamedIndividual
has db xref: nlx_52206
IAO_0000115: The Regional Biobank of Central Norway, henceforth called the Biobank, is a research facility which contains a collection of human biological material such as blood, tissue and urine samples, and a database which stores relevant information about the samples and the patients from whom the samples originate, as well as information obtained from analysis of the material. The material is collected as part of medical examinations, diagnosis or treatment. The Biobank is foreseen to give an increased knowledge about causes for diseases and their mechanisms, and thereby contributing to improve prophylactic health work, diagnostics and treatment. The Biobank is owned and operated by official authorities on a no commercial profit basis. The Biobank was established in collaboration between the Central Norwegian Regional Health Authority (data management and administration) and the Faculty of Medicine at the Norwegian University of Science and Technology (economics and personnel). The Biobank is approved by The Data Inspectorate of Norway, and by the Regional Committee for Medical Research Ethics, and all information in the Biobank is handled according to the guidelines of the Data Inspectorate.

SeraCare Lifesciences: Sample Storage Management and Processing Services
type: Resource
type: NamedIndividual
has db xref: nlx_52485
synonym: SeraCare Lifesciences: Sample Storage Management Processing Services
abbrev: SeraCare Sample Storage Management and Processing Services
IAO_0000115: SeraCare stores and manages over 19 million samples in our state-of-the-art biobank, and is supported by a range of processing and characterization services. Security. Backup. On-line inventory. Next day sample access. Analysis. Characterization. Anonymization. Transformation. Restoration. Compliance. Coordination. We handle your samples all the way through. SeraCare is well-equipped to perform a wide range of sample storage, management, and processing services. We have longstanding customer relationships with clinical and research laboratories, biopharma, and public health agencies, including the National Institutes of Health, the Centers for Disease Control, and the US Food and Drug Administration. * Our scientists have expertise in virology, immunology, molecular biology, and biochemistry * We have a proven legacy of custom assay design and custom product development to meet your specifications

NEI-AREDS Genetic Repository
type: Resource
type: NamedIndividual
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synonym: Age-Related Eye Disease Study
synonym: NEI Age-Related Eye Disease Study
synonym: NEI Age-Related Eye Disease Study Genetic Repository
synonym: NEI-AREDS Repository
abbrev: NEI-AREDS
IAO_0000115: The NEI-AREDS Genetic Repository is a collection of genetic material submitted by participants in the Age-Related Eye Disease Study (AREDS) which was sponsored by the National Eye Institute (NEI). The Repository stores DNA for use by investigators conducting genetics research into the causes of eye disease. The Age-Related Eye Disease Study was designed to learn about macular degeneration and cataract, two leading causes of vision loss in older adults. The study looked at how these two diseases progress and what their causes may be. In addition, the study tested certain vitamins and minerals to find out if they can help to prevent or slow these diseases. Participants in the study did not have to have either disease. (Enrollment was completed in January 1998.) Eleven medical centers in the United States took part in the study, and more than 4,700 people across the country were enrolled in AREDS. The study was supported by the National Eye Institute, part of the Federal government''s National Institutes of Health. The clinical trial portion of the study also received support from Bausch & Lomb Pharmaceuticals and was completed in October 2001. Data from AREDS is publicly available in the Database of Genotypes and Phenotypes (dbGaP). Genetic samples from 600 AREDS participants (200 controls, 200 Neovascular AMD cases, and 200 Geographic Atrophy cases) were selected using data available in March 2005 and then were genotyped using the Illumina 100K and the Affymetrix 100K gene chips. These genotype data are available in the dbGaP. DNA samples are distributed only to qualified professional persons who are associated with recognized research, medical, educational, or industrial organizations engaged in health-related research or health delivery. All orders for DNA samples must be submitted using the online catalog.

AIDS and HIV Research Lab Registry
type: Resource
type: NamedIndividual
has db xref: nlx_52705
synonym: AIDS HIV Research Lab Registry
IAO_0000115: The AIDS And HIV Research Lab Registry is a registry of lab heads ranked by total citation score. You may sort the rankings by total score, mean score, publication number and last 365 days. Results presented are Rank, Name, Affiliation, and Total score/Last 365 days. Clicking on the name of the lab head provides additional information including a picture, affiliation, citations, the researcher''s home page, and collaborative biography.

Arnaud Delormes Programs Overview
type: Resource
type: NamedIndividual
has db xref: nlx_53037
synonym: Programs overview
IAO_0000115: Software resource including non-EEG related Matlab functions, Neuron''s simulation files, C/C++ functions, Java, Unix tips, Flash 5 buttons and movies, Publishing photo albums using Linux (external page), and Publishing digital camera movies using Linux (external page). Non-EEG related Matlab functions *Qsubfunc *Gui Matlab functions *Function keyword input/output arguments processing *Web and Matlab help *Others C/C++ functions *Convolution *Chono *Format_biblio *Image processing library *Fusion sort Java *Simple scroll *Rebound scroll *Spiking neurons Unix tips *Send a mail automatically in non-interactive mode *Log in remotely and redirect/assess resources *Schedule automatically a task (for instance to check your quota)

COHORT Repository
type: Resource
type: NamedIndividual
has db xref: nlx_143811
synonym: Cooperative Huntington's Observational Research Trial Repository
IAO_0000115: A repository of information related to Huntington's disease and its causes, progression, treatments, and possible cures. It stores and accepts data and specimens to accelerate research on Huntington's disease and provides scientists with prospectively collected clinical data and biological specimens. The COHORT sample includes individuals which manifest Huntington's disease (HD), unaffected individuals known to carry the HD gene or who are at risk of carrying the HD gene, and family members who have no risk for HD (control subjects). Clinical data includes demographics, clinical features, family history, and genetic characteristics. Biological specimens include blood with a potential of collecting urine or other samples in the future. The COHORT biological specimen repository will provide research specimens for current and future scientific research aimed at developing useful biomarkers of HD.

JP McCarthy Cord Stem Cell Bank
type: Resource
type: NamedIndividual
has db xref: nlx_53223
synonym: J.P. McCarthy Cord Stem Cell Bank
IAO_0000115: The J.P. McCarthy Cord Stem Cell Bank at the Karmanos Cancer Institute is a public, non-profit stem cell bank with over 1,200 umbilical cord blood units in its inventory. The bank was founded in 2001 and is one of only 21 internationally recognized cord stem cell banks affiliated with the National Marrow Donor Program. The only bank of its kind in Michigan, it was created in anticipation of providing life-saving hope to people who have been diagnosed with cancer and serious blood disorders. Karmanos collects, processes and stores donated umbilical cord blood that becomes a readily available source of hematopoietic stem cells for transplant in children and adults with leukemia, lymphoma, sickle cell disease or other life-threatening conditions. The J.P. McCarthy Cord Blood Bank and Carls Processing Laboratory is also accredited by the Foundation for the Accreditation of Cellular Therapy (FACT). The accreditation signifies the highest standards of practice in collection, processing and transplantation. Karmanos is the only FACT accredited cord blood bank in Michigan and one of only nine in the United States. In the Detroit Metropolitan area, the number of hospitals participating in the collection of cord blood is rapidly increasing. Please consider donating your baby''s cord blood if you are delivering at one of our participating hospitals: Henry Ford Wyandotte Hospital in Wyandotte, MI, Providence Park Hospital in Novi, MI, St. Joseph Mercy Hospital in Ann Arbor

Michigan Neonatal Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_53327
IAO_0000115: The Michigan Neonatal Biobank (Biobank) is a storage and management facility for The Michigan Department of Community Health''s archive of dried blood spot cards. A 501(c)3 non-profit charitable organization, the Biobank is contracted to serve as the repository for storage and management of the samples in a temperature controlled facility at Wayne State University''s Biobanking Center of Excellence in Tech Town. The Biobank''s roots are planted in the State''s Newborn Screening Program which began in 1965 in the Department of Community Health. Newborn screening is a public health program required by Michigan law to find babies with rare but serious disorders that require early treatment. A few drops of blood taken from the baby''s heel are sent to the State Public Health Laboratory and are tested for 49 disorders. Each year more than 200 Michigan babies are found to have a disorder detected by Newborn Screening. Once screening in the State laboratory is complete, residual dried blood spot samples that are no longer needed for testing are each assigned a unique code which assures anonymity for the sample and its donor. The samples are then sent for storage in the Michigan Neonatal Biobank.

Selectome: a Database of Positive Selection
type: Resource
type: NamedIndividual
has db xref: biotools:selectome
has db xref: nif-0000-03451
synonym: Selectome
IAO_0000115: Database of positive selection based on a rigorous branch-site specific likelihood test. Positive selection is detected using CODEML on all branches of animal gene trees.

SepNet Central Sample Bank
type: Resource
type: NamedIndividual
has db xref: nlx_53583
synonym: Biobank Kompetenznetz Sepsis
abbrev: SepNetBiobank
IAO_0000115: It is the aim of the SepNet initiative to establish a central facility, essential to data and sample quality and homogeneity, that comprises a structured and easily accessible sample bank with probes of homogeneous quality originating from a well-characterized patient population enrolled in independent, innovative and internationally competitive prospective clinical sepsis trials. The SepNetBiobank is a core facility of SepNet. The object of this central sample resource is to organize and handle all relevant aspects of sampling, storage and delivery of samples in the SepNet collaboration to ensure homogeneity of the samples in terms of specimen quality and maintaining sampling standards. This will be achieved through central handling of samples collected in peripheral nationwide 17 regional centers and an additional 36 associated centers according to an agreed sampling scheme and pre-set standards for sample quality, sample handling and banking; quality assurance and all relevant parts of sample handling will be in the hands of the core unit, minimizing pre-analytical steps in the heterogeneous environment of the different regional centers. In the next few months a fully automated sample storage system will be implemented that allows handling of more than 200.000 individual aliquots expected after completion of the different ongoing and planned SepNet Trails. In the next six months a fully automated -80 degree C sample storage system will be implemented. After completion of the plannend and ongoing SepNet trials more than 59.710 expected primary samples (218.040 aliquots) will be stored in this system. This outstanding sample resource will provide the basis for scientific projects aming at improving patient care with sepsis e.g. advancement in diagnostics, risk stratification, therapy and outcome.

Genomedata
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type: NamedIndividual
has db xref: biotools:genomedata
has db xref: nlx_53677
has db xref: OMICS_02148
IAO_0000115: A format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. They have also developed utilities to load data into this format. Retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files. A reference implementation in Python and C components is available here under the GNU General Public License. The software has only been tested on Linux and Mac systems.

celltypes.org
type: Resource
type: NamedIndividual
has db xref: nlx_53797
IAO_0000115: Central repository of information on neuronal cell types mainly accumulating information on: Genetically labeled cell types in mouse brain and genetically engineered mouse lines for cell type research. Mouse lines are annotated with * Atlas for examining transgene expression patterns * Information on construct used to generate transgene * Associated publications * Anatomical regions where transgene is expressed (based on Atlas) * Information on where to obtain the animals Currently, the mouse lines in the database are mostly generated at Cold Spring Harbor Lab, Scripps Research Institute, Baylor College of Medicine and Brandeis University with few other exceptions. In the future, they will incorporate more mouse lines useful for neuronal cell type research. Cell types are annotated with * Anatomical region * Properties (frequently used terms in neuroscience research) * Mouse line used to define the cell type * Genome wide transcriptome data (if available) * Specific (marker) genes (if available) * Marker immunostaining data (if available) * Associated publications * Electrophysiological characterizations (when available) * Morphological characterizations (when available)

LifeLink Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_53810
IAO_0000115: Established in 1985, LifeLink Tissue Bank is a not-for-profit organization dedicated to serving patients in need of transplantation therapy. It is one of five divisions of the LifeLink Foundation and the largest not-for-profit tissue bank in the Southeast and one of the largest in the United States. LifeLink Tissue Bank is inspected and accredited by The American Association of Tissue Banks (AATB). Our goal is to provide the safest, most clinically effective allografts while remaining cognizant of the rising cost of medical care. Donors and their families are the core of our organization. We treat them with respect, show them compassion, and offer them comfort in knowing that their confidentiality is protected and their gifts optimally utilized. Our allografts are utilized by surgeons and hospitals that trust LifeLink to provide them with safe and clinically effective allografts. Every effort is made to ensure that our allografts are placed back in the hospitals of the communities that we serve with organ and tissue recovery services.

OpenAnesthesia.org
type: Resource
type: NamedIndividual
has db xref: nlx_54007
synonym: OA.org
synonym: OpenAnesthesia
synonym: OpenAnesthesia Wiki
IAO_0000115: OpenAnesthesia.org is a wiki promoting evidence-based medicine in anesthesiology, critical care and pain management. It is divided into several, major Units (Anesthesia Text, Critical Care Manual, Practice-Changing Articles, Controversies in Anesthesia, ABA keywords, Audio/Video Archives, CME, GME, Pharmacology...), each of which is subdivided into Chapters (or in some cases, even smaller subdivisions, such as sections, individual key words, topics, points of interest, or bibliographic references). The goal of Anasthesia Text is to collect and distribute evidence-based information regarding all aspects of anesthesia. This section is similar to a traditional textbook in the broad range of topics covered, but different in that it will provide this information in the form of a wiki (i.e. anyone can edit, add, or subtract to it). OpenAneshesia.org provides anesthesia residents with GME credit and Program Directors with a tool to document core competency activities for Accreditation Council for Graduate Medical Education (ACGME)-mandated learning portfolios. Residents are invited invited to read the Anesthesia & Analgesia article of the month and listen to an interview with one of the article''s authors. During the interview, the author will discuss the specifics of the article as well as general topics geared towards improving each resident''s appreciation of basic or clinical research. After listening to the podcast and reading the article, residents can answer 5 questions in order to demonstrate their mastery of the topics discussed (similar to the Anesthesia & Analgesia Continuing Medical Education (CME) section). Like the CME section, after demonstrating proficiency, a resident will receive a printable certificate that will specify which ACGME core competencies were addressed in the article and interview. The certificates can be put in each resident''s ACGME-required learning portfolio.

Samaritan Health Services
type: Organization
type: NamedIndividual
has db xref: grid.430072.2
has db xref: ISNI: 0000 0004 0392 9405
has db xref: nlx_143814
has db xref: Wikidata: Q30288491
abbrev: SHS
IAO_0000115: Samaritan Health Services (SHA) is a non-profit network of hospitals, physician clinics and health services caring for the communities of the mid-Willamette Valley and central Oregon Coast. We''ve joined together to provide innovative medicine and world-class quality in a way that''s consistent with the values of the places we serve. That includes care and compassion for everyone, regardless of the ability to pay. Samaritan Health Services is a values-driven, church-related organization governed by community members, physicians and other health care providers. We seek to be the first choice of consumers in the region and to lead collaborative efforts among those who share similar goals.

Encefalus.
type: Resource
type: NamedIndividual
has db xref: nlx_54131
synonym: Encefalus
synonym: Encefalus: Studying the complex interaction between brain
synonym: society and mind
IAO_0000115: This is a blog that combines an update of the current scientific research on psychology (and all its related disciplines) along with criticism, personal thoughts and commentary. Since psychology, along with its many other facets, is a social science I consider its connection with society to be an essential part of it. Therefore, the criticism and the commentary I make will often take things to the larger scale of society whether the research concerns neurology, cognitive psychology or anything else. Holding true to this spirit, this blog will many times incorporate current news from all over the world in an attempt to establish the missing link that differentiates mainstream psychology from the real out-of-the-lab world. I hope that this blog really brings something different to just a simple updating of the current research, because there are, indeed, many blogs that do this job. The author describes this blog as some occasional psycho-rant by a former student (now graduate) of psychology (and post graduate in artificial intelligence), while combining of course an update on the current research with a critical view and the occasional satiric spirit.

Open Medicine Live Wiki
type: Resource
type: NamedIndividual
has db xref: nlx_54196
synonym: Open Medicine: where articles Live
abbrev: Open Medicine Live
IAO_0000115: This project explores the use of a wiki as an online collaborative tool for improving and updating peer-reviewed systematic reviews. Posted on this wiki is a copy of the article: Second-line therapy in patients with type 2 diabetes inadequately controlled with metformin monotherapy: A systematic review and mixed treatment comparisons meta-analysis. Readers are invited to edit the article by adding to, deleting or modifying its contents.

SPH Biorepository
type: Resource
type: NamedIndividual
has db xref: nlx_54203
synonym: School of Public Health Biorepository
synonym: UC Berkeley Biorepository
IAO_0000115: Established in 2004, SPH Biorepository was built to create a centralized facility for many research programs, as well as for new ones; more effective use of the available storage space; development of new database management tools; and quality control of sample processing and banking. While maintaining ultimate control of the samples accumulated in their research projects, PIs will have the assurance of competent handling of their biological samples, reliable access, safe storage, and expert advice from the Biorepository personnel. In the long-term, the Biorepository will provide: * Safe and orderly storage of banked samples * Samples diversification in case of a major disaster *Leverage for additional funding for the new projects Over 145,000 thousands of various biological and environmental samples have been stored and archived through the CHAMACOS, Vitamin, FACES, IBD, and other projects. The Biorepository (Holland - Director) has accumulated substantial expertise in the development of customized databases to barcode and monitor sample location, transfer, and use.

Cardio-Facio-Cutaneous Syndrome International Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_54340
synonym: Cardio-Facio-Cutaneous International BioBank
synonym: CFC International BioBank
abbrev: CFC BioBank
IAO_0000115: CFC International holds the world''s largest collection of blood and tissue from people affected by CFC and their immediate relatives. It is the only centralized repository in the world. The CFC BioBank provides medical researchers with genetic and biological material from CFC patients and their families, so that research on CFC and other related syndromes can be performed. CFC International joined the Genetic Alliance BioBank in 2004 to make certain that your privacy and confidentiality are protected and your samples are available to any approved research project. The bank serves as a resource for researchers around the world who are willing to search to find the gene(s) responsible for the Cardio-Facio-Cutaneous Syndrome. As you know, Cardio-Facio-Cutaneous Syndrome is an extremely rare condition. Thus while access to cell lines is essential for studying the biology and genetics of the disorder, there are very few cell lines in existence. Because an integral part of CFC''s mission is to stimulate interest in CFC research, there is an increased need for cell lines. The CFC BioBank will ensure that need is met! The goals of The CFC BioBank are to promote: * Sufficient availability of cells for approved research projects * Incentive for new research projects * Study of the biochemical basis for CFC Syndrome * Discoveries leading to new treatments for children with CFC Syndrome If you are interested in donating to the CFC BioBank please call 607-772-9666, or e-mail us at bconger_at_cfcsyndrome.org and indicate your interest. Researchers with an interest in either donating CFC Syndrome cell lines or in applying to use material from the bank should also call or write.

Science in Society Conference
type: Resource
type: NamedIndividual
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IAO_0000115: Welcome to the website of the Fourth International Conference on Science in Society, to be held at the University of California, Berkeley, USA from 17 to 19 November 2012. This Conference will address disciplinary and interdisciplinary challenges in the sciences, and in particular the relationships of science to society. Key themes addressed by the Conference include the social impacts of science, the values and ethics of science, the pedagogies of science, the knowledge-making processes of science, the politics of science and the economics of science. At first glance, the scope and concerns of the Conference are enormous. However, in contrast to conferences with a specialist disciplinary focus, this Conference aims to explore, in an interdisciplinary spirit, linkages between different areas of concern and practices of investigation. We welcome presentation proposals which range from broad explorations of philosophical, theoretical, methodological and policy questions, to proposals which present finely grained evidence of the connections of science to society in microcosms of research, teaching and practice. Participants at the Conference will include researchers, teachers, administrators and policy makers from the basic natural-physical sciences, the applied sciences, the social sciences, history and philosophy of science, the humanities, and the professions. Plenary speakers will include some of the world's leading thinkers in the various fields which are concerned with the relationships of science to society, as well as numerous paper, colloquium and workshop presentations by practitioners, teachers and researchers. Participants are welcome to submit a presentation proposal either for a 30-minute paper, 60-minute workshop, or a jointly presented 90-minute colloquium session. Parallel sessions are loosely grouped into streams reflecting different perspectives or disciplines. Each stream also has its own talking circle, a forum for focused discussion of issues. For…

DCI Donor Services
type: Resource
type: NamedIndividual
has db xref: nlx_54729
abbrev: DCIDS
IAO_0000115: An affiliation of organ and tissue recovery organizations across the United States that is committed to saving and improving lives by connecting one life to another through donation and transplantation. DCI Donor Services (DCIDS) supports families who have sustained the loss of a loved one by providing an opportunity for organ, eye and tissue donation and by facilitating the recovery and transplantation of these gifts to help others in need. They also provide after-care support to donor families while at the same time working to inspire universal acceptance of donation throughout the hospitals and communities we serve to ensure every person in need receives the Gift of Life.

LifeGift Organ Donation Center
type: Resource
type: NamedIndividual
has db xref: nlx_54839
abbrev: LifeGift
IAO_0000115: Established in 1987, LifeGift is a not-for-profit organ procurement organization that recovers organs and tissue for individuals needing transplants in 109 Texas counties in North, Southeast and West Texas. Our Role * Help grieving families consider the decision to give the gift of life. Inform families of registered donors of their loved ones����?? wishes to donate. * Coordinate the organ and tissue recovery process with surgeons, other transplant professionals and transplant centers. Collect data for use in transplantation research. * Partner with hospitals to continually develop effective, government-regulated donation systems to help increase the number of donated organs available for transplant. * Educate the public about the need for organ and tissue donation. Serve the African-American, Latino and Asian minority communities with specific educational programs. * Continue to support and maintain contact with donor families following the donation process, facilitating communication between recipients and donor families, if both parties desire.

Inflammatory Breast Cancer Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_55116
synonym: IBC Research Foundation BioBank
synonym: ibcRF BioBank
abbrev: IBC BioBank
IAO_0000115: The IBC Research Foundation BioBank is a secure, privacy-protected collection of biological specimens from ibc-diagnosed patients (cases, and, unlike the former George Washington University IBC Registry, ibc patients who have died, those who are under legal age, and those living but unable to make decisions for themselves, may be consented to participate in the IBC Research Foundation BioBank by their authorized representative) and from those not diagnosed with ibc (controls), volunteering following a consent decision making process, and signing an Informed Consent. Clinical Data and a comprehensive questionnaire will also be obtained for those diagnosed with ibc. The Inflammatory Breast Cancer Research Foundation (ibcRF) has established a BioBank and Clinical Database. The BioBank contains non-tumor RNA and DNA, tumor RNA and DNA, blocks and slides from diagnostic pathology, and medical records describing clinical and pathologic findings at diagnosis.

BioDiscovery Nexus Copy Number
type: Resource
type: NamedIndividual
has db xref: OMICS_01122
synonym: Nexus Copy Number
abbrev: BioDiscovery
IAO_0000115: Software package provides statistical tools. Derives copy number and BAF from variety of NGS data including WES, WGS, targeted panel, and shallow sequencing as well as Microarray data. Multifaceted desktop software for rapid discovery of genomic alterations. Accepts data from various manufacturers and technologies including Infinium GSA and CytoScan XON.

CAS REGISTRY
type: Resource
type: NamedIndividual
has db xref: nlx_55136
synonym: CAS REGISTRY - The gold standard for substance information
synonym: Chemical Abstracts Service
abbrev: CAS
IAO_0000115: CAS REGISTRY, the gold standard for substance information, is the only integrated, comprehensive source of chemical information from a full range of disclosed material including patents, journals, and reputable web sources. When you need to positively identify a chemical substance, you can rely on the authoritative source for chemical names and structures of CAS REGISTRY. CAS databases are curated and quality-controlled by CAS scientists, and recognized by chemical and pharmaceutical companies, universities, government organizations, and patent offices around the world as authoritative. By combining these databases with advanced search and analysis technologies (SciFinder, STN, and Science IP products and services), CAS delivers the most current, complete, and cross-linked secure digital information environment for scientific discovery. You can identify your substance of interest by its CAS Registry Number, which is the best way to identify a substance, regardless of what name you have for it. You can also use CAS REGISTRY to locate * literature references to the substance * experimental and predicted property data (boiling and melting points, etc.) * commercial availability * preparative methods * spectra * regulatory information from international sources

PGN
type: Resource
type: NamedIndividual
has db xref: nlx_55223
synonym: PGN - Plant Genome Network
synonym: Plant Genome Network
IAO_0000115: Resource for the storage, retrieval and annotation of plant ESTs, with a focus on comparative genomics. PGN comprises an analysis pipeline and a website, and presently contains mainly data from the Floral Genome Project. However, it accepts submission from other sources. All data in PGN is directly derived from chromatograms and all original and intermediate data are stored in the database. The current datasets on PGN come from the floral genome project and includes the following species: Acorus americanus, Amborella trichopoda, Asparagus officinalis, Cucumis sativus, Eschscholzia californica, Eschscholzia californica, Illicium parviflorum, Ipomopsis aggregata, Liriodendron tulipifera, Mesembryanthemum crystallinum, Mimulus guttatus, Nuphar advena, Papaver somniferum, Persea americana, Prymnesium parvum, Ribes americanum, Saruma henryi, Stenogyne rugosa, Vaccinium corymbosa, Welwitschia mirabilis, Yucca filamentosa, Zamia fischeri. For functional annotation, blast is used to compare find the best match of each unigene sequence to in the Genbank NR database, and the in complete coding sequences from Arabidopsis. These annotations are stored in the database and serve as the primary source of annotation. The annotation framework will be extended to Gene Ontology annotations in the future.

University of Miami Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_55385
abbrev: UMTB
IAO_0000115: Established in 1970, the University of Miami Tissue Bank (UMTB) is the oldest academic institution of its kind in the United States. UMTB came about and evolved in an effort to provide safe and effective bone and soft tissue grafts to patients long before allograft bone transplantation was widely accepted. UMTB has always been focused on safety and the advancement of knowledge in allograft use. More scientific peer-reviewed articles, book chapters and innovations have come from UMTB either directly or indirectly than from any other organization of its kind. UMTB continues to be a leader in transplantation research and has maintained an impeccable safety record. As the only university-run tissue bank, UMTB works closely with surgeons and basic science investigators to advance the field of bone and soft tissue transplantation. Our scientific endeavors include clinical trials to confirm and improve graft efficacy for oral surgery, orthopedic tumor and spine surgery, and sports injuries. When warranted, we engage commercial entities for these studies. As a multidisciplinary organization of surgeons, pathologists, scientists and technicians, we have safely recovered, processed, distributed and implanted aseptically processed bone, cartilage and soft tissue grafts in thousands of patients. We make extraordinary efforts to ensure aseptic recovery and processing to protect the biologic activity, integrity, bio attributes, and safety of the graft. We believe that the American Association of Tissue Banks (AATB) has adopted appropriate guidelines for Tissue Banking in the United States and the University of Miami is a proud member of this organization.

Oscar3
type: Resource
type: NamedIndividual
has db xref: nlx_55584
synonym: Open Source Chemistry Analysis Routines
synonym: OSCAR
abbrev: Oscar
IAO_0000115: OSCAR is software for the semantic annotation of chemistry papers. The modules OPSIN (a name to structure converter) and ChemTok (a tokeniser for chemical text) are also available as standalone libraries. This tool for shallow, chemistry-specific parsing of chemical documents identifies (or attempts to identify): * Chemical names: singular nouns, plurals, verbs etc., also formulae and acronyms, some enzymes and reaction names. * Ontology terms: if you can do it by string-matching, you can get OSCAR to do it. * Chemical data: Spectra, melting/boiling point, yield etc. in experimental sections. In addition, where possible the chemical names that are detected are annotated with structures, either via lookup or name-to-structure parsing (OPSIN), and with identifiers from the chemical ontology ChEBI Current work on OSCAR3 by Peter Corbett focuses on its use in SciBorg, a framework for the deep parsing of chemical text. OSCAR3 also includes the Oscar Server, a Jetty-powered set of servlets. These provide the following services: * Parsing of text/HTML by OSCAR. * Text/InChI/SMILES/SMILES substructues/SMILES similarity search of papers, coupled with keyword and ontology-based search, using Lucene and the CDK. * List of all names found / all names that co-occur with a search term or terms. * Online management of a chemical/stopword lexicon. * Manual editing of SciXML fragments containing named entities, for creating of gold standards and training data. Oscar3 can be found on SourceForge: http://sourceforge.net/projects/oscar3-chem/

Language Map Experiment Management System
type: Resource
type: NamedIndividual
has db xref: nif-0000-00065
synonym: UW Integrated Brain Project Language Map Experiment Management System
abbrev: Language Map EMS
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. An experiment management system for researchers studying language organization in the brain. Data from thirteen patients are available as a public demo. Language Map EMS

HapMap 3 and ENCODE 3
type: Resource
type: NamedIndividual
has db xref: nlx_143820
abbrev: HapMap 3 and ENCORE 3
IAO_0000115: Draft release 3 for genome-wide SNP genotyping and targeted sequencing in DNA samples from a variety of human populations (sometimes referred to as the HapMap 3 samples). This release contains the following data: * SNP genotype data generated from 1184 samples, collected using two platforms: the Illumina Human1M (by the Wellcome Trust Sanger Institute) and the Affymetrix SNP 6.0 (by the Broad Institute). Data from the two platforms have been merged for this release. * PCR-based resequencing data (by Baylor College of Medicine Human Genome Sequencing Center) across ten 100-kb regions (collectively referred to as ENCODE 3) in 712 samples. Since this is a draft release, please check this site regularly for updates and new releases. The HapMap 3 sample collection comprises 1,301 samples (including the original 270 samples used in Phase I and II of the International HapMap Project) from 11 populations, listed below alphabetically by their 3-letter labels. Five of the ten ENCODE 3 regions overlap with the HapMap-ENCODE regions; the other five are regions selected at random from the ENCODE target regions (excluding the 10 HapMap-ENCODE regions). All ENCODE 3 regions are 100-kb in size, and are centered within each respective ENCODE region. The HapMap 3 and ENCORE 3 data are downloadable from the ftp site.

Handbook of Genetic Counseling
type: Resource
type: NamedIndividual
has db xref: nlx_79147
IAO_0000115: The Handbook of Genetic Counseling is a wikibook designed as an introduction to the discipline and practice of genetic counseling. The text provides an introduction to genetic counseling as a clinical practice and includes sample counseling outlines and letters for students of genetic counseling. Additional outline and letter examples are highly encouraged. Wikibooks contains books on many medical topics; however, no warranty whatsoever is made that any of the books are accurate.

LifeNet Health of Florida
type: Resource
type: NamedIndividual
has db xref: nlx_56256
synonym: LifeNet Health of Florida Inc.
IAO_0000115: Founded in 1982 and headquartered in Virginia Beach, VA, LifeNet Health Inc., is a leading biomedical alloengineering organization and organ and tissue donation agency whose mission is saving lives and restoring health. LifeNet Health of Florida is a fully owned subsidiary dedicated to the recovery of tissue in Northern Florida, improving the awareness of tissue donation and educating the public about donation in the Northern Florida Community. Our mission is to improve upon the awareness of tissue donation within the community as well as to provide human tissue for transplant. We strive to give back to the community by providing an extensive public education program regarding donation, as well as being involved and making contributions that we feel will benefit the local community as a whole. Our efforts with total quality management have solidified our belief that LifeNet Health of Florida, Inc., must be driven by excellence in service and uncompromising quality. By the continuous improvement of processes and services leading to a better understanding of the entire donor process for both hospital personnel and members of our community.

emedicinehealth: Dementia Due to HIV Infection
type: Resource
type: NamedIndividual
has db xref: nlx_143822
abbrev: Dementia Due to HIV Infection
IAO_0000115: A narrative resource that provides a wealth of information on topic including: * Dementia Due to HIV Infection Overview * Dementia Due to HIV Infection Causes * Dementia Due to HIV Infection Symptoms * Exams and Tests * Dementia Due to HIV Infection Treatment * Self-Care at Home * Medical Treatment * Next Steps * Follow-up * Prevention * Outlook * Support Groups and Counseling * For More Information * Web Links * Multimedia * Synonyms and Keywords Additional information includes: * HIV AIDS Myths and Facts Slideshow Pictures * Take the HIV/AIDS Quiz * AIDS Retrospective Slideshow Pictures

WebMD
type: Resource
type: NamedIndividual
has db xref: nlx_143824
IAO_0000115: WebMD has created an organization that we believe fulfills the promise of health information on the Internet. We provide credible information, supportive communities, and in-depth reference material about health subjects that matter to you. We are a source for original and timely health information as well as material from well known content providers. The WebMD content staff blends award-winning expertise in journalism, content creation, community services, expert commentary, and medical review to give our users a variety of ways to find what they are looking for. And that, we believe, requires dedicated, full-time staff professionals with state-of-the-art expertise in: * Health news for the public * Creating and maintaining up-to-date medical reference content databases * Medical imagery, graphics, and animation * Communities * Live web events * User experience * Interactive tools Our board-certified physicians, award-winning journalists, and trained community moderators are solely dedicated to your daily information experience on WebMD. Our content staff includes individuals who hold advanced degrees in journalism, medical illustration, health communications, clinical informatics, nursing, and medicine. WebMD verifies the qualifications of all medical professionals on the site; including health professionals, experts, editorial professionals and contributors with a specialty license. You may search for information or use the Health A-Z option. Additionally, Drugs & Supplements, Living Healthy, Eating & Diet, Parenting & Pregnancy, Teen Health, and Pet Health tabs are available.

HUPO Antibody Initiative
type: Resource
type: NamedIndividual
has db xref: nlx_56399
synonym: Human Antibody Initiative
synonym: HUPO HAI
synonym: HUPO Human Antibody Initiative
abbrev: HAI
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022.The mission of the Human Antibody Initiative (HAI) aims to promote and facilitate the use of antibodies for proteomics research. The initiative consists of two separate activities; (1) the generation of a catalogue of validated antibodies from many different sources and (2) a protein atlas for the expression and localization of human proteins in normal and disease tissue. The two separate activities have as their primary deliverables to generate databases with free public accessibility. The Antibody Resource database (www.antibodypedia.org) is aimed to produce a comprehensive catalogue of validated antibodies towards human proteins. This initiative depends on input from a large number of academic groups and commercial companies. The Protein Atlas initiative (www.proteinatlas.org) is aimed to provide comprehensive and annotated database of high-resolution images showing tissue profiles in normal and cancer tissues. Both databases will be open to the public without restriction (no passwords).

SysMO JERM Ontology of Systems Biology for Micro-Organisms
type: Resource
type: NamedIndividual
has db xref: nlx_157602
abbrev: JERM
IAO_0000115: An ontology to describe the entities and relationships in the SEEK database, a Systems Biology environment for the sharing and exchange of data and models. The SysMO-SEEK database contains the work of the SysMO consortium (Systems Biology of Micro-Organisms) https://seek.sysmo-db.org/

UTHealth BioBank
type: Resource
type: NamedIndividual
has db xref: nlx_62871
synonym: CCTS Biomedical Informatics Group at UTHealth BioBank
synonym: Clinical and Translational Sciences BioBank
synonym: UTHealth CCTS BioBank
synonym: UTHealth Clinical and Translational Sciences BioBank
abbrev: CCTS BioBank
IAO_0000115: The University of Texas Health Science Center at Houston (UTHealth) Clinical and Translational Sciences (CCTS) BioBank employs a federated rather than a centralized model which encourages participation by sample owners who are concerned about guaranteeing their ownership of samples and sample information about patients, samples and related clinical data. In a federated model, individual sites agree on shared policies and procedures for data and sample sharing and oversight. Samples remain with and are governed by the contributing principal investigator at each site. The contributing investigator has final authority whether or not to collaborate or to release samples to qualified researchers. The goal of SLED (Sample Location and Enhanced Distribution) is to help researchers overcome two of the biggest obstacles preventing their research from beginning: 1) location of samples and related data, and 2) requesting of samples and related data. Prior to SLED''s inception the existing system was limited to providing links to samples and data and relying on phone calls to sample owners to facilitate sharing. Collaboration between the CTSA Biobank Consortium and the informatics team at the University of Texas School of Biomedical Informatics is ongoing during this effort. The initial design was constructed using best practices offered by NIH, NCI, and other biobank industry leaders to support and to improve synergy and interaction among various research efforts. Through SLED, researchers will be able to search for samples using a variety of criteria including availability, clinical data, consent criteria, patient demographics, patient diagnoses, study data, and sample type at local and national biobank sites.

PEDSCRIPT
type: Resource
type: NamedIndividual
has db xref: nlx_154528
IAO_0000115: Software tool that allows scripting of simple modifications to pedigree files. (entry from Genetic Analysis Software)

SubMito
type: Resource
type: NamedIndividual
has db xref: nlx_56452
IAO_0000115: SubMito is the first computational system for predicting protein submitochondria locations from its primary sequence. SubMito is designed and implemented with Java. This site is a web-like front end for SubMito system. Users can access SubMito on the server side by uploading a FASTA file or entering sequence below. The prediction result will be saved on server, and a link to the result file will be provided. Since there may be several sessions running at the same time on the server, the responding of the server side SubMito may be very slow. Another way to use SubMito is to download a local version of the software. The online service can accept 2 forms of input. One is single sequence, the other is uploaded FASTA file. If you want to predict submitochondria location for a single sequence, you can paste your sequence in the text box. Optionally, you can choose to write some remarks in the text field labeling Enter your remark. Then, press the Submit button to perform the prediction. The result will be saved in a FASTA format file, and you can download it at any time in the coming 48 hours.

TETRA
type: Resource
type: NamedIndividual
has db xref: OMICS_01474
synonym: TETRA - Fragment assignment by intrinsic tetranucleotide frequencies
IAO_0000115: Standalone software programs that can be used to calculate how well tetranucleotide usage patterns in DNA sequences correlate. Such correlations can provide valuable hints on the relatedness of DNA sequences.

Southwest France Tumour Bank
type: Resource
type: NamedIndividual
has db xref: nlx_56834
synonym: Canceropole Grand Sud-Ouest Virtual Tumour Bank
synonym: Canc��rop��le Grand Sud-Ouest Virtual Tumour Bank
synonym: GSO virtual biobank
synonym: Southwest France Tumor Bank
synonym: Southwest France Virtual Tumor Bank
synonym: SW France Tumour Bank
synonym: SW France Virtual Tumor Bank
synonym: Tumorotheque Virtuelle du Canceropole GSO
abbrev: SW France Tumor Bank
IAO_0000115: The Virtual Tumour Bank of the Canceropole Grand Sud-Ouest''s mission is to federate the cancer research of four French regions: Aquitaine, Languedoc-Roussillon, Limousin and Midi-Pyrenees. This site allows access to an inventory of the specimens stored in the tumor banks of the Greater South-West region, within the laboratories of Pathology of the University Hospital Centers and Cancer Centers of Bordeaux, Limoges, Montpellier, Nimes and Toulouse. You may search by disease or multiple criteria. These specimens are removed from patients primarily to confirm and accurately characterize their cancer diagnosis, and are therefore stored by the tumor bank for diagnostic and/or therapeutic purposes. These samples can be re-qualified for scientific research pending that a number of conditions are met, including the absence of refusal from the person (in compliance with French regulations). So far, the tumor bank is a major tool for cancer treatment and research. This inventory is a further evidence of the coordination effort between the eight concerned tumor banks that have been mobilized at the service of patients and research within the framework of the Canceropole Grand Sud-Ouest programs. These biological resources are made available to research groups that conduct basic or translational programs in the field of oncology. They will not be made available for projects in fields other than oncology.

Alien hunter
type: Resource
type: NamedIndividual
has db xref: nlx_56835
synonym: Alien_hunter: Interpolated Variable Order Motifs for Identification of Horizontally Acquired DNA
IAO_0000115: Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. An IVOM approach exploits compositional biases using variable order motif distributions and captures more reliably the local composition of a sequence compared to fixed-order methods. Optionally the predictions can be parsed into a 2-state 2nd order Hidden Markov Model (HMM), in a change-point detection framework, to optimize the localization of the boundaries of the predicted regions. The predictions (embl format) can be automatically loaded into the freely available Artemis genome viewer.

Southern Alberta Organ and Tissue Donation Program
type: Resource
type: NamedIndividual
has db xref: nlx_57488
synonym: HOPE Program
IAO_0000115: The Southern Alberta Organ and Tissue Donation Program is an integrated donation program for organs, occular tissue and non-occular tissue. These services are provided by the Southern Alberta Organ Donation Program, Lions Eye Bank & the Southern Alberta Tissue Program. This service provides: * coordination of donation, allocation, recovery and distribution of organs for transplantation for Southern Alberta; * recovery, processing, storage and distribution of occular and non-occular tissues for transplantation; * public , professional education and awareness; * research and statistics; * bereavement support.

Blood and Tissue Center of Central Texas
type: Resource
type: NamedIndividual
has db xref: nlx_57236
synonym: Travis County Medical Society Blood Bank
IAO_0000115: The Blood and Tissue Center of Central Texas is a 501(c)(3) not-for-profit organization. Its mission is to safeguard the community''s gifts of blood and tissue with uncompromising quality and excellence in customer service. The Center is licensed by the US Food and Drug Administration, accredited by the American Association of Blood Banks and American Association of Tissue Banks, and is a proud member of America''s Blood Centers. The Blood and Tissue Center today is the exclusive provider and guardian of the community blood supply for more than 37 medical facilities in a ten-county service area of Central Texas. In 2010, over 56,000 whole blood donations and 7,700 apheresis platelet donations were collected. These donations are tested extensively to assure suitability for transfusion and processed into life saving components: red blood cells, plasma, and platelets, which go to help Central Texas patients. The Center works with the Marrow Donor Program of Central and South Texas to increase the number of Central Texans on the National Marrow Donor Registry. The Tissue Services division was established in 1985 due to the increasing demand for allograft tissue. Today, The Tissue Center surgically recovers tissue from approximately 300 donors each year and assists with donor family services. The Tissue Center''s main facility is located in Austin with a satellite office in Corpus Christi.

Psychology Wiki: Neuroinformatics
type: Resource
type: NamedIndividual
has db xref: nlx_57306
synonym: Psychology Wiki - Neuroinformatics
IAO_0000115: Psychology wiki is an up-to-date, authoritative statement of knowledge, theory, and practice in the whole field of psychology reflecting generally accepted academic standards. A topic covered in this wiki portal includes Neuroinformatics. The Neuroinformatics wiki page currently offers the following categories: overview, history, collaboration with other disciplines, research programs and groups, technologies and developments, references, external links, research centers, and more. Neuroinformatics is a research field that encompasses the development of neuroscience data, knowledge and application of computational models and analytical tools for the integration and analysis of experimental data and for improving existing theories about nervous system and brain. Neuroinformatics provides tools, databases, models, networks technologies and models for the clinical and research purposes in the neuroscience community and other fields.

Alabama Head Injury Foundation
type: Resource
type: NamedIndividual
has db xref: nlx_143826
synonym: Alabama Head Injury Foundation: Improving Life After Traumatic Brain Injury
abbrev: AHIF
IAO_0000115: The Alabama Head Injury Foundation (AHIF) was founded in 1983 to increase public awareness of Traumatic Brain Injury (TBI) and to stimulate the development of supportive services. Today, AHIF is among the largest state brain injury associations in the nation with model programs and statewide services. Its mission is to improve the quality of life for people who have survived traumatic brain injuries and for their families. Whether the injury is mild or severe the life of the injured person and their family is changed forever. The impact can be both emotionally and financially devastating. AHIF provides the information to help clients and families understand the results of injury. AHIF helps access available resources and provides services and programs which meet the unique needs of individuals with traumatic brain injury (TBI) as well as spinal cord injury (SCI) in certain programs.

MD Anderson Clone Bank
type: Resource
type: NamedIndividual
has db xref: nlx_57463
synonym: MD Anderson Cancer Center Clone Bank
synonym: University of Texas MD Anderson Cancer Center Clone Bank
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The MD Anderson Cancer Center Clone Bank consists of 802 murine cDNA clones, purchased from Research Genetics, Inc. These clones were sequence verified. A listing of the following are available: * Currently available clones (xls) * Top five blast hits for incorrect sequences (xls)

Community Tissue Services - CTS
type: Resource
type: NamedIndividual
has db xref: nlx_57465
synonym: Community Tissue Services
abbrev: CTS
IAO_0000115: Community Tissue Services (CTS), a not-for-profit tissue bank, was founded in Dayton, Ohio in 1986 as a division of the Community Blood Center. The tissue bank was established to help patients in need of life saving or life enhancing tissue grafts. CTS'' goal is to educate the community of the importance of tissue donation so that families can make informed decisions about the options of donation. CTS serves the public through recovery, processing and distribution of human tissue grafts used for transplantation. Since 1994, CTS has expanded its Dayton, Ohio operations into Texas, Oregon, California, Indiana, Pennsylvania and Tennessee, with over 300 employees nationwide. CTS is an accredited member of the American Association of Tissue Banks and CTS-CTIR is ISO 13485 certified. Strongly committed to providing the highest quality of tissues for transplantation, the tissue bank complies with all federal and state regulations. CTS is currently one of the largest US tissue banks, distributing nearly 10% of the tissue grafts in the United States. CTS is the largest nonprofit provider of skin grafts to surgeons for severe burn patients.

NLM Catalog
type: Resource
type: NamedIndividual
has db xref: nlx_62909
IAO_0000115: The NLM Catalog provides access to NLM bibliographic data for journals, books, audiovisuals, computer software, electronic resources and other materials. Links to the library''s holdings in LocatorPlus, NLM''s online public access catalog, are also provided.

Entrez GEO Profiles
type: Resource
type: NamedIndividual
has db xref: nlx_57723
synonym: Gene Expression Omnibus Profiles
synonym: GEO Profiles
IAO_0000115: The GEO Profiles database stores gene expression profiles derived from curated GEO DataSets. Each Profile is presented as a chart that displays the expression level of one gene across all Samples within a DataSet. Experimental context is provided in the bars along the bottom of the charts making it possible to see at a glance whether a gene is differentially expressed across different experimental conditions. Profiles have various types of links including internal links that connect genes that exhibit similar behaviour, and external links to relevant records in other NCBI databases. GEO Profiles can be searched using many different attributes including keywords, gene symbols, gene names, GenBank accession numbers, or Profiles flagged as being differentially expressed.

LinkedCT
type: Resource
type: NamedIndividual
has db xref: nlx_57779
synonym: Linked Clinical Trials
synonym: LinkedCT Live Databrowse
synonym: LinkedCT.org
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023.The Linked Clinical Trials (LinkedCT) project aims at publishing the first open Semantic Web data source for clinical trials data. The data exposed by LinkedCT is generated by (1) transforming existing data sources of clinical trials into RDF, and (2) discovering links between the records in the trials data and several other data sources. You may download static data dumps. The LinkedCT data space is published according to the principles of publishing Linked Data. These principles greatly enhance adaptability and usability of data on the web. Each entity in LinkedCT is identified by a unique HTTP dereferenceable Uniform Resource Identifier (URI). When the URI is looked up, related RDF statements about the entity is returned in HTML or RDF/XML based on the user''s agent. Moreover, a SPARQL endpoint is provided as the standard access method for RDF data.

DISCO
type: Resource
type: NamedIndividual
has db xref: nlx_143827
synonym: DISCO: Extensible Web resource DISCOvery
synonym: registration and interoperation framework
IAO_0000115: DISCO is an information integration approach designed to facilitate interoperation among Internet resources. It consists of a set of tools and services that allows resource providers who maintain information to share it with automated systems such as NIF. NIF is then able to harvest the information and keep those sets of information up-to-date. How is this accomplished? By using a series of files and/or scripts which are then placed in the root directory of the resource developer''s resource. (NIF can also host the files on its servers and crawl for changes there.) Once the files of the resource providers are in place, and DISCO is notified, the DISCO server can then recognize and consume the information shared, providing machine understandable information to NIF Integrator Servers (also known as Aggregators) about your resource. What can DISCO do for my resource? * Inform search engines about your resource and keep your NIF Registry resource description up-to-date. * Expose your data (semi-structured datasets or fields within your structured database) through NIF''s Data Federation you choose what data will be shared. * Create links from an NCBI database (e.g., PubMed, Protein, Nucleotide, etc.) to your data records in NIF using Entrez LinkOut. * Advertise your terminology or ontological information. * Share your resource''s news with the NIF community., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Aurora Healthcare Biorepository
type: Resource
type: NamedIndividual
has db xref: nlx_57835
synonym: Open-Source Robotic Biorepository and Informatics Technology
synonym: ORBIT - The Biorepository Program
abbrev: ORBIT
IAO_0000115: The Open-Source Robotic Biorepository & Informatics Technology is a platform that aims to make blood samples and health related information available to researchers. This resource is intended to help researchers understand human biology so they can develop treatments that are effective for each individual. In the simplest terms, ORBIT is a large library of blood specimens. Patient recruitment for ORBIT is being rolled out of Aurora''s 13 hospitals and 120 clinics in eastern Wisconsin, starting with its Milwaukee facilities. So far, more than 70 percent of patients have agreed to participate. If patients agree to participate, blood left over from their medical tests is sent to the ORBIT lab. Here a robot extracts the DNA from the blood, bar codes the sample and stores it in a freezer. The barcode allows the informatics technology to link each sample with the appropriate privacy-protected electronic medical record. The open source aspect of ORBIT is intended to expand scientific discovery. Researchers who use ORBIT specimens will return their research results to ORBIT to minimize study repetition and to allow researchers from around the world to build on previous results.

National Comorbidity Survey
type: Resource
type: NamedIndividual
has db xref: nlx_143828
abbrev: NCS
IAO_0000115: The baseline NCS, fielded from the fall of 1990 to the spring of 1992, was the first nationally representative mental health survey in the U.S. to use a fully structured research diagnostic interview to assess the prevalences and correlates of DSM-III-R disorders. The baseline NCS respondents were re-interviewed in 2001-02 (NCS-2) to study patterns and predictors of the course of mental and substance use disorders and to evaluate the effects of primary mental disorders in predicting the onset and course of secondary substance disorders. In conjunction with this, an NCS Replication survey (NCS-R) was carried out in a new national sample of 10,000 respondents. The goals of the NCS-R are to study trends in a wide range of variables assessed in the baseline NCS and to obtain more information about a number of topics either not covered in the baseline NCS or covered in less depth than we currently desire. A survey of 10,000 adolescents (NCS-A) was carried out in parallel with the NCS-R and NCS-2 surveys. The goal of NCS-A is to produce nationally representative data on the prevalences and correlates of mental disorders among youth. The NCS-R and NCS-A, finally, are being replicated in a number of countries around the world. Centralized cross-national analysis of these surveys is being carried out by the NCS data analysis team under the auspices of the World Health Organization (WHO) World Mental Health Survey Initiative. In order to provide an easily accessible database which can be updated and checked on a regular basis, we have created a public use file system containing all the documents from the NCS and NCS-R programs. These file systems can be accessed through the Internet and either downloaded onto a disk or printed. We will update the system on a regular basis to add newly completed paper abstracts and other documents. In addition, the NCS and NCS-R data can be accessed through ICPSR (Inter-university Consortium for Political and Social Research). Any updates to t…

Sapien Games
type: Resource
type: NamedIndividual
has db xref: nlx_58009
synonym: and the Science of Human Interaction
synonym: Politics
synonym: Sapien Games: Evolution
IAO_0000115: Sapien Games is a blog at the intersection of Nicholas Saij Horton''s interests in Evolutionary Science and Political Theory. He is a graduate student in mathematics at Portland State University. His areas of study are Quantum Game theory and Mathematical Modeling in the Behavioral Sciences including Biological Evolution, Economics, and Political Science.

National Tsing Hua University; Hsinchu; Taiwan
type: Organization
type: NamedIndividual
has db xref: nlx_59919
synonym: National Tsing Hua University
synonym: National Tsing Hua University; Hsinchu City; Taiwan
abbrev: NTHU
IAO_0000115: Research university in Hsinchu City, Taiwan. Public institution that traces its roots back to 1911, when it was established in Beijing as Tsing Hua Academy.

Human Biological Data Interchange
type: Resource
type: NamedIndividual
has db xref: nlx_143829
synonym: Human Biological Data Interchange (HBDI)
abbrev: HBDI
IAO_0000115: Database of medical history and genealogical data on over 6700 families who are affected by type 1 diabetes and a repository of DNA and immortalized cell lines collected from 500 families. This database and repository was originally created to help researchers uncover the genetic causes of type 1 diabetes but today, it is also used by researchers who study type 2 diabetes, diabetic complications, autoimmune diseases, kidney disease, and other disorders. The following resources and services are available to researchers through HBDI: * International Type 1 Diabetes Database: This database includes more than 6700 families with diabetes, related complications and other genetic diseases. There are extensive genealogical and medical histories for more than 90,000 individuals. NDRI conducts searches of the database for approved research requests. * HBDI Catalog: The catalog contains 503 family pedigrees with associated cell lines, DNA, and serum for research. Also available are HLA-typing and auto-antibody test results for diabetes families in the catalog. * HBDI Repository: The HBDI repository contains cell lines, DNA, and HLA typing information from 480 families, and frozen buffy coats from 23 families, all with Type 1 diabetes. They have recently expanded the repository to include specimens from individuals with rare diseases. * Customized Collections: NDRI will collect data from patients and physicians, conduct phone interviews and collect blood and other specimens for research on request., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

JCVI GenProp
type: Resource
type: NamedIndividual
has db xref: nlx_58176
synonym: Genome Properties
synonym: Genome Properties Database
synonym: JCVI CMR Genome Properties
IAO_0000115: The Genome Properties system consists of a suite of Properties which are carefully defined attributes of prokaryotic organisms whose status can be described by numerical values or controlled vocabulary terms for individual completely sequenced genomes. The system has been designed to capture the widest possible range of attributes and currently encompasses taxonomic terms, genometric calculations, metabolic pathways, systems of interacting macromolecular components and quantitative and descriptive experimental observations (phenotypes) from the literature. You may search the Genome Properties Database in 1 of 3 ways: * Search For Predicted Properties in the CMR: The Genome Property Search allows you to search the Genome Property database for state information for selected genomes and properties. * Perform a Keyword Search for a Specific Property: Lists all Genome Properties that match a specific text string. You can choose to search All Fields within a genome property or the Property Name. * Browse Top Level Genome Properties: Click on the properties to see the specific genome property report page. The Genome Properties system presents key aspects of prokaryotic biology using standardized computational methods and controlled vocabularies. Properties reflect gene content, phenotype, phylogeny and computational analyses. The results of searches using hidden Markov models allow many properties to be deduced automatically, especially for families of proteins (equivalogs) conserved in function since their last common ancestor. Additional properties are derived from curation, published reports and other forms of evidence. Genome Properties system was applied to 156 complete prokaryotic genomes, and is easily mined to find differences between species, correlations between metabolic features and families of uncharacterized proteins, or relationships among properties.

WSDbfetch (SOAP)
type: Resource
type: NamedIndividual
has db xref: nlx_58252
synonym: WSDbfetch
IAO_0000115: WSDbfetch is a webservice implementation of Dbfetch, a generic DB retrieval system that allows you to retrieve entries from various up-to-date biological databases using entry identifiers or accession numbers. It aims to provide programmatic access for sequence retrieval. This involves a service running on a SOAP server responding to remote client invocations. This is equivalent to the CGI based dbfetch service and like the CGI service a request can return a maximum of 200 entries.

Bio-Options
type: Resource
type: NamedIndividual
has db xref: nlx_58415
synonym: BIO - OPTIONS
abbrev: BIO-OPTIONS
IAO_0000115: BIO - OPTIONS provides human tissues and biological materials to researchers and scientists for molecular and genomic research. These high quality, well characterized biological specimens are available for drug and biomarker discovery, validation of drug targets and development of diagnostic tests and devices. BIO - OPTIONS specializes in providing fresh tumor tissue, blood and other biological fluids delivered the same day or overnight for your studies. We collect specimens from virtually all disease states through our extensive network of physicians, hospitals, and clinical laboratories. All of our specimens are collected at facilities located in the United States in compliance with all applicable federal and state laws and regulations and ethical guidelines. Collection facilities are located on the East and West coasts and Midwest. The officers of BIO - OPTIONS consist of licensed physicians with extensive medical training and experience. This enables us to work directly with physicians and support staff to insure that collection protocols provide the high quality specimens needed for research without compromising patient care. Protocols are designed to work within the workflow of physician offices and hospital operating rooms so that specimens are timely processed and preserved and well characterized.

EyeWiki
type: Resource
type: NamedIndividual
has db xref: nlx_58463
IAO_0000115: EyeWiki is an ophthalmic wiki where ophthalmologists, other physicians, patients and the public can view an eye encyclopedia of content written by ophthalmologists covering the vast spectrum of eye disease, diagnosis and treatment. Any qualified ophthalmologist, or ophthalmologist in training, is invited to contribute content to the wiki and post it immediately. Categories: *Cataract / Anterior Segment *Cornea / External Disease *Glaucoma *Miscellaneous *Neuro-ophthalmology / Orbit *Oculoplastics / Orbit *Oncology / Pathology *Pediatric Ophthalmology / Strabismus *Refractive Management / Intervention *Retina / Vitreous *Uveitis

Cancer Center Tissue Bank - Fudan University
type: Resource
type: NamedIndividual
has db xref: nlx_59788
synonym: Institutional Tissue Bank of Fudan University Shanghai Cancer Center
synonym: ITB of FUSCC
synonym: Tissue bank of FUSCC
abbrev: ITB
IAO_0000115: The Institutional Tissue Bank (ITB) of Fudan University Shanghai Cancer Center was established in 2006 with the goal of serving as a central repository for human tissue samples for cancer research and possible personalized medicine for the institution. The Institutional Research Board oversees the fulfilling of informed consent of each patient whose samples are collected. The ITB''s collection procedures meet the global quality standards and provide high quality tissue samples. The quality control for morphology, RNA, DNA and protein has been set up to ensure the sample quality. Routine frozen section from tissue aliquot is made for every piece of sample to ensure the component of tumor tissue and the pathological feature is the same as the diagnosed tumor. Agilent 2100 Bioanalyzer was used to provide RNA and DNA quality parameters. The Tissue Bank occupies 500 m2, with sufficient space for sample preparation and storage, data registration, data tracking/access, related equipments and monitor system. Variant samples including blood, tumor tissue, and body fluids are collected and serve as alternative permanent patient tissue records. Annotation of collected samples is captured through linking the medical record and pathological report system to tissue bank software. Frequent tumor types such as lung cancer, breast cancer, gastric cancer, urological tumors, gynecological tumors and esophageal cancers, head & neck cancers, as well as infrequent cancer types such as malignant soft tissue sarcomas, pancreatic cancer, gall bladder cancer, and other rare cancers are all collected and stored. Tumor tissues are stored with matched normal tissues. Serum and plasma are isolated from coagulation plus and coagulation minus blood samples. White blood cells are stored as well. Tissues are stored both in RNALater at -20 degrees C and -80 degrees C after snap frozen. Samples have been increased from 4,000 in 2008 to 10,783 in 2009. To the end of September 2010, over 30,000 samples …

British Columbia Tumour Tissue Repository
type: Resource
type: NamedIndividual
has db xref: nlx_58550
synonym: BC Cancer Agency TTR
synonym: BC Cancer Agency Tumor Tissue Repository
synonym: BC Cancer Agency Tumour Tissue Repository
synonym: BCCA Tumour Tissue Repository
abbrev: BCCA-TTR
abbrev: TTR
IAO_0000115: A provincial biobank resource to support translational cancer research at the BC Cancer Agency, across Canada and internationally. This biobank collects biospecimens (tissues and blood), and clinical information and processes these to create anonymous cases that can be studied by cancer researchers to understand how cancer develops, how it grows, how it spreads, and how it responds to treatment. These tissues and data are obtained from patients who undergo surgery to treat a tumor and who have generously provided their consent for the TTR to collect tissues that are unused after diagnosis has been completed. The TTR is a provincial program that currently comprises a core biobank at the Vancouver Island Center, Victoria, that offers participation in the program to patients in Victoria and Nanaimo. The TTR works with other banks and expert translational research groups in BC, to create expanded capacity for collection and opportunities for research access to tissue resources. The TTR operates under the management and oversight of the director, a scientific advisory board, and the UBC BCCA Research Ethics Board. The TTR operates within organizational policies and a commitment to protection of donor privacy that is embodied in all standard operating procedures and aspects of the repository. The TTR is also a founding member and contributor to the development of provincial (BC BioLibrary) and national (CTRNet) initiatives to promote biobanking.

BioReliance Biorepository
type: Resource
type: NamedIndividual
has db xref: nlx_58806
IAO_0000115: The BioReliance Biorepository offers secure cell storage of eukaryotic, prokaryotic and viral biological materials. Our vapor phase liquid nitrogen and -80����??C freezers offer complete flexibility and protection. Each bank is certified free from mycoplasma and tested for sterility prior to storage and then divided and stored in separate validated vessels. Our continuously monitored facilities in US and UK follow cGMP.

MetaCluster-TA
type: Resource
type: NamedIndividual
has db xref: OMICS_01473
IAO_0000115: A software for binning and annotating short paired-end reads.

Neuroscience News
type: Resource
type: NamedIndividual
has db xref: nlx_143830
synonym: Neurosciencenews
synonym: NeuroscienceNews.com
IAO_0000115: Science website dedicated strictly to neuroscience research news including brain research news, neuroscience jobs, neuroscience forums, social network, student resources and events. They scour news sources every weekday and choose only neuroscience research related news headlines and links to post. They attempt to link to the original neuroscience research news release as much as possible to enable readers to bypass opinion and get straight to the news. In a few cases, the original neuroscience research article is not available without registration, so they will link to a secondary source to ensure that readers get the neuroscience news as soon as possible. Neuroscience News staff encourages visitors to submit neuroscience research articles, brain research news, neuroscience article reviews, breaking neuroscience news tips, original neuroscience blog posts, neuroscience book reviews and suggestions to be reviewed, implemented and possibly published on Neuroscience News.

Neuroscience News: Neuroscience Jobs
type: Resource
type: NamedIndividual
has db xref: nlx_143832
abbrev: Neuroscience Jobs
IAO_0000115: Database listing of jobs where neuroscience students, neuroscience research professionals, neuroscience professors and anyone looking for a neuroscience job can use the interface to find jobs in their area or post neuroscience jobs needing to be filled. Neuroscience News members are encouraged to use the resources for neuroscience job information and also consider joining up to our Neuroscience Jobs Group. Members of the Neuroscience Jobs group are allowed to post jobs available and job positions sought. Neuroscience jobs offers, job listings, neuroscience resumes, networking and more can be found in the group.

SI622 Project evaluation service
type: Resource
type: NamedIndividual
has db xref: nlx_59642
synonym: SI 622 Course Projects
IAO_0000115: SI 622 is a Masters-level Human-Computer Interaction course taught in the School of Information at the University of Michigan on a yearly basis during the Winter semester. Students learn and apply a number of methods for assessing the usability and usefulness of interactive systems such as websites or software applications. The course is based around a semester-long group project in which groups of 3-4 students select a system to study and then proceed to conduct a series of evaluations and other analyses, generating reports and recommendations along the way. If you would like to obtain a free, high-quality assessment of your website or software product, you can submit a proposal for a course project. If a student group chooses your project, they will perform a series of evaluations of your product and give you detailed and actionable feedback on the usability problems they find.

DELLY
type: Resource
type: NamedIndividual
has db xref: biotools:delly2
has db xref: OMICS_00313
synonym: Structural variant discovery by integrated paired-end and split-read analysis
IAO_0000115: Integrated structural variant prediction software that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout genome.

New York Firefighters Skin Bank
type: Resource
type: NamedIndividual
has db xref: nlx_59846
synonym: New York Firefighter''s Skin Bank
IAO_0000115: Established nearly 30 years ago, the New York Firefighters Skin Bank is the only comprehensive skin bank in New York State, providing allograft skin grafts to patients throughout the region. Allograft skin grafts enable burn victims to fight infection, maintain their fluids and body heat, and control pain. The Skin Bank also provides cryopreservation services so that patients can bank their own skin for future autologous transplantation.

GSDS - Golden State Donor Services
type: Resource
type: NamedIndividual
has db xref: nlx_60283
synonym: Golden State Donor Services
abbrev: GSDS
IAO_0000115: Golden State Donor Services (GSDS) is the nonprofit, federally designated transplant donor network serving two and a half million people in the greater Sacramento area. We are committed to saving and improving lives by connecting one life to another through donation and transplantation. We support potential donor families in their time of loss, provide care for them through the donation process and coordinate the recovery of organs and tissues for transplant. We also provide after-care support to donor families while at the same time working to inspire universal acceptance of donation to ensure every person in need receives the ����??Gift of Life.����?? GSDS'' designated service area includes 11 counties in Northern California, (Amador, Calaveras, Colusa, El Dorado, Nevada, Placer, Sacramento, Sierra, Sutter, Yolo, and Yuba), as well as the communities of Santa Rosa and Reno. Currently GSDS has agreements with 30 hospitals. In Golden State Donor Services'' area, more than 1000 people now wait for an organ transplant, (heart, liver, lungs, kidneys, intestine or pancreas).

Ganfyd - Get A Note From Your Doctor
type: Resource
type: NamedIndividual
has db xref: nlx_60295
synonym: ganfyd
synonym: ganfyd.org
abbrev: GANFYD
IAO_0000115: Simply put ganfyd is an evolving textbook of medicine: a free medical knowledge base that anyone can read and any registered medical practitioner may edit. This collaborative medical reference by medical professionals and invited non-medical experts is based around the wiki format, enabling true sharing of knowledge. Please join and help us to create a great source of information and experience! Ganfyd is the first of its type and relies on your contributions to make it a truly world-class resource. Contents: * Medical Specialties * Surgical Specialties * Primary Care * Public Health * Laboratory-based specialties * Imaging Specialties * Basic Medical Sciences * Miscellaneous * Women''s health * Survival Guides * How-tos & Practical Advice * Resources for Trainees * Computing * Medical Dictionary

The Scientist
type: Resource
type: NamedIndividual
has db xref: nlx_60297
synonym: The Scientist: Magazine of the Life Sciences
synonym: TheScientist
IAO_0000115: The Scientist is the magazine for life science professionalsa print and digital publication dedicated to covering a wide range of topics central to the study of cell and molecular biology, genetics, and other life-science fields. Through innovative print articles, online stories, and multimedia features, the magazine explores the latest scientific discoveries, trends in research, innovative techniques, new technology, business, and careers. It is read by leading researchers in industry and academia who value penetrating analyses and broad perspectives on life-science topics both within and beyond their areas of expertise. Written by prominent scientists and professional journalists, articles in The Scientist are concise, accurate, accessible, and entertaining.

QuickGO
type: Resource
type: NamedIndividual
has db xref: biotools:quickgo
has db xref: nlx_60318
has db xref: OMICS_02276
synonym: Quick GO
IAO_0000115: A web-based browser for Gene Ontology terms and annotations, which is provided by the UniProtKB-GOA group at the EBI. It is able to offer a range of facilities including bulk downloads of GO annotation data which can be extensively filtered by a range of different parameters and GO slim set generation. The software for QuickGO is freely available under the Apache 2 license. QuickGO can supply GO term information and GO annotation data via REST web services.

UK Multiple Sclerosis Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_60486
abbrev: UK MS Tissue Bank
IAO_0000115: Procures brain, spinal cord and other tissues bequeathed by donors and makes them available to scientists investigating the cause and treatment of multiple sclerosis. The Tissue Bank achieves this aim by addressing the following objectives: # Increasing the awareness of the importance of human tissue to research amongst the MS and scientific communities. # Being sensitive to the needs of the tissue donor and responsive to the requirements of scientists when collecting and processing donated tissue. # Making available high quality, well-documented samples of tissue to research scientists working to better understand MS. There are approximately 85 000 people with multiple sclerosis in the United Kingdom. The varied symptoms experienced by all these people result from damage taking place within their brain and spinal cord. Understanding the exact nature of this damage is essential if we are to better treat the condition. Vital information about how the brain and spinal cord are damaged in multiple sclerosis can be obtained by using a multitude of experimental approaches to study the affected tissue from people with MS and ''control'' tissue from people without the disease. The donation of tissue for research is therefore fundamental to furthering our understanding of the causes of multiple sclerosis and to developing more effective treatments for the disease. The UK Multiple Sclerosis Tissue Bank welcomes requests for tissue samples for use in research into the cause and treatment of multiple sclerosis. It has available post mortem, cryopreserved brain and spinal cord tissue both fixed and unfixed, and cerebrospinal fluid from patients with and without a history of multiple sclerosis. Freshly dissected tissue samples, or those preserved using unconventional techniques may also be made available by prior arrangement.

UCL/UCLH Biobank for Studying Health and Disease
type: Resource
type: NamedIndividual
has db xref: nlx_143838
synonym: UCL / UCLH Biobank for Studying Health Disease
synonym: UCL Biobank for studying Health Disease
synonym: UCL/UCLH Biobank for Studying Health Disease
abbrev: UCL Biobank for studying Health and Disease
IAO_0000115: The UCL/UCLH Biobank for Studying Health and Disease has been primarily established to support the Research Programme and scientific needs, of the Pathology Department UCLH & the UCL Cancer Institute. The establishment of the core programme enables a centralised approach to the management and integration of all research groups working within these institutions, providing appropriate structure and support. The biobank has policies and guidelines to guarantee compliance with HTA legislation and to ensure quality standards will be maintained. The biobank stores normal and pathological specimens, surplus to diagnostic requirements, from relevant tissues and bodily fluids, as well as human tissue used in xenograft experiments. Stored tissues include; snap-frozen or cryopreserved tissue, formalin-fixed tissue, paraffin-embedded tissues, and slides prepared for histological examination. Tissues include resection specimens obtained surgically or by needle core biopsy. Bodily fluids include; whole blood, serum, plasma, urine, cerebrospinal fluid, milk, saliva and buccal smears and cytological specimens such as sputum and cervical smears. Fine needle aspirates obtained from tissues and bodily cavities (eg. pleura and peritoneum) are also collected. Where appropriate the biobank also stores separated cells, protein, DNA and RNA isolated from collected tissues and bodily fluids described above. Some of the tissue and aspirated samples are stored in the diagnostic archive.

Tumorbank Bern
type: Resource
type: NamedIndividual
has db xref: nlx_60955
synonym: Tumor Bank Bern
synonym: Tumorbank Bern - TBB
synonym: Tumorbank Bern TBB
abbrev: TBB
IAO_0000115: Tumorbank Bern - TBB collects high quality clinical samples since 2003 for translational research selected by expert pathologists under controlled conditions of normal and diseased tissue from different origin. The Tumor Bank is approved by the Ethical Commission of Bern, we only collect samples with written informed patient consent. Origin of Tissue: Thoracic Surgery, Gynecology, Urology, Visceral Surgery, Orthopedic Surgery, Head and Neck Surgery, Neurosurgery Tumorbank Bern TBB holds 12,000 samples from 3600 Patients. Please contact us to check if we have samples for your field of research.

OSU College of Pharmacy Bachelor of Science in Pharmaceutical Sciences (BSPS) Program Overview
type: Resource
type: NamedIndividual
has db xref: nif-0000-02101
synonym: OSU Bachelor of Science in Pharmaceutical Sciences
synonym: OSU BSPS Program College of Pharmacy
synonym: OSU College of Pharmacy Bachelor of Science in Pharmaceutical Sciences (BSPS) Program
synonym: OSU College of Pharmacy Bachelor of Science in Pharmaceutical Sciences Program
synonym: OSU College of Pharmacy BSPS
abbrev: OSU BSPS
IAO_0000115: Bachelor of Science in Pharmaceutical Sciences (BSPS) provides training for success in variety of healthcare or research-oriented/non-clinical graduate programs and careers. Emphasizes integrated science learning, hands-on laboratory experiences and career development.

GeneDB Lmajor
type: Resource
type: NamedIndividual
has db xref: nlx_60997
synonym: GeneDB Leishmania major
synonym: Leishmania major strain Friedlin
synonym: Leishmania major strain Friedlin homepage on GeneDB
synonym: Leishmania major strain Friedlin on GeneDB
abbrev: GeneDB L. major
abbrev: GeneDB_Lmajor
IAO_0000115: Database of the most recent sequence updates and annotations for the L. major genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Trypanosomatid research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. Leishmania species cause a spectrum of human diseases in tropical and subtropical regions of the world. We have sequenced the 36 chromosomes of the 32.8-megabase haploid genome of Leishmania major (Friedlin strain) and predict 911 RNA genes, 39 pseudogenes, and 8272 protein-coding genes, of which 36% can be ascribed a putative function. These include genes involved in host-pathogen interactions, such as proteolytic enzymes, and extensive machinery for synthesis of complex surface glycoconjugates. The Pathogen Genomics group at the Wellcome Trust Sanger Institute played a major role in sequencing the genome of Leishmania major (see Ivens et al.) Details of the centres involved and which chromosomes they sequenced, are given. The sequence data were obtained by adopting several parallel approaches, including complete cosmid sequencing, whole chromosome shotguns and/or BAC sequencing/skimming. The Leishmania parasite is an intracellular pathogen of the immune system targeting macrophages and dendritic cells. The disease Leishmaniasis affects the populations of 88 counties worldwide with symptoms ranging from disfiguring cutaneous and muco-cutaneous lesions that can cause widespread destruction of mucous membranes to visceral disease affecting the haemopoetic organs. In collaboration with GeneDB, the EuPathDB genomic sequence data and annotations are regularly deposited on TriTrypDB where they can be integrated with other datasets and queried using customized queries.

IPBIR - Integrated Primate Biomaterials and Information Resource
type: Resource
type: NamedIndividual
has db xref: nlx_143841
synonym: Integrated Primate Biomaterials and Information Resource
synonym: Integrated Primate Biomaterials Information Resource
synonym: IPBIR - Integrated Primate Biomaterials Information Resource
synonym: IPBIR Repository
abbrev: IPBIR
IAO_0000115: The purpose of the IPBIR - Integrated Primate Biomaterials and Information Resource is to assemble, characterize, and distribute high-quality DNA samples of known provenance with accompanying demographic, geographic, and behavioral information in order to stimulate and facilitate research in primate genetic diversity and evolution, comparative genomics, and population genetics. Further research in these areas will advance our understanding of human origins, the biological basis of cognitive processes, evolutionary history and relationships, and social structure, and will provide critical scientific information needed to facilitate conservation of biological diversity. The derived DNA will be openly available to the broad scientific community who agree to restrict use to non-commercial purposes. DNA and cell culture samples are distributed only to qualified professional persons who are associated with recognized research, medical, or educational organizations engaged in research.

Stanford Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_61352
IAO_0000115: The Stanford Tissue Bank was established with seed funding from the Bio-X Program and the Department of Pathology, and currently receives support from the Stanford Cancer Institute. The goal of the Tissue Bank is to facilitate biomedical research using tissues at Stanford, by providing services for the procurement, storage, distribution, and study of tissues. Current Tissue Bank activities and services include collecting and banking freshly-frozen tissue specimens from excess surgical material and from autopsy, providing fresh tissue specimens for viable cell studies, processing and banking blood components, maintaining a tissue database with links to clinicopathological data, performing histological staining and pathological review, and coordinating patient consent and assuring regulatory compliance. As a centralized shared resource, the Tissue Bank adds value through experience, efficiency, standardization, accountability, protection of patient confidentially, and timely completion of research. An oversight committee serves to guide policies, prioritize resources, and review service requests to ensure equitable usage.

BAMS Neuroanatomical Ontology
type: Resource
type: NamedIndividual
has db xref: nlx_61376
synonym: BAMS Ontology
IAO_0000115: Ontology designed for neuroscience. Includes complete set of concepts that describe parts of rat nervous system, growing set of concepts that describe neuron populations identified in different brain regions, and relationships between concepts.

Amino Acid-Nucleotide Interaction Database
type: Resource
type: NamedIndividual
has db xref: nlx_61417
abbrev: AANT
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016. AANT, the Amino Acid-Nucleotide Interaction Database, contains information derived from all of the protein/nucleic acid complexes with experimentally determined structures in the Protein Data Bank. You can visualize the AANT models using the simple web interface, which relies on the Chime plug-in. You can also download these models for further analysis using publicly available tools for manipulating PDB structures. The software that generates AANT uses HBPLUS to predict hydrogen bond interactions between single bases and single amino acid residues within these complexes. The AANT software uses this information to break down a single PDB structure into scores of individual interactions between either the base, sugar, or phosphate of a nucleotide and the side chain or peptide backbone of a amino acid. The software then superimposes all the interactions between a particular moiety of a nucleotide and a particular moiety of a amino acid residue into a single 3D model, centering on a particular point in the base, sugar, or phosphate. The AANT software then groups geometrically similar interactions into clusters.

TAIR
type: Resource
type: NamedIndividual
has db xref: nlx_61477
has db xref: OMICS_01662
has db xref: r3d100010185
synonym: AGI LocusCode
synonym: The Arabidopsis Information Resource
IAO_0000115: Database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive linkouts from data pages to other Arabidopsis resources. The data can be searched, viewed and analyzed. Datasets can also be downloaded. Pages on news, job postings, conference announcements, Arabidopsis lab protocols, and useful links are provided.

CompostBin
type: Resource
type: NamedIndividual
has db xref: OMICS_01472
IAO_0000115: A DNA-composition-based binning algorithm for classifying metagenomic reads. It has the ability to accurately bin raw sequence reads without need for assembly or training. It applies principal component analysis to project the data into an informative lower-dimensional space, and then uses the normalized cut clustering algorithm on this filtered data set to classify sequences into taxon-specific bins.

IntegromeDB
type: Resource
type: NamedIndividual
has db xref: nlx_63198
synonym: Integrome DB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016. Search engine that integrates over 100 curated and publicly contributed data sources and provides integrated views on the genomic, proteomic, transcriptomic, genetic and functional information currently available. Information featured in the database includes gene function, orthologies, gene expression, pathways and protein-protein interactions, mutations and SNPs, disease relationships, related drugs and compounds.

HD Community BioRepository
type: Resource
type: NamedIndividual
has db xref: nlx_143842
synonym: HD Community
IAO_0000115: HD Community BioRepository is a secure, centralized repository that stores and distributes quality-controlled, reliable research reagents. This repository currently provides access to huntingtin DNAs, polyclonal antibodies (with antigenic peptides) and cell lines. Monoclonal antibodies and hybridomas will be added in the near future. Working together with the Coriell Institute for Medical Research, CHDI Foundation established this secure, centralized repository to store and distribute quality-controlled and reliable research reagents to give research scientists unobstructed access to biomaterials and to support the discovery of therapeutics that will slow or prevent Huntington's disease. Huntington's disease is a fatal, familial disease caused by a mutation in the huntingtin gene. The mutation causes brain cells to malfunction, resulting in cognitive and physical impairments that, over the course of the disease, isolate and constrain the individual. There is currently no way to stop or reverse the course of Huntington's disease. Researchers currently not collaborating with CHDI Foundation may request these Huntington's disease resources from the HD Community BioRepository through the website; CHDI collaborators are asked to contact Mithra Mahmoudi at CHDI Management. Materials will be sent after completing a simple online MTA. Recipients are asked to cover the costs of shipping and handling. Persons with Huntington's disease bioresources interested in making them available to the research community through the HD Community BioRepository should also contact CHDI Management.

CHDI Foundation
type: Resource
type: NamedIndividual
has db xref: nlx_143844
synonym: CHDI Foundation Inc
abbrev: CHDI
IAO_0000115: A private, not-for-profit research organization that serves as an international collaborative enabler in order to discover drugs that slow the progression of Huntington's disease (HD). The activities of CHDI extend from exploratory biology to the identification and validation of therapeutic targets, and from drug discovery and development to clinical studies and trials. CHDI works with biotech and pharmaceutical companies and funds and works with academic HD researchers at universities.

Autism Research Resource
type: Resource
type: NamedIndividual
has db xref: nlx_143845
synonym: Autism Resource
synonym: The Autism Research Resource
IAO_0000115: A genetic resource to support the study of autism in families where more than one child is affected or where one child is affected and one demonstrates another significant and related developmental disorder. An open bank of anonymously collected materials documented by a detailed clinical diagnosis forms the basis of this growing database of information about the disease. The Autism Resource is housed at the Coriell Institute for Medical Research in New Jersey, which holds the world''s largest collection of human cells for use in genetic research. The Autism Research Resource has been built through a full collaboration between Coriell and clinical services at the UMDNJ-Robert Wood Johnson Medical school, New Brunswick campus, which provides clinical information and diagnosis. All clinical interviews were conducted face-to-face. Further multiplex families will be added to the resource in a continuing program of diagnosis and Repository development. The Autism Research Resource includes cell lines and DNA from families with more than one child who meets criteria for autistic disorder. An additional group of families is included in which monozygotic twins meet all criteria for autistic disorder. Also included in this resource, however, are families in which one child meets the criteria for autistic disorder while another child displays behavior with a broader phenotype of falling within the spectrum of autistic disorder. A small number of multiplex families is included in which one child meets all criteria for autistic disorder and a second has a behavioral disorder falling outside the autism spectrum. Pedigrees are provided for each family. Where clinical statements are noted for individuals other than the affected children and parent(s), these should be judged as reported. All family relationships have been verified by confirming the molecular identities, established using a panel of six microsatellite markers.

Yerkes Collection Non-Human Primate Resource
type: Resource
type: NamedIndividual
has db xref: nlx_143848
abbrev: Yerkes Repository
IAO_0000115: The Yerkes National Primate Research Center of Emory University is an international leader in biomedical and behavioral research. For more than seven decades, the Yerkes Research Center has been dedicated to advancing scientific understanding of primate biology, behavior, veterinary care and conservation, and to improving human health and well-being. The Yerkes Non-Human Primate Resource at Coriell includes viable and contaminant-free Pan troglodytes cell cultures and high quality DNA samples derived from these cultures, both subjected to rigorous quality control.

Philius
type: Resource
type: NamedIndividual
has db xref: biotools:philius
has db xref: nlx_62426
IAO_0000115: Web server that predicts protein transmembrane topology and signal peptides. Hidden Markov models (HMM) have been successfully applied to the tasks of transmembrane protein topology prediction and signal peptide prediction. They expand upon this work by making use of the more powerful class of dynamic Bayesian networks (DBN). Their model, Philius, is inspired by a previously published HMM, Phobius, and combines a signal peptide sub-model with a transmembrane sub-model. They introduce a two-stage DBN decoder which combines the power of posterior decoding with the grammar constraints of Viterbi-style decoding. Philius also provides protein type, segment, and topology confidence metrics to aid in the interpretation of the predictions.

Hollings Cancer Center Tissue Biorepository and Research Pathology Services Shared Resource
type: Resource
type: NamedIndividual
has db xref: nlx_62775
synonym: Hollings Cancer Center Tissue Biorepository Research Pathology Services Shared Resource
abbrev: HCC Tissue Biorepository
IAO_0000115: The Hollings Cancer Center Tissue Biorepository & Research Pathology Services Shared Resource provides investigators with a centralized infrastructure that promotes biomedical research involving the use and study of human biospecimens. The shared resource is comprised of four integrated components: Biospecimens and data bank, Laser Capture Microdissection, Tissue Microarray, and Research Pathology Services. These components, along with extensive staff expertise, offer a comprehensive means by which researchers can utilize valuable human biospecimens and cutting edge technology to support basic, translational and clinical research. Services: * Biospecimen and Data Bank ** Collecting, processing, and banking of tissue, saliva, urine, blood, plasma, serum, and other tissue derivatives; including those for protocol driven studies ** Retrieval of banked specimens linked to clinicopathologic data, while maintaining patient confidentiality, for research use ** Quality control of collected tissue by the Tissue Biorepository Director, a trained pathologist: verification of diseased state and assessment of tumor purity, etc ** Quality control of DNA/RNA/protein isolated from collected tissue using the Agilent Bioanalyzer * Laser Capture Microdissection ** Identification, localization, and microdissection of targeted cell populations (from human and animal tissue sources) ** Extraction of DNA/RNA/protein from microdissected samples. ** Quality analysis and quality control of isolated nucleic acid using Agilent Bioanalyzer * Tissue Microarray ** Create custom and standard TMAs ** Consultation and technical support in the construction and analyses of TMA * Research Pathology Services ** Macrodissection of tissue prior to isolation of DNA/RNA/protein to increase tumor purity ** Immunohistochemistry and In-situ hybridization ** Quantitative image analysis on conventional and TMA sections, including tissue scoring, Ki-67 labeling index, microvascular density counting, and tissue mi…

Center for Cancer Research
type: Organization
type: NamedIndividual
has db xref: grid.417768.b
has db xref: ISNI: 0000 0004 0483 9129
has db xref: nlx_inv_1005030
abbrev: CCR
abbrev: RC
IAO_0000115: funding opps.asp

Washington Regional Transplant Community - WRTC
type: Resource
type: NamedIndividual
has db xref: nlx_62810
synonym: Washington Regional Transplant Community
abbrev: WRTC
IAO_0000115: Founded in 1986, Washington Regional Transplant Community (WRTC) is federally designated as the organ procurement organization (OPO) for Washington, DC, Northern Virginia and suburban Maryland since 1988. This non-profit organization provides full-service organ, tissue and eye recovery. WRTC responds to potential donors at more than 44 area healthcare institutions and serves approximately 5.13 million Washington-area residents. It coordinates with all five area transplant centers and the United Network for Organ Sharing (UNOS). WRTC provides support to more than 4,000 donor family members and acts as the community and professional education resource for organ and tissue donation in the Washington, DC, region.

Nonpareil
type: Resource
type: NamedIndividual
has db xref: OMICS_01419
IAO_0000115: Estimate average coverage and create Nonpareil curves for metagenomic datasets.

Nucleotide database
type: Resource
type: NamedIndividual
has db xref: nlx_62971
has db xref: SCR_016578
abbrev: nucest
IAO_0000115: Nucleotide database as collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.

Compugen
type: Organization
type: NamedIndividual
has db xref: grid.418916.3
has db xref: ISNI: 0000 0004 0506 4804
has db xref: nlx_63124
has db xref: Wikidata: Q5157220
synonym: Compugen Ltd
abbrev: CGEN
IAO_0000115: Drug discovery company providing pharma with protein and antibody therapeutics in the fields of Oncology and Immunology.

Vanderbilt BioVU
type: Resource
type: NamedIndividual
has db xref: nlx_63125
synonym: BioVU DNA Databank
synonym: BioVU: Vanderbilt''s DNA Databank
synonym: BioVU: Vanderbilts DNA Databank
abbrev: BioVU
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. BioVU is a research resource providing a View into biology at the level of DNA and other important macromolecules. BioVU has two major components. The first is a repository of DNA samples (extracted from discarded blood samples) that are coded solely by a Research Unique Identifier (RUI) derived from the Medical Record Number (MRN) using a one-way hash function. This is a computer algorithm that creates a transformation of each MRN such that the resulting RUI (which is in this instance is a 512 byte identifier) is unique, and has the property that it is not possible to infer or compute the MRN that generated it. As of early 2009, over 50,000 DNA samples were in the biobank, with new samples being added at the rate of approximately 700 per week. The second component of the resource is the creation of a database known as the Synthetic Derivative which is a collection of de-identified information extracted from VUMC''s electronic clinical information systems, indexed by the same one-way RUI used to track samples, and with content changed by deletion or permutation of all identifiers contained within each record. The Synthetic Derivative search interface is available to Vanderbilt researchers via the StarBRITE research portal created and maintained by the Vanderbilt Institute for Clinical and Translational Research. This user interface enables investigators meeting protocol approval criteria and other user agreement requirements to receive protocol-specific sets of data derived from DNA samples and from the Synthetic Derivative., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Jackson Laboratory
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100005946
has db xref: grid.249880.f
has db xref: ISNI: 0000 0004 0374 0039
has db xref: nlx_63162
synonym: Jackson Lab
synonym: JAX Lab
abbrev: JAX
IAO_0000115: An independent, nonprofit organization focused on mammalian genetics research to advance human health. Their mission is to discover the genetic basis for preventing, treating, and curing human disease, and to enable research for the global biomedical community. Jackson Laboratory breeds and manages colonies of mice as resources for other research institutions and laboratories, along with providing software and techniques. Jackson Lab also conducts genetic research and provides educational material for various educational levels.

FslAtlasIntegration
type: Resource
type: NamedIndividual
has db xref: nlx_144317
IAO_0000115: FslAtlasIntegration is a documentation site for FSL coordinate reporting and atlas integration. Links to references are available to internal FMRIB systems. Some of this material is drawn from Matthew Brett' '''s webpages on MNI-Talairach Atlas Differences and Localization in Brain Mapping. http://www.mrc-cbu.cam.ac.uk/Imaging/Common/mnispace.shtml

SAS - Sequence Annotated by Structure
type: Resource
type: NamedIndividual
has db xref: nlx_63340
synonym: Sequence Annotated by Structure
abbrev: SAS
IAO_0000115: SAS is a tool for applying structural information to a given protein sequence. It uses FASTA to scan a given protein sequence against all the proteins of known 3D structure in the Protein Data Bank (PDB). The resultant multiple alignment can be colored according to different structural features and the matching 3D structures can be superimposed and viewed in RasMol. Use the form to identify your protein sequence of interest by: a) providing a PDB code, b) providing a UniProt code or accession number, c) pasting in your sequence, or d) uploading a PDB file. By default the whole PDB will be searched, but you can restrict the search using the Search Option box at the bottom.

BioPig
type: Resource
type: NamedIndividual
has db xref: biotools:biopig
has db xref: OMICS_01225
IAO_0000115: Software providing a framework for genomic data analysis using Apache Pig and Hadoop.

Central England Haemato-Oncology Research Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_63387
synonym: Central England Haemato-Oncology Research Biobank (CEHRB)
abbrev: CEHRB
IAO_0000115: The Central England Haemato-Oncology Research Biobank stores excess material from oncology samples referred for diagnostic testing and disease monitoring at the West Midlands Regional Genetics Laboratory (WMRGL). The bank is housed within the WMRGL. Types of material stored include viable cells, fixed cell suspensions, DNA, RNA / cDNA, and plasma. The material is made available to all cancer research groups both locally and nationally. Excess sample (mainly from blood and bone marrow) is stored from diagnostic patient material and from samples received throughout their disease course. The WMRGL serves a population of about 5.5 million and is the largest UK NHS genetic Lab. Due to the large patient population CEHRB is able to collate sufficient research material from all classifications of neoplastic haematological disorders including those that are rare.

Johns Hopkins University; Undergraduate Neuroscience Program
type: Resource
type: NamedIndividual
has db xref: nlx_63501
synonym: JHU Undergraduate Neuroscience
synonym: Johns Hopkins University; Undergraduate Program in Neuroscience
IAO_0000115: Undergraduate Program in Neuroscience offers broad overview of field, as well as more advanced training in one of four specialized areas: cellular and molecular, cognitive, computational, or systems neuroscience.

Genethon DNA and Cell Bank
type: Resource
type: NamedIndividual
has db xref: nlx_63525
synonym: Genethon DNA Cell Bank
IAO_0000115: Since its creation in 1990, the mission of the Genethon''s DNA and Cell Bank is to promote advances in genetic research by providing the scientific community with a high quality cell and human tissue products resource. Europe''s leading bank for genetic diseases, it serves the whole of the medical and scientific community. Each year, Genethon''s DNA and Cell Bank: * Produces approximately 2,000 lymphoblastoid cell lines * Performs approximately 3,000 DNA extractions * Prepares primary myoblast and fibroblast cultures from approximately 100 biopsies Genethon has developed a computer database for ensuring sample management and traceability, which has been submitted to and approved by the CNIL. The Genethon DNA and Cell Bank has been AFNOR certified, according to French biological research center standard NF S 96-900. The activities of the DNA and Cell Bank are as follows: * Collecting blood or DNA from patients affected with genetic diseases and their families with the minimum identification data necessary for the monitoring and follow-up of samples. * Processing the samples in order to make them available to the scientific community and perpetuating DNA preservation (serum isolation and DNA extraction), isolating lymphocytes and establishing lymphoblastoid B lines and primary cultures (mainly myoblasts and fibroblasts). * Storing samples for future research and preserving the genetic heritage by ensuring the long-term physical security of the preserved samples. * Distributing samples as necessary for ongoing research while complying with the principles and laws of bioethics and using the best available technologies at minimum cost.All these activities are carried out following Standard Operating Procedures (SOP) validated by the Quality Assurance department at Genethon. The Bank is open to researchers in France or abroad wishing to store samples or use the services provided (extraction, establishment of cell lines etc.). Each sample received at Genethon is coded in o…

University of Michigan Autism and Communication Disorders Center
type: Resource
type: NamedIndividual
has db xref: nlx_63680
abbrev: UMACC
IAO_0000115: At the UMACC our mission is to improve the lives of individuals with autistic spectrum disorders and their families through the education of current and future leaders in the field, research that enhances the understanding of causation, intervention, prevention, and course, and provision of clinical services to individuals, families and the community. At UMACC, research and training initiatives strengthen clinical services by incorporating the latest research findings and sharing this information with families. At the same time, families have the opportunity to be a part of the research studies-and help expand scientific knowledge through their participation.

ResearchGate: Research Jobs
type: Resource
type: NamedIndividual
has db xref: nlx_143851
IAO_0000115: Job board for science professionals worldwide. You may search through international listings in science and research or post your job listing for free. Advanced filters are available and you may also research jobs by field. Currently, fields include: Agricultural Science, Anthropology, Biology, Chemistry, Computer Science, Design, Economics, Education, Engineering, Entertainment and Arts, Geoscience, History, Law, Linguistics, Literature, Mathematics, Medicine, Other, Philosophy, Physics, Political Science, Psychology, Religious Studies, Social Science, Space Science

ModBase
type: Resource
type: NamedIndividual
has db xref: nif-0000-03153
IAO_0000115: A database of three-dimensional protein models calculated by comparative modeling. ModBase is organized into datasets, which are either available to the public, to the academic community, or to specific users. 20 unique amidohydrolase and 41 unique enolase structures have been determined have been included in the database.

University of Michigan Biorepository
type: Resource
type: NamedIndividual
has db xref: nlx_63960
abbrev: MICHER Biorepository
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 24,2025. In 2009, the Medical School and the Michigan Institute for Clinical & Health Research (MICHR) unveiled a new biorepository for U-M researchers in need of a controlled storage environment for biological samples. MICHR is pleased to be able to add to its many services for the research community a centralized biological repository for controlled storage of biological samples, and related services (including DNA, RNA, and other downstream preparation) within the U-M campus. The biorepository, located in the CAP/CLIA-certified Michigan Center for Translational Pathology (MCTP) laboratory at the U-M Traverwood facility on Huron Parkway, will store biologic material, including blood and urine. Sample accessioning and tracking will be accomplished using the caTISSUE suite of programs, and samples will be processed and stored in compliance with CAP/CLIA guidelines. Initially, all samples will be used only with the authorization of the individual investigator who directed the project under which the samples were obtained. Samples will be used in accordance with the relevant informed consent. Long-term plans include federating the database in order to facilitate sharing of data and samples between research teams.

Simons Simplex Collection
type: Resource
type: NamedIndividual
has db xref: nlx_64171
abbrev: SSC
IAO_0000115: Repository of genetic samples from approximately 3,000 families, each of which has one child affected with an Autism Spectrum Disorder (ASD) and parents unaffected with ASD. A central database characterizing all of the study subjects is available to any qualified researcher and biospecimens are freely available to SFARI grant holders, and to other researchers on a modest fee-for-use basis. Each genetic sample will have an associated collection of data that provides a precise characterization of the individual (phenotype). Rigorous phenotyping will maximize the value of the resource for a wide variety of future research projects into the causes and mechanisms of autism. The Simons Simplex Collection is operated by SFARI in collaboration with twelve university-affiliated research clinics.

University of Texas at Dallas School of Behavioral and Brain Sciences
type: Organization
type: NamedIndividual
has db xref: nif-0000-02104
synonym: University of Texas at Dallas School of Behavioral Brain Sciences
synonym: UT Dallas School of Behavioral and Brain Sciences
abbrev: UT Dallas BBS
IAO_0000115: Mission of the School of Behavioral and Brain Sciences is to understand the intersection of mind, brain and behavior; enhance the health, education, and quality of life of children and families; and create and implement technologies and therapies that repair and strengthen human abilities. The School is housed in Green Hall on the main UT Dallas campus in Richardson. It also has satellite research centers and facilities in downtown Dallas.

LMAT
type: Resource
type: NamedIndividual
has db xref: OMICS_02285
synonym: Livermore Metagenomics Analysis Toolkit
IAO_0000115: Open-source software tool to assign taxonomic labels to as many reads as possible in very large metagenomic datasets and report the taxonomic profile of the input sample. The quick "single pass" analysis of every read allows read binning to support additional more computationally expensive analysis such as metagenomic assembly or sensitive database searches on targeted subsets of reads.

Proteopedia - Life in 3D
type: Resource
type: NamedIndividual
has db xref: nlx_64233
abbrev: Proteopedia
IAO_0000115: Free, collaborative 3D, interactive encyclopedia of proteins and other molecules, it collects, organizes and disseminates structural and functional knowledge about protein, RNA, DNA, and other macromolecules, and their assemblies and interactions with small molecules, in a manner that is relevant and broadly accessible to students and scientists. With a free user account, users can edit pages in Proteopedia. Click on the green links to change the 3D image or click and drag the molecules. Categories include Diseases & Related Topics, Enzymes, Gene Expression & Replication, Metabolism, Signaling & Transport, Structural Biology and Miscellaneous. Currently, Proteopedia has 93,912 articles (pages), and 2,366 registered users (May 2013). Among other pages, Proteopedia contains one page (or article) for every entry in the World Wide Protein Data Bank. Proteopedia is updated weekly with new entries shortly after they are released by the Protein Data Bank. Most of these pages, which are titled with a four-character PDB identification code, are seeded automatically to include a default view of the asymmetric unit, the abstract of the publication, green links to sites and ligands, and molecule-specific links to other viewers and databases. When you go to a random page, you nearly always get one of these automatically-seeded, PDB-code-titled pages (click Random Page in the navigation box at the upper left), because of their abundance. In addition to one article about each entry in the Protein Data Bank (PDB identification code-titled articles), there are articles titled with the name of a molecule or a subject, instead of a PDB identification code. Some of these articles that have substantial content are listed at Topic Pages, or you can browse a complete list of articles not titled with a PDB identification code. There are also articles About Macromolecular Structure.

AbundanceBin
type: Resource
type: NamedIndividual
has db xref: OMICS_01471
IAO_0000115: An abundance-based software tool for binning metagenomic sequences, such that the reads classified in a bin belong to species of identical or very similar abundances. AbundanceBin also gives estimations of species abundances and their genome sizes -two important characteristic parameters for a microbial community.

ScienceNOW
type: Resource
type: NamedIndividual
has db xref: nlx_144226
synonym: ScienceNOW - UP TO THE MINUTE NEWS FROM SCIENCE
IAO_0000115: ScienceNOW is science headline news from all realms of science, including biology, genetics, medicine, stem cells, evolution, animals, climate change, the environment, physics, astronomy, and science policy. This free content is produced by Science Magazine''s award-winning team of journalists.

AFTOL
type: Resource
type: NamedIndividual
has db xref: nlx_64804
synonym: Assembling the Fungal Tree of Life
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented Jan 13, 2022; To enhance the understanding of the evolution of the Kingdom Fungi, 1500+ species were sampled for eight gene loci across all major fungal clades, plus a subset of taxa for a suite of morphological and ultrastructural characters with resulting data: AFTOL Molecular Database (generated by WASABI - Web Accessible Sequence Analysis for Biological Inference), Blast search the AFTOL Database (generated by WASABI), AFTOL primers (generated by WASABI), AFTOL primers by species (generated by WASABI), AFTOL alignments, and the AFTOL Structural and Biochemical Database. Users may submit samples to the AFTOL project. AFTOL is a collaboration centered around four universities in the United States: Duke University (Francois Lutzoni and Rytas Vilgalys), Clark University (David Hibbett), Oregon State University (Joey Spatafora), and University of Minnesota (David McLaughlin). Participants throughout the world have donated vouchers, taxon samples, and gene sequences. The aim of the project is to reconstruct the fungal tree of life using all available data for eight loci (nuclear ribosomal DNA: LSU, SSU, ITS (including 5.8s, ITS1 and ITS2); RNA polymerase II: RPB1, RPB2; elongation factor 1-alpha; mitochondrial SSU rDNA, and mitochondrial ATP synthase protein subunit 6). A further objective of this study is to summarize and integrate current knowledge regarding fungal subcellular features within this new phylogenetic framework. The name of the bioinformatic package developed for AFTOL is WASABI which provides an efficient communication platform to facilitate the collection and dissemination of molecular data to (and from) the laboratories and participants. All molecular data can be viewed, downloaded, verified, and corrected by the participants of AFTOL. A central goal of the WASABI interface is to establish an automated analysis framework that includes basecalling of newly generated chromatograms, contig assembly, qual…

Gift of Life Donor Program
type: Resource
type: NamedIndividual
has db xref: nlx_64894
abbrev: Gift of Life
IAO_0000115: Gift of Life Donor Program, the nonprofit organization serving the eastern half of Pennsylvania, southern New Jersey and Delaware, is responsible for recovering and distributing organs and tissues used in life-saving and life-enhancing transplants. Founded in 1974 by the Greater Delaware Valley Society of Transplant Surgeons, Gift of Life is one of the oldest and largest of 58 organ procurement organizations (OPO) in the United States. Gift of Life is part of the nationwide organ and tissue sharing network run by the United Network for Organ Sharing (UNOS). In addition, Gift of Life coordinates life-enhancing tissue transplants for area residents who are in need of corneas for sight-restoring procedures, as well as skin, tissue and bone to repair injuries. Gift of Life partners with 150 acute care hospitals to offer families from around the region the option of donation.

Queen Square Brain Bank
type: Resource
type: NamedIndividual
has db xref: nlx_143854
synonym: Queen Square Brain Bank for Neurological Disorders
synonym: UCL Brain Bank
abbrev: QSBB
IAO_0000115: A brain bank which holds an archive of brains donated by individuals with neurodegenerative disease and others who serve as neurologically normal controls. It specializes in parkinsonian movement disorders, including Parkinson's disease and multiple system atrophy, and holds the national collection of brains donated by individuals with progressive supranuclear palsy (PSP). Recently the collection has been developed to include donated brains from prospectively studied people with familial dementias. The QSBB also banks brains donated by people with dystonia and Gilles de la Tourette syndrome. The Brain Bank aims to provide brain tissue for neuropathological studies and for scientific research both in the UK and worldwide. The large collection of tissue is backed up by clinical documentation and all material is fully evaluated by the neuropathologists at QSBB. Brain tissue is stored as formalin-fixed, wax embedded blocks and is frozen, either at -20 degrees C or at -80 degrees C (flash-frozen). Tissue can be provided as slide-mounted sections, or as small blocks for neurochemistry, proteomics and DNA and RNA analysis. Flash-frozen material has excellent histological preservation and is suitable for in situ hybridization and immunohistochemistry. Case-control studies are matched for post-mortem delay and agonal status and are supplied blind.

chem-bla-ics
type: Resource
type: NamedIndividual
has db xref: nlx_66624
IAO_0000115: Egon Willighagen''s blog deals with chemblaics in the broader sense. Chemblaics (pronounced chem-bla-ics) is the science that uses computers to solve problems in chemistry, biochemistry and related fields. The big difference between chemblaics and areas such as chem(o)?informatics, chemometrics, computational chemistry, etc, is that chemblaics only uses open source software, open data, and open standards, making experimental results reproducible and validatable. And this is a big difference! Egon Willighagen is a postdoctoral research associate at the Karolinska Institute in Stockholm. Open source programming is my main hobby resulting in participation in, amongst many others, Bioclipse, CDK and Jmol. This blog is personal and may not reflect university''s views.

Gene Logic Biorepository and Biobanking
type: Resource
type: NamedIndividual
has db xref: nlx_65731
synonym: Gene Logic Biorepository Biobanking
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 08, 2013. A biorepository containing thousands of biosamples from international pharmas, biotechs, hospitals, medical centers, private physicians and universities. As a part of our custodial activities, we have on-site power generators, extra supplies of liquid nitrogen and regular inspections. Sample tracking is handled by our LIMS system, which is connected to our laboratory service work, ensuring integrity of sample tracking and sample identification. Our biorepository group also handles sample collection kits, constructing kits with relevant tubes, accession sheets and barcode labels. The group also tracks expiration of tubes. Having a biorepository is also major advantage for serving the needs of clinical trials. It decreases costs, as there is lesser need for shipping samples. It mitigates the risk associated with sample transfer and handling. It simplifies trial management, fewer partners to manage. It simplifies chain of custody, sample transfer occurs under a single LIMS at a single site with teams that work together each day. It simplifies processing any sample repeats, no tracking, cost or risks associated with inter-company transfers. We can also supply sample collection kits complete with accession sheets and matched barcode labels.

PSP Association
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100008177
has db xref: grid.481174.f
has db xref: ISNI: 0000 0000 9330 6674
has db xref: nlx_143855
synonym: Progressive Supranuclear Palsy Association
IAO_0000115: The PSP Association is dedicated to the support of people with Progressive Supranuclear Palsy (PSP) and those who care for them. We also support those with the related, but rarer, disease Cortico Basal Degeneration (CBD). We fund research to better understand the possible causes of PSP and CBD, to find ways to achieve earlier and better diagnosis and to develop treatments that could potentially slow down, or even halt, the progression of these diseases. We support patients, families and carers through the services we offer on a UK-wide basis, through our Nurse Specialist helpline, our Local Support Groups, our publications (including the comprehensive Carers'' Information Pack) and our Annual Symposium for carers and therapists. We raise awareness of PSP and CBD on a local and national level and work in partnership with the relevant bodies and umbrella organisations in the UK to seek to make a positive difference to the lives of people with PSP and CBD. Registered charity numbers: England & Wales 1037087 / Scotland: SC041199.

Daily Scan
type: Resource
type: NamedIndividual
has db xref: nlx_144233
synonym: GenomeWeb - The Daily Scan
synonym: The Daily Scan - What''s Worth Reading on the Web
synonym: The Daily Scan from GenomeWeb
IAO_0000115: A roundup of the most interesting mainstream media articles, blog posts, and peer-reviewed literature relevant to genomic and proteomic scientists. Published daily online and by e-mail bulletin.

SeqWright Biorepository
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_65768
abbrev: SeqWright BioRepository
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented on August 17, 2021.Convenient, cost-effective and reliable storage solutions including maintaining, storing and monitoring your biological samples. Avoid costly purchases of ultra-low temperature freezers, sample track…

Telethon Network of Genetic Biobanks
type: Resource
type: NamedIndividual
has db xref: nlx_65989
abbrev: TNGB
IAO_0000115: Network of non profit association of Italian repositories to form catalogue of biospecimens and associated data. Used to collect, process, preserve and distribute biological samples and related clinical data from individuals affected by rare diseases, their relatives or from healthy control individuals, with standards complying with Italian laws and international recommendations. You may browse sample catalogue by diagnosis or use advanced search option. Request for samples is granted only if project is in agreement with TNGB mission and after receiving signed material transfer agreement form.

New York Organ Donor Network - NYODN
type: Resource
type: NamedIndividual
has db xref: nlx_66050
synonym: New York Organ Donor Network
abbrev: NYODN
IAO_0000115: The New York Organ Donor Network is the nonprofit, federally designated organ procurement organization (OPO) for the greater New York Metropolitan area. Established in 1978, the Donor Network is the second largest OPO in the United States, serving a culturally and ethnically diverse population of 13 million people. Working closely with transplant centers and hospitals, we: * Coordinate organ, tissue and eye donation for transplant in the New York region * Educate the public and health care professionals about donation and transplantation * Promote the importance of signing up on the New York State Donate Life Registry. We work closely with 10 transplant centers, more than 90 hospitals, and various tissue and eye banks. The Donor Network is accredited by the Association of Organ Procurement Organizations (AOPO) and a member of the United Network for Organ Sharing (UNOS), which oversees the organ transplant waiting list in the U.S.

Wistar Institute Collection at Coriell
type: Resource
type: NamedIndividual
has db xref: nlx_143856
abbrev: Wistar Collection
IAO_0000115: Collection of cell lines developed by Wistar scientists that includes a group of hybridomas that produce monoclonal antibodies that are useful in influenza research and vaccine development, melanoma cell lines derived from patients with diseases ranging from mild dysplasia to advanced metastatic cancer and a range of human endothelial cell lines.

USIDNET DNA and Cell Repository
type: Resource
type: NamedIndividual
has db xref: nlx_143858
synonym: US Immunodeficiency Network DNA and Cell Repository
synonym: US Immunodeficiency Network DNA Cell Repository
synonym: US Immunodeficiency Network Repository
synonym: USIDNET DNA Cell Repository
abbrev: USIDNET Repository
IAO_0000115: The USIDNET DNA and Cell Repository has been established as part of an NIH-funded program - the US Immunodeficiency Network - to provide a resource of DNA and functional lymphoid cells obtained from patients with various primary immunodeficiency diseases. These uncommon disorders include patients with defects in T cell, B cell and/or granulocyte function as well as patients with abnormalities in antibodies / immunoglobulins, complement and other host defense mechanisms. All samples in this Repository have been de-identified to protect the privacy of the individual donors. The USIDNET also operates a Patient Data Registry in addition to this Repository and certain clinical data relating to a specific sample may be available through the Registry for some of the patient samples in the Repository collection. Materials in the collection are being made available at modest cost to qualified investigators in academic and commercial organizations in an effort to stimulate research to increase understanding of these orphan diseases and to promote development of new treatments. Requestors are required to complete a Statement of Research Intent briefly describing their proposed use of materials obtained from the Repository and must sign an Assurance agreeing to conditions established by USIDNET for distribution of samples from its collection. Requestors wishing to obtain additional clinical data specific to individual samples in the Repository collection must make a separate application for that information to the Registry (see www.usidnet.org) Physicians or Patients wishing to submit cell samples for the Repository collection should first contact Coriell to arrange for the Repository to send them the correct sample collection tubes as well as prepaid mailers for returning the collected sample(s) to Coriell. Separate collection and shipping procedures may be involved depending on how many samples are to be shipped at one time and whether the shipment will involve freshly obtain…

University of Colorado Denver; Colorado; USA
type: Organization
type: NamedIndividual
has db xref: GRID grid.241116.1; ISNI 0000000107903411; Crossref Funder ID 100010346; Wikidata Q1468161
has db xref: nlx_54335
synonym: University of Colorado Denver
synonym: University of Colorado Denver Anschutz Medical Campus
synonym: University of Colorado Denver Anschutz Medical Campus;Colorado; USA
synonym: University of Colorado Health Sciences Center
synonym: University of Colorado Health Sciences Center; Colorado; USA
abbrev: CU Denver
IAO_0000115: University of Colorado Denver is a public research university in Denver. It is part of the University of Colorado system.

UniProt DAS
type: Resource
type: NamedIndividual
has db xref: nlx_66230
synonym: UniProt DAS Reference Server
synonym: UniProt Protein DAS Server
IAO_0000115: The distributed annotation system (DAS) is a client-server system in which a single client integrates information from multiple servers. The UniProt DAS server provides access to sequence and annotation from UniProt, UniParc and IPI. Researchers can then provide annotation of their own results in the context of UniProt annotation, IPI annotation and UniParc cross references through the use of suitable DAS client such as Dasty2, the Ensembl DAS client or SPICE. The server also gives access to Gene Ontology Annotation of UniProt sequences (GOA) and theoretical tryptic digests of protein sequences in UniProt and IPI. An extremely useful resource for users of DAS is the DAS Registration Server that supports registry and discovery of DAS services. The datasources provided by the UniProt DAS server are all registered with this service.

Brain Bank for Autism
type: Resource
type: NamedIndividual
has db xref: nlx_66413
synonym: Brain Bank for Autism & Related Developmental Research
synonym: Brain Bank for Autism and Related Developmental Research
synonym: UK Brain Bank for Autism
IAO_0000115: Encourages and facilitates brain tissue donation for use in the best scientific studies to better understand the biological basis of autism down to the cellular and molecular levels and through that understanding bring about the development of effective interventions for those affected by autism spectrum disorders. To ensure the best co-ordinated use of brain tissue, the UK Brain Bank for Autism works in collaboration with the Autism Tissue Program in the US and shares the same Tissue Advisory board. The Brain Bank for Autism & Related Developmental Research was established in 2009. It is an initiative to develop a similar program in the UK to the Autism Tissue Program, which has been developed in the US since 1998. Our Brain Bank is the first extension outside the US of the Autism Tissue Program and is integrated with it. The Brain Bank is based at Oxford University, where it forms part of the Thomas Willis Oxford Brain Collection. It operates in accordance with all UK legal and ethical requirements. The donation of post-mortem brain tissue for this research program is of fundamental importance to our understanding of the causes of autism and to help us develop more effective diagnostic measures and interventions. A separate brain bank for autism is necessary because we need to understand how, in autism, the brain develops over time and how the brain functions as a whole. However, our Brain Bank will promote close cooperation across all relevant brain banks in order to take the research forward. Our research focuses on: * people within the autism spectrum or their family members * people not affected by autism but who are affected by epilepsy * individuals without autism or epilepsy.

Living Legacy Foundation of Maryland
type: Resource
type: NamedIndividual
has db xref: nlx_66483
synonym: The Living Legacy Foundation
synonym: The Living Legacy Foundation of Maryland
synonym: The LLF
abbrev: LLF
abbrev: LLF of MD
abbrev: The LLF of MD
IAO_0000115: The Living Legacy Foundation is the non-profit organ and tissue donation program serving the state of Maryland, with the exception of three counties (Charles, Montgomery, and Prince Georges). We facilitate the life-saving process of organ and tissue donation, celebrate the generous gifts of organ and tissue donors, support our donor families and educate others about the importance of registering as a donor. Our organization was incorporated in 1990, consolidating the former Maryland Organ Procurement Center and the Maryland Tissue Bank. The U.S. Department of Health and Human Services, Centers for Medicare and Medicaid Services accredits us as an organ procurement organization, and the State of Maryland licenses us as a Tissue Bank. Our tissue bank is accredited by the American Association of Tissue Banks. We are governed by a 25 member Board of Directors, which includes general public members, transplant recipient representatives and donor family members. Our Board also includes transplant physicians, surgeons and administrators from the two Baltimore organ transplant centers (the University of Maryland Medical Center and The Johns Hopkins Hospital).

Beaumont Hospitals Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_66501
abbrev: Beaumont BioBank
IAO_0000115: BioBank is a new Beaumont research center that is focused on developing innovative methods for early detection of disease and personalized treatment plans through leading edge analysis techniques and state of the art technologies. Biomarkers from tissue, blood or fluids, are used to develop the next generation of care management, taking it from bench to bedside. Beaumont BioBank will work to: * collect high-quality biological specimens from any specialty at Beaumont * store, analyze and record specimens in an efficient, organized and accessible manner using leading-edge technologies * connect specialties and specialists with each other across traditional hospital or laboratory departments to provide a multidisciplinary research structure * facilitate translational research that links molecular laboratory techniques that enable us to apply biomarker discoveries to clinical outcome studies in a speedy and direct manner

Central Biomaterial Bank - German Heart Failure Network
type: Resource
type: NamedIndividual
has db xref: nlx_69537
synonym: Competence Network Heart Failure Central biomaterial bank
synonym: Heart Failure Competence Network Central biomaterial bank
abbrev: CNHF Central Biomaterial Bank
IAO_0000115: The goal of this project is the creation of an extensive biomaterials bank. Materials (blood, serum, plasma, DNA) from all patients who participate in studies in the network will be collected for this purpose. The objective is a consistently high quality standard for the processing, storage and management of all samples. The biomaterials bank is an investment in the future by the network. It enables the competence network and the research community in general to acquire new scientific knowledge about the development, progression and prognosis of the different forms of heart failure. Each time a patient is documented in a study in the competence network, blood (EDTA whole blood and serum) is drawn from the patient, sent by post to the central biomaterials bank and processed there in the central incoming sample laboratory according to specified standards. In the first two subsidization periods, a total of 100,000 samples from approximately 10,000 patients was documented and processed (aliquoting, DNA extraction). These samples are stored in climate-controlled rooms used especially for this purpose at the biomaterial bank of the Experimental and Clinical Research Center (ECRC) in Berlin-Buch at temperatures between -20 and -80 degrees C. As the central infrastructure project for all samples, the biomaterials bank is deeply involved in the networking. There are also intensive collaborations with other competence networks (e.g. the Competence Network for Congenital Heart Defects) and biobanks. The biomaterial bank of the Heart Failure Competence Network also participates in domestic and European pilot projects for networking biomaterial banks (BBMRI, ESFRI, etc.). The goal of these projects is to develop uniform methods for sample processing and use.

PXE International Registry and BioBank
type: Resource
type: NamedIndividual
has db xref: nlx_66505
synonym: PXE International Blood and Tissue Bank
synonym: PXE International Registry BioBank
synonym: PXE International Tissue Bank
abbrev: PXE International BioBank and Clinical Data Registry
IAO_0000115: The PXE International BioBank and Clinical Data Registry is the centralized sample repository and registry for pseudoxanthoma elasticum (PXE). It enables translational research and treatment discovery. PXE International, Inc. holds the world' '''s largest collection of blood and tissue from people affected by PXE and their families. It is the only centralized repository for PXE samples in the world. The PXE International BioBank has tens of thousands of samples, including DNA, tissue from every organ in the body, full body donations postmortem, and many special samples such as eyes, urine, breast tumor tissue and so on. The PXE International Clinical Data Registry ties the biological samples to the clinical record and stores self reported data (surveys and questionnaires), medical records (from any specialist), images (CT scans, MRIs and so on) and anything else that can be scanned or typed in. We are using these samples for genetic research ������?? examining the many mutations, the effect of the mutations on the cell and the future of possible interventions. PXE International established the PXE International Blood and Tissue Bank to make certain that your privacy and confidentiality are protected and your samples are available to any approved research project. Researchers interested in either donating PXE DNA, tissue and cell lines or in applying to use material from the bank should call 202.362.9599 or email Sharon Terry.

TaxSOM
type: Resource
type: NamedIndividual
has db xref: OMICS_01468
IAO_0000115: A tool for taxonomic classification of DNA fragments, as they are typically obtained in metagenome projects. The classification is based on taxon-specific DNA base composition characteristics (genomic signatures). Classification of query sequences is achieved by mapping the query sequences to the genomic signatures of sequences with known taxonomic affiliations. The mapping is done via the Self-Organizing Map (SOM) algorithm. TaxSOM offers two modes of operation: * mapping query sequences to a pre-calculated SOM * mapping query sequences to a custom SOM

University of Colorado School of Medicine; Colorado; USA
type: Organization
type: NamedIndividual
has db xref: nlx_77807
synonym: University of Colorado Denver School of Medicine
synonym: University of Colorado School of Medicine
abbrev: CU School of Medicine
IAO_0000115: One of the medical schools in the U.S., consistently ranked among the top in the nation.

Systems Biology Graphical Notation
type: Resource
type: NamedIndividual
has db xref: nlx_66628
abbrev: SBGN
IAO_0000115: The Systems Biology Graphical Notation (SBGN) project aims to develop high quality, standard graphical languages for representing biological processes and interactions. Each SBGN language is based on the consensus of the broad international SBGN community of biologists, curators and software developers. Over the course of its development many individuals, organizations and companies made invaluable contributions to the SBGN through participating in discussions and meetings, providing feedback on the documentation and worked examples, adopting the standard and spreading the word. Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: process diagram, entity relationship diagram and activity flow diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling. A list of software packages known to provide (or have started to develop) support for SBGN notations is available.

USIDNET: US Immunodeficiency Network
type: Resource
type: NamedIndividual
has db xref: nlx_143859
synonym: United States Immunodeficiency Network
synonym: US Immunodeficiency Network
abbrev: USIDNET
IAO_0000115: Research consortium to advance scientific research in the primary immune deficiency diseases (PIDD) and: * Assemble and maintain a registry of patients with primary immunodeficiency diseases to provide a minimum estimate of the prevalence of each disorder in the United States. Provide a comprehensive clinical picture of each disorder and act as a resource for clinical and laboratory research. * Establish a multifaceted mentoring program to introduce new investigators into the field and stimulate interest and research in primary immune deficiency diseases. * Establish an advisory/review committee to maintain a cell/DNA Repository of biologic material from well-characterized PIDD patients for the advancement of scientific research USIDNET operates a large database of patient information for your use. The purpose and scope of this project is to assemble and maintain a registry of residents with primary immunodeficiency diseases. The project was started with the Registry of U.S. Residents with Chronic Granulomatous Disease. Since then, the registry has been expanded and now collects data on all primary immunodeficiency disorders. The following are just a few of the diseases housed in the registry: Chronic Granulomatous Disease, Common Variable Immunodeficiency Disease, DiGeorge Anomaly, Hyper IgM Syndrome, Leukocyte Adhesion Defect, Severe Combined Immunodeficiency Disease, Wiskott-Aldrich Syndrome, X-Linked Agammaglobulinemia Physicians who would like to register their patients or access the registry are encouraged to contact Onika Davis or Lamar Hamilton, USIDNET team, at odavis (at) primaryimmune.org, or lhamilton (at) primaryimmune.org

Capralogics
type: Organization
type: NamedIndividual
has db xref: nlx_152324
synonym: Capralogics Inc.
IAO_0000115: An Antibody supplier

Immune Deficiency Foundation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100003011
has db xref: grid.434854.a
has db xref: nlx_143860
abbrev: IDF
IAO_0000115: National non-profit patient organization dedicated to improving the diagnosis, treatment and quality of life of persons with primary immunodeficiency diseases through advocacy, education and research. One of the greatest challenges faced by individuals diagnosed with primary immunodeficiency disease is finding the right information and resources when they need it. With knowledge and foresight from their personal experience, the Immune Deficiency Foundation (IDF) was founded by families of children with primary immunodeficiency diseases and their physicians to help meet those needs. It is with the spirit and energy of this keen perspective that IDF exists today, thriving as an organization dedicated to individuals living with primary immunodeficiencies. Since 1980, IDF has provided accurate and timely information for the nearly quarter-million Americans who have been diagnosed with a primary immunodeficiency disease. Governed by a Board of Trustees and supported by a Medical Advisory Committee comprised of some of the world''s leading clinical immunologists, as well as hundreds of grassroots volunteers and a compassionate, professional staff IDF has provided individuals and their families with vital knowledge and made tremendous strides in: * Helping the patient and medical community gain a broader understanding of primary immunodeficiency diseases through education and outreach efforts; * Promoting, participating, and funding research that has helped characterize primary immunodeficiency diseases and given patients and physicians substantially improved treatment options; * Addressing patient needs through public policy programs by focusing on issues such as insurance reimbursement, patient confidentiality, ensuring the safety and availability of immune globulin therapy, and maintaining and enhancing patient access to treatment options. Today, thousands of individuals and families affected by primary immunodeficiency diseases depend on IDF for advocacy, education and…

Southeast Tissue Alliance, Inc. - SETA
type: Resource
type: NamedIndividual
has db xref: nlx_66784
synonym: Southeast Tissue Alliance
abbrev: SETA
IAO_0000115: The Southeast Tissue Alliance recovers tissues and provides them to leading tissue processing companies. One of the most important aspects of this process is ensuring that donor families understand tissue donation and are fully supported as they make the gifts that change the lives of others. To promote tissue donation, we also work throughout the community to increase awareness, educate health professionals and further donation-related research. The Southeast Tissue Alliance is accredited by the American Association of Tissue Banks, which ensures that our services are of the highest quality and are provided in the most professional manner.

Multipoint Identical-by-descent Method
type: Resource
type: NamedIndividual
has db xref: nlx_154482
abbrev: MIM
IAO_0000115: Software application using multipoint IBD method for partitioning genetic variance of quantitative traits to specific chromosome regions using data on nuclear families. (entry from Genetic Analysis Software)

National University of Ireland; Galway; Ireland
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100001634
has db xref: grid.6142.1
has db xref: ISNI:0000 0004 0488 0789
has db xref: nlx_149500
has db xref: Wikidata:Q644478
synonym: National University of Ireland
synonym: National University of Ireland Galway
abbrev: NUI Galway
IAO_0000115: Located in the city of Galway in Ireland.

Brain Research Trust
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100000368
has db xref: grid.468558.2
has db xref: ISNI: 0000 0004 0623 3016
has db xref: nlx_143861
IAO_0000115: Brain Research Trust is a Registered Charity (no. 1137560) and a Company Limited by Guarantee (no. 7345516) promoting and supporting vital research. With the help of our donors, Brain Research Trust supports world-class research at University College London' '''s Institute of Neurology (IoN), London. We were able to provide a record 2.3m pounds to research grants in the 09/10 financial year and has been supporting its vital research program for almost 40 years. Brain Research Trust comprises a dedicated fundraising team, a supportive Board of Trustees and a knowledgeable Scientific Advisory Panel who all work together closely to ensure your money goes towards the best neurological research projects. Some of the conditions into which we fund research include: Alzheimer' '''s Disease, Ataxia, Brain Tumours, Creutzfeldt-Jakob Disease, Dystonia, Epilepsy, Huntington' '''s Disease, Migraine, Motor Neurone Disease, Multiple Sclerosis, Parkinson' '''s Disease, Progressive Supranuclear Palsy, Stroke. The Institute of Neurology also carries out research into Autism, Aphasia, Guillain-Barre Syndrome, M��ni��re' '''s Disease, Multiple Systems Atrophy (MSA), Myasthenia Gravis, Niemann-Pick Disease, Shy-Drager Syndrome, Tay-Sachs Disease and Tourette Syndrome.

National Biobank of Finland
type: Resource
type: NamedIndividual
has db xref: nlx_67744
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023.To guarantee the top level of expertise in modern genetic and biological analyses, we have built an infrastructure that facilitates the collection of genome-wide information on the genetic background of diseases as well as functional information on the molecules that are critical in the disease process. Furthermore we have established the necessary storage, database and computational resources for the expert analyses of the massive amount of collected biological information. Our scientific expertise, technology platforms and large nationwide sample collections facilitate a highly competitive environment for research and education in molecular medicine of the 21st century. The biobanking wet lab effort is concentrated to KTL/Biomedicum Large scale DNA extraction and storage facility. The facility presently houses DNA from more than 200 000 individuals and is co-ordinated by National Public Health Institute. It is equipped with state of the art bar coding system for sample tracking, an automated Gentra DNA extraction equipment, liquid handling robots, storage facilities, and tailor made data management tools for optimal confidentiality and quality control.

CDC Cell and DNA Repository
type: Resource
type: NamedIndividual
has db xref: nlx_143863
synonym: Centers for Disease Control and Prevention Cell and DNA Repository
IAO_0000115: A repository which houses DNA samples prepared from reference cell lines and are available for use in molecular genetic testing. The CF samples contain mutations associated with unique populations, combinations of IVS8 poly-thymidine tract variants, and mutations not previously available. Three DNA samples with homozygous MTHFR-related mutations are available. Hemochromatosis-associated samples include a compound HFE heterozygote and other combinations of HFE alleles. DNA samples with triplet repeats at the intermediate-range are available for HD and Fragile X syndrome. Mutations were confirmed in all cell lines from which the DNA has been prepared by reference testing and multi-laboratory pilot testing. Control DNA samples negative for all mutations are also available. Laboratories are encouraged to contact Coriell Cell Repositories to inquire about obtaining samples or donating samples as possible candidates for transformation.

CalBioreagents
type: Organization
type: NamedIndividual
has db xref: nlx_152323
IAO_0000115: An Antibody supplier

ILSbio
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_68031
synonym: ILSbio LLC
synonym: ILSbio LLC (Integrated Laboratory Services - Biotech)
synonym: ILSbio: Wolrd''s Most Comprehensive Tissue Collection Network
synonym: Integrated Laboratory Services - Biotech
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented on August 17, 2021.Biospecimens and support services to advance translational research including a wide range of specimen types, including matched sets of normal and diseased tissue, Formalin-Fixed, Paraffin-Embedded (…

Mouse Brain Architecture Project
type: Resource
type: NamedIndividual
has db xref: nlx_146201
synonym: MBA Project
synonym: Mouse Brain Architecture
IAO_0000115: An atlas project whose goal is to enerate brainwide maps of inter-regional neural connectivity that specify the inputs and outputs of every brain region, at a "mesoscopic" level of analysis. A 3D injection viewer is used to view the mouse brain. To determine the outputs of a brain region, anterograde tracers are used which are taken up by neurons locally ("the input"), then transported actively down the axons to the "output regions." The whole brain is then sliced thinly, and each slice is digitally imaged. These 2-D images are reconstructed in 3D. The majority of the resulting 3-D brain image is unlabeled. Only the injected region and its output regions have tracer in them, allowing for identification of this small fraction of the connectivity map. This procedure is repeated identically, to account for individual variability. To determine the inputs to the same brain region as above, a retrograde tracer is injected in the same stereotaxic location ("the input"), and the process is repeated. In order to accumulate data from different mice (each of whom has a slightly different brain shape and size), 3-D spatial normalization is performed using registration algorithms. These gigapixel images of whole-brain sections can be zoomed to show individual neurons and their processes, providing a "virtual microscope." Each sampled brain is represented in about 500 images, each image showing an optical section through a 20 micron-thick slice of brain tissue. A multi-resolution viewer permits users to journey through each brain, following the pathways taken through three-dimensional brain space by tracer-labeled neuronal pathways. A key point is that at the mid-range "mesoscopic" scale, the team expects to assemble a picture of connections that are stereotypical and probably genetically determined in a species-specific manner. By dividing the volume of a hemisphere of the mouse brain into 250 equidistant, predefined grid-points, and administering four different kinds of tracer …

California Cryobank, Inc.
type: Resource
type: NamedIndividual
has db xref: nlx_68136
synonym: California Cryobank
abbrev: CCB
IAO_0000115: Founded in 1977, California Cryobank (CCB) is a full-service sperm bank providing a comprehensive resource for frozen donor sperm, private semen cryopreservation, and specialized reproductive services (including egg and embryo storage and artificial insemination guidance). We are extremely proud of our 30 years of reproductive success. The demand for expert services has grown exponentially as discussion of reproductive challenges has continued to become more mainstream. At California Cryobank we understand that regardless of how much information and education you bring to the process, there can still be significant apprehension accompanying such big steps as sperm donation and donor insemination. CCB''s commitment to making our clients as comfortable as possible is what sets us apart and makes us so much more than just another sperm bank. Our services are entirely patient-centric; from the education that we provide����??answering questions and providing step-by-step timetables that let patients know what to expect in the weeks and months to come from donor sperm selection through insemination����??to the guidance that we offer. Our team is comprised of physicians, lab technicians, genetic counselors, Client Service Consultants, and Donor Matching Consultants. Every facet of our services is completely and expertly led by one of our experienced and compassionate team members. And while our sperm donor program is the foundation of our service, California Cryobank provides a full range of services for our clients including cord blood banking and access to our CCB Sibling Registry.

ETEX Corporation
type: Commercial Organization
type: NamedIndividual
has db xref: nlx_68272
synonym: ETEX Corp
abbrev: ETEX
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Develop, manufacture and market proprietary, nanocrystalline calcium-phosphate-based biomaterials that promote the repair and regeneration of bone damaged by trauma or disease. ETEX focuses on expanding applications through combinations with cells, biologics, or therapeutic agents delivered in minimally invasive and easy to use systems.

Leiomyosarcoma Cell and DNA Repository
type: Resource
type: NamedIndividual
has db xref: nlx_143864
synonym: Leiomyosarcoma Cell DNA Repository
synonym: LMS Cell and DNA Repository
synonym: LMS Cell DNA Repository
synonym: LMS Leiomyosarcoma Cell and DNA Repository
synonym: LMS Leiomyosarcoma Cell DNA Repository
abbrev: LMS Repository
IAO_0000115: The Leiomyosarcoma Cell and DNA Repository has been established with an award from the National Leiomyosarcoma Foundation. This foundation provides leadership in supporting research of Leiomyosarcoma, improving treatment outcomes of those affected by this disease as well as fostering awareness in the medical community and general public. The resources available include highly-characterized, viable, and contaminant-free cell cultures and high quality, well-characterized DNA samples derived from these cultures, both subjected to rigorous quality control. Leiomyosarcoma is a rare form of cancer, which affects about four people in every million. It spreads through the blood stream and can affect the lungs, liver, blood vessels, or any other soft tissue in the body. Presently there is no cure, only remission if it can be attained, and this rare cancer can reappear anywhere at any time. Because of its rarity, few doctors know how to treat it and it attracts very little research. Cell cultures or DNA are distributed only to qualified professional persons who are associated with recognized research, medical, educational, or industrial organizations engaged in health-related research or health delivery. Before cell cultures or DNA samples can be shipped, the principal investigator must sign an ASSURANCE FORM (Material Transfer Agreement) detailing the terms and conditions of sale. This agreement must be renewed annually. In addition, before receiving lymphoblast or other virus-transformed cell cultures users should read the MINIMUM SAFETY GUIDELINES RECOMMENDED FOR WORKING WITH HUMAN CELL CULTURES.

Code4Lib Journal
type: Resource
type: NamedIndividual
has db xref: nlx_68308
IAO_0000115: This article is an appeal to technically-oriented library staff to initiate collaborative, bottom-up data-analysis efforts across their libraries. We discuss successful strategies used at North Carolina State University (NCSU) Libraries for initiating cross-departmental outreach for data-analysis work, as well as structuring and storing data, and disseminating findings. We present several specific examples of collaborative data-analysis projects undertaken at NCSU Libraries. Although the primary goal of the Code4Lib Journal is to provide practical solutions for technologists working in libraries, it has a lot to offer non-technologists. Technology affects all of the work that our libraries are doing and will define what the future of libraries will look like.

SEVENS
type: Resource
type: NamedIndividual
has db xref: nif-0000-03455
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. SEVENS summarizes GPCR (G-protein coupled receptor) genes that are identified with high accuracy from 43 eukaryote genomes, by a pipeline integrating such software as a gene finder, a sequence alignment tool, a motif and domain assignment tool, and a transmembrane helix predictor. This treats a larger data space (than that in currently available other databases), which should include not only the expressed sequences but also the newly identified sequences that cannot be detected by in vivo experiments, although they definitely exist on the genome sequence and are just waiting for the opportunity to express their functions. SEVENS provides the infrastructure of general information of GPCR universe for comparative genomics. We developed an automatic system for identifying GPCR (G-protein coupled receptor) genes from various kinds of genomes, by integrating such software as a gene finder, a sequence alignment tool, a motif and domain assignment tool, and a transmembrane helix predictor. SEVENS enables us to perform a genome-scale overview of the GPCR universe using sequences that are identified with high accuracy (99.4% sensitivity and 96.6% specificity). Using this system, we surveyed the complete genomes of 7 eukaryotes and 224 prokaryotes, and found that there are 4 to 1016 GPCR genes in the 7 eukaryotes, and only a total of 16 GPCR genes in all the prokaryotes. Our preliminary results indicate that 11 subfamilies of the Class A family, the Class 2(B) family, the Class 3(C) family and the fz/smo family are commonly found among human, fly, and nematode genomes. We also analyzed the chromosomal locations of the GPCR genes with the Kolmogorov-Smirnov test, and found that species-specific families, such as olfactory, taste, and chemokine receptors in human and nematode chemoreceptor in worm, tend to form clusters extensively, whereas no significant clusters were detected in fly and plant genomes. How…

Brighter Ideas Inc.
type: Organization
type: NamedIndividual
has db xref: nlx_152322
synonym: Bii
synonym: Brighter Ideas Inc
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 17,2021. An Antibody supplier

NCBI BioSystems Database
type: Resource
type: NamedIndividual
has db xref: biotools:biosystems
has db xref: nlx_69646
has db xref: r3d100011033
synonym: BioSystems Database
synonym: NCBI BioSystems
abbrev: BioSystems
IAO_0000115: Database that provides access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez. A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. BioSystem records list and categorize components, such as the genes, proteins, and small molecules involved in a biological system. The companion FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems. A number of databases provide diagrams showing the components and products of biological pathways along with corresponding annotations and links to literature. This database was developed as a complementary project to (1) serve as a centralized repository of data; (2) connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system; and (3) facilitate computation on biosystems data. The NCBI BioSystems Database currently contains records from several source databases: KEGG, BioCyc (including its Tier 1 EcoCyc and MetaCyc databases, and its Tier 2 databases), Reactome, the National Cancer Institute's Pathway Interaction Database, WikiPathways, and Gene Ontology (GO). It includes several types of records such as pathways, structural complexes, and functional sets, and is desiged to accomodate other record types, such as diseases, as data become available. Through these collaborations, the BioSystems database facilitates access to, and provides the ability to compute on, a wide range of biosystems data. If you are interested in depositing data into the BioSystems database, please contact them.

HIV Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_68685
synonym: Spanish HIV BioBank
abbrev: HIV BioBank
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 15, 2011. The Spanish HIV BioBank was created with the objectives of processing, storing and providing distinct samples from HIV/AIDS patients, categorized according to strictly defined characteristics, free of charge to research projects. Strict compliance to ethical norms is always guaranteed. HIV BioBank possesses nearly 50,000 vials containing different prospective longitudinal study sample types. More than 1,700 of these samples are now used in 19 national and international research projects. (2009) The HIV BioBank represents a novel approach to HIV research that might be of general interest not only for basic and clinical research teams working on HIV, but also for those groups trying to establish large networks focused on research on specific clinical problems. It also represents a model to stimulate cooperative research among large numbers of research groups working as a network on specific clinical problems. The HIV BioBank is able to very efficiently release samples to different research project not only in Spain but also in other countries.

National LeioMyoSarcoma Foundation
type: Resource
type: NamedIndividual
has db xref: nlx_143866
synonym: NLMSF.org
abbrev: NLMSF
IAO_0000115: A volunteer, not for profit organization providing leadership in supporting research of LeioMyoSarcoma, improving treatment outcomes of those affected by this disease as well as fostering awareness in the medical community and general public. All dollars go to research and awareness. Leiomyosarcoma is a rare form of cancer, which affects about four people in every million. It spreads through the blood stream and can affect the lungs, liver, blood vessels or any other soft tissue in the body. Presently there is no cure, only remission if it can be attained, and this rare cancer can reappear anywhere and at any time. Because of its rarity, few doctors know how to treat it and it attracts little research. The National LeioMyoSarcoma Foundation hosts several Fundraising events throughout the year.

Human Reference Genetic Material Repository
type: Resource
type: NamedIndividual
has db xref: nlx_143868
synonym: J. Craig Venter Institute Human Reference Genome (HuRef)
abbrev: HuRef Repository
IAO_0000115: The Human Reference Genetic Material Repository makes available DNA from a single individual, J. Craig Venter, whose genome has been sequenced and assembled. The DNA samples are prepared from a lymphoblastoid cell line established at Coriell Cell Repositories from a sample of peripheral blood. The DNA samples are available in 50 microgram aliquots. The lymphoblastoid cell line is not available for distribution. The human DNA sample provided is that of J. Craig Venter whose DNA from white blood cells and sperm was sequenced using Sanger chemistry (ABI Capillary Electrophoresis Platforms 3700 and 3730xl), assembled using the Celera Assembler and was published in PLoS Biology . J. Craig Venter, born on 14 October 1946, is a Caucasian male of self-reported European-American ancestry. The data available on this sample, whose genome assembly is referred to as HuRef, includes: * Whole Genome Shotgun Sequencing data * Sequence trace set deposited by JCVI in the NCBI trace archive * Human Genome Browser displaying sequence assembly, DNA variants and gene annotations Additional data sets from this study include: * Full set of Sanger reads used for genome assembly * SNP and insertion/deletion variant on the human genome sequence coordinates (NCBI version 36) * Affymetrix 500K GeneChip data * Illumina HumanHap650Y Genotyping BeadChip data Given the amount of data publicly available the genomic content of this sample, HuRef will be useful as a reference for many genetic studies.

SGD
type: Resource
type: NamedIndividual
has db xref: biotools:sgd
has db xref: nif-0000-03456
has db xref: OMICS_01661
has db xref: r3d100010419
synonym: Saccharomyces Genome Database
synonym: SGD LOCUS
synonym: SGD REF
IAO_0000115: A curated database that provides comprehensive integrated biological information for Saccharomyces cerevisiae along with search and analysis tools to explore these data. SGD allows researchers to discover functional relationships between sequence and gene products in fungi and higher organisms. The SGD also maintains the S. cerevisiae Gene Name Registry, a complete list of all gene names used in S. cerevisiae which includes a set of general guidelines to gene naming. Protein Page provides basic protein information calculated from the predicted sequence and contains links to a variety of secondary structure and tertiary structure resources. Yeast Biochemical Pathways allows users to view and search for biochemical reactions and pathways that occur in S. cerevisiae as well as map expression data onto the biochemical pathways. Literature citations are provided where available.

Toronto Public Library Health Information
type: Resource
type: NamedIndividual
has db xref: nlx_69561
synonym: CHIS Wiki
synonym: Consumer Health Information Service Wiki
synonym: Toronto Public Library Health and Wellness
synonym: Toronto Public Library Health and Wellness Wiki
synonym: Toronto Public Library''s Health and Wellness Wiki
IAO_0000115: This site, created and maintained by the Business, Science & Technology Department of the Toronto Public Library, is designed to help you find reliable, understandable health information for you and your family. It can help you access a wide range of health and medical information online, and supports people in gaining greater control over their own health through access to health information. Resources include articles, books, health guides, reading list and websites.

Defense Centers of Excellence for Psychological Health and Traumatic Brain Injury
type: Resource
type: NamedIndividual
has db xref: nlx_143873
synonym: Defense Centers of Excellence for PH and TBI
abbrev: DCoE
IAO_0000115: The Defense Centers of Excellence for Psychological Health and Traumatic Brain Injury (DCoE) was established in November 2007 to integrate knowledge and identify, evaluate and disseminate evidence based practices and standards for the treatment of psychological health and TBI within the Defense Department. DCoE is part of the Military Health System, which provides a ''continuum of care'' from initial accession to deployment to discharge. DCoE works across the entire continuum of care to promote resilience, rehabilitation and reintegration for warriors, families and veterans with psychological health concerns and traumatic brain injuries. DCoE leads a groundbreaking collaborative effort that includes the Department of Veterans Affairs (VA), civilian agencies, community leaders, advocacy groups, clinical experts and academic institutions that are dedicated to expanding the state of knowledge of psychological health and TBI. In addition, DCoE''s Real Warriors Campaign is working to encourage help-seeking behavior for warriors with post-traumatic stress or mTBI. DCoE brings together six directorates and three centers. Their joint goal is to maximize opportunities for warriors and families to thrive through a collaborative global network to promote resilience, recovery and reintegration for PH and TBI.

VA Polytrauma / TBI System of Care
type: Resource
type: NamedIndividual
has db xref: nlx_143875
synonym: Polytrauma / TBI System of Care
synonym: Polytrauma System of Care
synonym: VA Polytrauma System of Care
abbrev: PSC
IAO_0000115: A network of specialized rehabilitation programs serving Veterans and Service Members with both combat and civilian related Traumatic Brain Injury (TBI) and polytrauma. Services available include: interdisciplinary evaluation and treatment, development of a comprehensive plan of care, case management, patient and family education and training, psychosocial support, and application of advanced rehabilitation treatments and prosthetic technologies.

Urgencyclopedie
type: Resource
type: NamedIndividual
has db xref: nlx_69234
synonym: Urgencyclopédie
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Urgencyclop?die is a wiki in French about first aid, rescue and emergency medicine. Anyone who registers may contribute.

University of Texas MD Anderson Cancer Center
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100007313
has db xref: grid.240145.6
has db xref: ISNI: 0000 0001 2291 4776
has db xref: nif-0000-24365
has db xref: nlx_69261
has db xref: SCR_008276
has db xref: Wikidata: Q1525831
synonym: M.D. Anderson Cancer Center
synonym: UT M.D. Anderson Cancer Center
synonym: UT MD Anderson Cancer Center
abbrev: MD Anderson Cancer Center
IAO_0000115: The mission of The University of Texas MD Anderson Cancer Center is to eliminate cancer in Texas, the nation, and the world through outstanding programs that integrate patient care, research and prevention, and through education for undergraduate and graduate students, trainees, professionals, employees and the public. VISION: We shall be the premier cancer center in the world, based on the excellence of our people, our research-driven patient care and our science. We are Making Cancer History.

Hema-Quebec
type: Organization
type: NamedIndividual
has db xref: grid.292497.3
has db xref: ISNI: 0000 0001 2111 8890
has db xref: nlx_69414
has db xref: Wikidata: Q3144906
IAO_0000115: Hema-Quebec''s mission is to efficiently provide adequate quantities of safe, optimal blood components, substitutes, human tissues and cord blood to meet the needs of all Quebecers; provide and develop expertise along with specialized and innovative services and products in the fields of transfusion medicine and human tissue transplantation. Hema-Quebec is driven by the commitment, support and recognition of its employees as well as the trust of its partners to remain the standard of quality and innovation with respect to the safe procurement of blood products, human tissues and stem cells.

MIGHEALTHNET (Migrant Health)
type: Resource
type: NamedIndividual
has db xref: nlx_69465
synonym: Mighealthnet
IAO_0000115: The MIGHEALTHNET wiki has been set up to gather information about the health of migrants and ethnic minorities in the United Kingdom. It forms part of the project MIGHEALTHNET, currently being carried out in 16 countries and co-funded by DG SANCO, the Health and Consumer Protection Directorate-General of the European Commission. We invite you to add your contributions to it and to pass on the address of this site to others who may be interested. This website is part of an EU Project that aims to give professionals, policy makers including health authorities, researchers, educators and representatives of migrant and minority groups easy access to a dynamically evolving body of knowledge and a virtual network of expertise. It will stimulate the formation of networks of individuals and organizations concerned with migrant and minority health.

LifeSource
type: Resource
type: NamedIndividual
has db xref: nlx_69466
IAO_0000115: LifeSource is the non-profit organization dedicated to saving lives through organ and tissue donation in the Upper Midwest. We serve more than 6 million people in communities across Minnesota, North Dakota, South Dakota and portions of western Wisconsin. As the federally-designated organization that manages organ and tissue donation in our region, we are dedicated to working with our hospital and community partners to support donor families, facilitate the donation of organs and tissues to transplant recipients and encourage the people in our communities to register as donors.

NuChart
type: Resource
type: NamedIndividual
has db xref: OMICS_00525
IAO_0000115: An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations.

Repository of molecular brain neoplasia data
type: Resource
type: NamedIndividual
has db xref: nif-0000-00230
synonym: REMBRANDT (Repository of Molecular Brain Neoplasia Data)
synonym: REMBRANDT - Repository of Molecular Brain Neoplasia Data
synonym: REpository for Molecular BRAin Neoplasia DaTa (REMBRANDT)
abbrev: REMBRANDT
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 28,2023. REMBRANDT is a data repository containing diverse types of molecular research and clinical trials data related to brain cancers, including gliomas, along with a wide variety of web-based analysis tools that readily facilitate the understanding of critical correlations among the different data types. REMBRANDT aims to be the access portal for a national molecular, genetic, and clinical database of several thousand primary brain tumors that is fully open and accessible to all investigators (including intramural and extramural researchers), as well as the public at-large. The main focus is to molecularly characterize a large number of adult and pediatric primary brain tumors and to correlate those data with extensive retrospective and prospective clinical data. Specific data types hosted here are gene expression profiles, real time PCR assays, CGH and SNP array information, sequencing data, tissue array results and images, proteomic profiles, and patients' ''' response to various treatments. Clinical trials' ''' information and protocols are also accessible. The data can be downloaded as raw files containing all the information gathered through the primary experiments or can be mined using the informatics support provided. This comprehensive brain tumor data portal will allow for easy ad hoc querying across multiple domains, thus allowing physician-scientists to make the right decisions during patient treatments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

National Temporal Bone Pathology Resource Registry
type: Resource
type: NamedIndividual
has db xref: nlx_69775
synonym: National Institute on Deafness and Other Communication Disorders National Temporal Bone Hearing Balance Pathology Resource Registry
synonym: National Temporal Bone Registry
synonym: NIDCD National Temporal Bone Hearing & Balance Pathology Resource Registry
synonym: NIDCD National Temporal Bone Hearing and Balance Pathology Resource Registry
IAO_0000115: A non-profit organization that promotes research on hearing and balance disorders. The Registry database allows researchers to perform simple searches to locate specimens of interest. The results show the laboratories where specimens that match the query are located. Investigators should contact the individual laboratories for studying the specimens or for access to the sections. The Registry also serves the public and the scientific community through the dissemination of public information on temporal bone donation and research, enrollment of temporal bone donors, publication of The Registry, a newsletter for researchers, conservation of existing human temporal bone collections, and professional educational activities for physicians and scientists.

Blood Borne Pathogens Laboratory
type: Resource
type: NamedIndividual
has db xref: nlx_70104
synonym: Blood Borne Pathogens Surveillance Project
abbrev: BBPSP
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. To develop a method to look for known and emerging blood borne diseases, a secure bank of samples has been established to test for known blood borne infectious agents and genetic changes causing or modifying the clotting disease, and to be available for testing for newly discovered viruses and clotting gene changes as they are found. The objectives of this project are: * To collect blood samples for a sample bank of plasma, DNA, and RNA to screen for known and emerging blood borne diseases. * To identify the mutation leading to each consenting patient''s bleeding disorder, and to characterize other known and yet to be discovered genes that affect blood coagulation. * To collect encoded, non-nominal data into a central database from an electronic chart known as CHARMS, which is currently kept in each hemophilia clinic in Canada to correlate with results from 1 and 2.

Susan G. Komen Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_70500
synonym: Komen Tissue Bank
synonym: Susan G. Komen for the Cure Tissue Bank
synonym: Tissue Bank at the IU Simon Cancer Center
abbrev: KTB
IAO_0000115: The goals of the Susan G. Komen for the Cure Tissue Bank at the IU Simon Cancer Center are to acquire biomolecule and tissue specimens from the entire continuum of breast development: puberty to menopause and to make these specimens or the digital data derived from them available and accessible to researchers across the globe.

ProViDE
type: Resource
type: NamedIndividual
has db xref: OMICS_01463
synonym: Program for Viral Diversity Estimation
synonym: ProViDE: Program for Viral Diversity Estimation
IAO_0000115: A similarity based binning algorithm that uses a customized set of alignment parameter thresholds / ranges, specifically suited for the accurate taxonomic labelling of viral metagenomic sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

UnifiedGenotyper
type: Resource
type: NamedIndividual
has db xref: OMICS_00080
IAO_0000115: A multiple-sample, technology-aware SNP and indel caller.

CBLAST
type: Resource
type: NamedIndividual
has db xref: nlx_70506
synonym: NCBI Related Structure Search
synonym: NCBI Related Structures
IAO_0000115: The NCBI Related Structures tool allows you to find 3D structures from the Molecular Modeling Database (MMDB) that are similar in sequence to a query protein. Although the query protein may not yet have a resolved structure, the 3D shape of a similar protein sequence can shed light on the putative shape and biological function of the query protein. CBLAST is a tool that compares a query protein sequence against all protein sequences from resolved 3D structures by using protein BLAST against the PDB data set. The purpose is to find representative 3D structures for the query and/or its homologs, as available. Each record in the Entrez Protein database has been CBLAST''ed and the search results are available as Related Structures in the Links menu of Entrez Protein records. You can also enter a protein query sequence directly into the CBLAST search page in order to find its sequence-similar 3D structure records. The search results can be viewed in Cn3D (hence the name CBLAST), which displays an alignment of the query protein to the related structure''s sequence and allows you to interactively examine the sequence-structure relationship.

Data.gov
type: Resource
type: NamedIndividual
has db xref: nlx_70953
has db xref: r3d100010078
synonym: Data.gov Catalogs
IAO_0000115: Catalog of data sets that are generated and held by the Federal Government, including data, tools and resources to conduct research, develop web and mobile applications, design data visualizations, etc. Data.gov provides descriptions of the Federal datasets (metadata), information about how to access the datasets, and tools that leverage government datasets. The data catalogs will continue to grow as datasets are added. Federal, Executive Branch data are included in the first version of Data.gov.

RHEA
type: Resource
type: NamedIndividual
has db xref: nlx_70986
has db xref: r3d100010891
IAO_0000115: Manually annotated reaction database where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest) which provides detailed information about structure, formula and charge. Rhea provides built-in validations that ensure both elemental and charge balance of the reactions. The database has been populated with the reactions found in the Enzyme Commission (EC) list (and in the IntEnz and ENZYME databases), extending it with additional known reactions of biological interest. While the main focus of Rhea is enzyme-catalyzed reactions, other biochemical reactions are also included. Rhea is a manually annotated resource and it provides: stable reaction identifiers for each of its reactions; directionality information if the physiological direction of the reaction is known; the possibility to link several reactions together to form overall reactions; extensive cross-references to other resources including enzyme-catalyzed and other metabolic reactions, such as the EC list (in IntEnz), KEGG, MetaCyc and UniPathway; and chemical substructure and similarity searches on compounds in Rhea.

Ohio State Biorepository
type: Resource
type: NamedIndividual
has db xref: nlx_71208
synonym: HTRN Biorepository
synonym: HTRN Biorepository & Biospecimen Resource
synonym: HTRN Biorepository and Biospecimen Resource
synonym: HTRN Biorepository Biospecimen Resource
synonym: Human Tissue Resource Network Biospecimen Bank
abbrev: HTRN Biospecimen Bank
IAO_0000115: The HTRN biospecimen bank is comprised of samples for the Ohio State University Cancer and Leukemia Group B Pathology Coordinating Office (CALGB-PCO) and the Ohio State University Midwestern Division of the Cooperative Human Tissue Network (CHTN). The CALGB-PCO banks biospecimens donated by patients enrolled in clinical trials. Samples can include tumor and normal tissue, plasma, serum, whole blood and white blood cells and urine. All of these samples are used later in correlative studies. The Midwestern Division of the CHTN stores a temporary biospecimen bank of tumor and normal tissue, tissue slides and paraffin embedded tissue blocks for research investigators throughout the country and Canada who are trying to find a cure for cancer. As part of the HTRN biospecimen bank, a Rees Scientific equipment monitoring system helps to secure the integrity and quality of samples stored in the biorepository. Scientific research within the HTRN is currently underway to determine the best methods in tissue storage for long term use. The NCI First-Generation Guidelines for NCI-Supported Biorepositories and the NCI Best Practices for Biospecimen Resources are continuously reviewed and adapted by the HTRN.

Orthopaedic Surgery
type: Resource
type: NamedIndividual
has db xref: nlx_71236
synonym: Orthopaedic Surgery (wikibook)
synonym: Orthopedic Surgery
IAO_0000115: Orthopaedic Surgery is a collaborative wikibook of orthopedic surgery. *Preface *Chapter 1: Basic Sciences *Chapter 2: Upper Limb *Chapter 3: Foot and Ankle *Chapter 4: Spine *Chapter 5: Hand and Microsurgery *Chapter 6: Pediatric Orthopedics *Chapter 7: Adult Reconstruction *Chapter 8: Sports Medicine *Chapter 9: Musculoskeletal Tumors *Chapter 10: Injury *Chapter 11: Surgical Procedures *Chapter 12: Rehabilitation *Chapter 13: Practice

SOrt-ITEMS
type: Resource
type: NamedIndividual
has db xref: OMICS_01465
synonym: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences
synonym: SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences
IAO_0000115: Sequence orthology based software for improved taxonomic estimation of metagenomic sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

PARENTE
type: Resource
type: NamedIndividual
has db xref: nlx_154508
IAO_0000115: Software application for parentage inference using molecular data from diploid codominant markers (entry from Genetic Analysis Software)

Patient-Reported Outcomes Measurement Information System
type: Resource
type: NamedIndividual
has db xref: nlx_143881
synonym: Patient Reported Outcomes Measurement Information System
synonym: PROMIS
IAO_0000115: Repository of person centered measures that evaluates and monitors physical, mental, and social health in adults and children.

The Scientists Labbies
type: Resource
type: NamedIndividual
has db xref: nlx_71430
synonym: The Scientist''s Labbies
IAO_0000115: Enter your science video, website, or multimedia for a chance to win this year''s multimedia awards! It''s time for you to send us your best videos, interactive multimedia, websites, blogs, or any other techie creation meant for sharing the latest in life science research with the world. You only have until May 6th (2011) to enter, so post your submission today! We''re calling all scientists, research groups, teachers, and bio-enthusiasts who''ve gone the extra mile to communicate their work in style. The entries will be rated by a panel of judges and the winners will be announced in our September issue. We''ll also ask you, our readers, to pick your favorites. All entries must be created with funding from an individual or single research grant (no entries created with funding from a corporation or research institution will be accepted). All videos must be 10 minutes or less, and all entries must relate to the life sciences. Entries will be judged on scientific content, concept/originality, entertainment value, and production quality. Winners will be featured in a full-length article in the September issue of The Scientist, complete with a presentation of their multimedia mastery on our website.

RAIphy
type: Resource
type: NamedIndividual
has db xref: OMICS_01464
IAO_0000115: A semi-supervised metagenomic fragment classification software program that utilizes the genome signatures to characterize the DNA sequences and taxonomic classification is based on an information theoretic measure referred as Relative Abundance Index (RAI). A DNA sequence of unknown source is classified and taxonomically labeled based on the phylogenetic profiles of the previously sequenced genomes. The profiles are iteratively updated using the unknown DNA sequences and the classification results. After a few cycles, the metagenome is classified into operational taxonomic units.

Alabama Organ Center
type: Resource
type: NamedIndividual
has db xref: nlx_71444
abbrev: AOC
IAO_0000115: The Alabama Organ Center (AOC) is the federally designated organ procurement organization for the state of Alabama. We work with all of the hospitals in the state to coordinate their donation services. Like all organ procurement organizations, the AOC is a non-profit organization. We provide a variety of services: * Hospital education * Public education * Screening of potential donors * Coordination of the donation process * Family support The AOC is committed to providing a better quality of life for those who require an organ or tissue transplant, while respecting the families who share the gift of life.

Human DNA Polymerase Gamma Mutation Database
type: Resource
type: NamedIndividual
has db xref: nlx_71693
has db xref: OMICS_01639
IAO_0000115: Database that lists all known mutations in the coding region of the POLG gene and describes the associated disease. Human DNA polymerase is composed of two subunits, a 140 kDa catalytic subunit encoded by the POLG on chromosome 15q25, and a 55kDa accessory subunit encoded by the POLG2 gene on chromosome 17q23-24. A number of mutations have been mapped to the gene for the catalytic subunit of DNA polymerase, POLG, and found to be associated with mitochondrial diseases. The nucleotide changes are numbered from the initiation Methionine codon and are based on the cDNA (accession U60325.1) and gene sequence (accession AF497906.1).

TRACK TBI Network
type: Resource
type: NamedIndividual
has db xref: nlx_143882
synonym: TBI Network
synonym: Transforming Research and Clinical Knowledge in Traumatic Brain Injury Network
synonym: Transforming Research and Clinical Knowledge in Traumatic Brain Injury: Multicenter Implementation of the TBI Common Data Elements
synonym: Traumatic Brain Injury Network
IAO_0000115: Network evaluating consensus-based common data elements (CDE) for traumatic brain injury (TBI) and psychological health (TBI-CDE, www.commondataelements.ninds.nih.gov/TBI.aspx) while extensively phenotyping a cohort of TBI patients across the injury spectrum from concussion to coma. Institutions that participate in the TBI Network will be able to track the outcomes of patients through a 3, 6 and 12-month followup program and compare outcomes with other participating institutions. For the three acute care centers, patients were enrolled that presented to the emergency department within 24 hours of head injury and required computed tomography (CT). For the rehabilitation center, referrals from acute hospitals were enrolled. Patients were consented to participate in components: clinical profile; blood draws for measurement of proteomic and genomic markers; 3T MRI within 2 weeks; three-month Glasgow Outcome Scale-Extended (GOS-E); and six-month TBI-CDE Core outcome assessments. A web-enabled database, imaging repository, and biospecimen bank was developed using the TBI-CDE recommendations. A total of 605 patients were enrolled. Of these subjects, 88% had a GCS 13-15, 5% had a GCS 9-12, and 7% had a GCS of 8 or less. Three-month GOS-E''s were obtained for 78% of the patients. Comprehensive 6-month outcome measures, including PTSD assessment, are ongoing until September 2011. Blood specimens were collected from 450 patients. Initial CTs for 605 patients and 235 patients with 3T MRI studies were transferred to an imaging repository. The TRACK TBI Network will provide qualified institutions access to a web-based version of key forms in tracking TBI outcomes for Quality Improvement and institutional benchmarking.

National University of Malaysia; Selangor; Malaysia
type: Organization
type: NamedIndividual
has db xref: nlx_151798
synonym: National University of Malaysia
synonym: Universiti Kebangsaan Malaysia
abbrev: NUM
abbrev: UKM
IAO_0000115: UKM affirms integration of faith in Allah and constructive knowledge along with amalgamation of theory and practice as core fundamentals in advancement of knowledge, building of educated society and development of university.

National Stem Cell Bank
type: Resource
type: NamedIndividual
has db xref: nlx_72054
abbrev: NSCB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 17, 2011. The US government contract funding the National Stem Cell Bank (NSCB) ended on February 28, 2010. A repository for the pluripotent stem cells lines listed on the NIH Human Pluripotent Stem Cell Registry. These cells were derived prior to August 2001 using excess IVF embryos and were eligible for use in federally funded research under previous presidential policy. The eligibility of these lines will not be known until the NIH issues final stem cell guidelines in July 2009. The goal of the NSCB is to grow, characterize and distribute the cell lines listed on the registry, and to provide comprehensive technical support to stem cell researchers around the world. Starting February 2, 2010, these materials can be ordered from the Wisconsin International Stem Cell Bank (the WISC Bank) operated by WiCell Research Institute, for delivery after February 28, 2010.

Pfam
type: Resource
type: NamedIndividual
has db xref: biotools:pfam
has db xref: nlx_72111
has db xref: OMICS_01696
has db xref: r3d100012850
synonym: PFAM
synonym: Pfam Database
synonym: Pfam protein families database
synonym: Protein Families Database
IAO_0000115: A database of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Users can analyze protein sequences for Pfam matches, view Pfam family annotation and alignments, see groups of related families, look at the domain organization of a protein sequence, find the domains on a PDB structure, and query Pfam by keywords. There are two components to Pfam: Pfam-A and Pfam-B. Pfam-A entries are high quality, manually curated families that may automatically generate a supplement using the ADDA database. These automatically generated entries are called Pfam-B. Although of lower quality, Pfam-B families can be useful for identifying functionally conserved regions when no Pfam-A entries are found. Pfam also generates higher-level groupings of related families, known as clans (collections of Pfam-A entries which are related by similarity of sequence, structure or profile-HMM).

European Bioinformatics Institute
type: Organization
type: NamedIndividual
has db xref: grid.225360.0
has db xref: ISNI: 0000 0000 9709 7726
has db xref: nlx_72386
has db xref: Wikidata: Q1341845
synonym: EBI
synonym: European Molecular Biology Laboratory - European Bioinformatics Institute
abbrev: EMBL-EBI
IAO_0000115: Non-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL.

Bioreclamation
type: Organization
type: NamedIndividual
has db xref: nlx_72707
synonym: BioreclamationIVT
synonym: BioreclamationIVT - The complete resource for all biologicals
IAO_0000115: BioIVT, formerly BioreclamationIVT, is global provider of biological specimens and services. Provides biological and in vitro products specializing in control and disease state matrices manufactured from human and animal whole blood, plasma, serum, tissues and other fluids which are used in drug discovery, compound development, clinical and research diagnostics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

ZFIN Antibody Database
type: Resource
type: NamedIndividual
has db xref: nlx_74236
synonym: ZFIN Antibodies
synonym: ZFIN Gene Expression Antibodies
IAO_0000115: The ZFIN Antibody Database is a database of zebrafish gene expression antibodies.

IMPACT Prognostic Calculator
type: Resource
type: NamedIndividual
has db xref: nlx_143884
synonym: International Mission for Prognosis and Analysis of Clinical Trials in TBI Prognostic Calculator
IAO_0000115: A calculator that calculates the prediction models for 6 month outcome after Traumatic Brain Injury. Based on extensive prognostic analysis the IMPACT investigators have developed prognostic models for predicting 6 month outcome in adult patients with moderate to severe head injury (Glasgow Coma Scale <=12) on admission. By entering the characteristics into the calculator, the models will provide an estimate of the expected outcome at 6 months. We present three models of increasing complexity (Core, Core + CT, Core + CT + Lab). These models were developed and validated in collaboration with the CRASH trial collaborators on large numbers of individual patient data (the IMPACT database). The models discriminate well, and are particularly suited for purposes of classification and characterization of large cohorts of patients. Extreme caution is required when applying the estimated prognosis to individual patients. The sequential prediction models may be used as an aid to estimate 6 month outcome in patients with severe or moderate traumatic brain injury (TBI). However, the prediction rule can only complement, never replace, clinical judgment and can therefore be used only as a decision-support system.

Biobanque de Picardie
type: Resource
type: NamedIndividual
has db xref: nlx_73857
IAO_0000115: A secure repository of biological samples and data dedicated for medical and research purposes. These biological samples are linked to consenting patient relative data. Biobanque de Picardie provides quality and traceability services for establishment, conservation and use of biological samples collections. It houses collections of human tissue in a variety of areas of disease. Samples are used in basic research and translational studies, physiopathology of diseases and identification of new diagnostic, and as prognostic or therapeutic biomarkers. Biobanque de Picardie also develops healthy or pathological human primary stem cell banks, such as: mesenchymal stem cells in umbilical cord (HUC-MSC), primary hepatocytes (HPH), peripheral blood mononuclear cells (PBMC), and fibroblasts. Biological samples are stored at - 80 degrees C in electric freezers, at - 196 degrees C in liquid nitrogen or -130 degrees C in nitrogen vapor.

Ontario Tumour Bank
type: Resource
type: NamedIndividual
has db xref: nlx_74199
synonym: Ontario Tumor Bank
abbrev: OTB
IAO_0000115: The Ontario Tumour Bank is a province-wide biorepository and data bank focused on collection of tumor-related human biospecimens. It provides academic and industry cancer researchers with a diverse selection of high quality tumor-related specimens and data obtained directly by dedicated tumour bank staff, who follow a stringent set of procedures and ethical guidelines. The biospecimens and clinical data are an important resource for scientists engaged in translational research who are developing better diagnostic tools and new drug therapies. Researchers depend on the Ontario Tumour Bank to provide research biospecimens of high quality, diversity, and integrity. Operating at state-of-the-art hospitals and cancer centers across Ontario, the Ontario Tumour Bank coordinates the collection, storage, analysis, annotation, and distribution of tumor and peripheral blood samples. Working in collaboration with local pathologists, medical oncologists, surgeons and other hospital personnel, specially trained staff obtain patient consent, collect tissues and assemble comprehensive clinical information about each donor and the corresponding samples.

Brain Tumor Action Network
type: Resource
type: NamedIndividual
has db xref: nlx_143887
abbrev: BTAN
IAO_0000115: The Brain Tumor Action Network is a not-for-profit 501(c)(3) organization established to bring awareness to the general public about brain tumors and to educate and empower brain tumor survivors, their families and friends. We foster grassroots advocacy on federal and state legislative issues affecting brain tumor survivors, their families and friends by providing information on brain tumor-related public issues and effective advocacy. BTAN has the following goals: * To encourage those living with brain tumors, their families and friends to become advocates for brain tumor awareness. * To foster grassroots advocacy on federal and state legislative issues affecting brain tumor survivors, their families and friends by providing information (and training) on brain tumor related public issues and effective advocacy. * To work independently and in collaboration with other brain tumor related organizations on behalf of the brain tumor community family. * To increase brain tumor awareness nationally through the Hidden Under Our Hats, National Brain Tumor Awareness Project in Washington, DC and at various treatment centers, conferences and fund raisers. * To raise funds to support specific research projects. * To create a PILOT respite care program for brain tumor survivors and their families at Moffitt Cancer Center & Research Institute (Tampa, FL). The respite care fund would assist brain tumor patients and their family members with additional care and support from home health care workers.

Albert Einstein College of Medicine Department of Pathology
type: Organization
type: NamedIndividual
has db xref: nlx_144336
IAO_0000115: An educational and research department at the Albert Einstein College of Medicine. Research is mainly focused on genomics and cancer biology, immunopathology, infectious disease, and neuropathology.

Brain Tumor Foundation For Children
type: Resource
type: NamedIndividual
has db xref: nlx_143888
synonym: Brain Tumor Foundation For Children Inc.
abbrev: BTFC
IAO_0000115: Established in 1983 in Atlanta, GA, the Brain Tumor Foundation for Children (BTFC) was the first nonprofit organization in the United States to focus on pediatric brain tumor disease. The mission of the Brain Tumor Foundation for Children is to provide financial assistance, social support, and information for families of children with brain and spinal cord tumors; fund research projects that improve treatment options and search for a cure; and raise public awareness of the disease and advocate on behalf of children who are affected.

Distributed String Mining Framework
type: Resource
type: NamedIndividual
has db xref: biotools:dsm
has db xref: OMICS_04171
abbrev: dsm-framework
IAO_0000115: Software package providing distributed string mining for High-Throughput Sequencing data that provides a content-based exploration and retrieval method for whole metagenome sequencing samples.

Pplacer
type: Resource
type: NamedIndividual
has db xref: OMICS_01462
synonym: pplacer: phylogenetic placement and downstream analysis
IAO_0000115: Software that places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.

UK Stem Cell Bank
type: Resource
type: NamedIndividual
has db xref: nlx_74499
abbrev: UKSCB
IAO_0000115: The UK Stem Cell Bank was established to provide a repository of human embryonic, fetal and adult stem cell lines as part of the UK governance for the use of human embryos for research. Its role is to provide quality controlled stocks of these cells that researchers worldwide can rely on to facilitate high quality and standardized research. It is also ready to prepare stocks of ''clinical grade'' cell lines as seed stocks for the development of therapies. The bank exists to establish and make available fully characterized and quality-controlled cell banks. These will be supplied to scientific research teams and eventually to pharmaceutical companies, to enable the development of broad-ranging cell therapies. The bank will support the development of stem cell therapy in the UK by: * Creating and growing a supply of well-characterized stem cell lines for researchers in the UK and abroad. This will allow the research teams to establish the basis for therapeutic applications. * Creating, a bank of stem cell lines, under conditions consistent for the preparation of pharmaceutical products which provide cultures that could be supplied for the production of medicines for human use. For researchers deriving human embryonic stem cell lines in the UK, it is a condition of the Human Fertilization and Embryology Authority (HFEA) license that a sample of all human embryonic stem cell lines derived in the UK must be deposited in the UK Stem Cell Bank. The UK Stem Cell Bank does not collect, process, store or distribute Umbilical Cord Blood either for its own use or on behalf of others. A catalog of currently available stem cells is available or you may search for a particular stem cell.

Florida Brain Tumor Association
type: Resource
type: NamedIndividual
has db xref: nlx_143890
synonym: South Florida Brain Tumor Association
abbrev: FBTA
IAO_0000115: The mission of the Florida Brain Tumor Association (FBTA) is to provide hope, support and education to brain tumor survivors, their families and friends; to conquer brain tumors by funding research into their causes and cures; and to enrich the quality of life of those touched by brain tumors. In October, 1991, the Florida Brain Tumor Association (formerly South Florida Brain Tumor Association) began due to a desperate need from brain tumor survivors and families who were searching for support and a safe place to share their life changing experiences. Beginning in Boca Raton, Florida, as a grass roots organization and a handful of people, the first support group was conceived. Today, there are many additional FBTA support groups, from coast to coast in the state of Florida. The Florida Brain Tumor Association (FBTA) has become a major force in the brain tumor community. We host many fundraisers yearly, donating funds for research to brain tumor centers. The FBTA has hosted over 20 three day conferences, seminars and meetings, attracting thousands of survivors, families and health care professionals in the United States and Canada. Many of the most renowned physicians in the world travel from far and near to present at FBTA conferences. We are proud and grateful for their commitment and dedication to our cause. The FBTA is a not-for-profit 501(c)(3) organization that is supported by contributions from individuals, corporations, and foundations. We are the only organization of this kind, relying on the strength and dedication of our members, who are brain tumor survivors, family members and friends. Our Medical Advisory Board is also voluntary; we are very thankful to them for their generous gifts of time.

TPEHG DB
type: Resource
type: NamedIndividual
has db xref: nlx_74635
synonym: Term-Preterm ElectroHysteroGram DataBase
synonym: The Term-Preterm EHG Database
IAO_0000115: It was obtained from 1997 to 2005 at the University Medical Centre Ljubljana, Department of Obstetrics and Gynecology. The records were obtained during regular check-ups either around the 22nd week of gestation or around the 32nd week of gestation. The women participating in the study represented a sample of the general population. In all, almost 1300 records were obtained during these years, and a preliminary database was built and used for studies by Ivan Verdenik, Gorazd Kavek, Marjan Pajntar and iva Novak-Antoli

Autism Speaks
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100000073
has db xref: grid.427598.5
has db xref: ISNI: 0000 0004 4663 7867
has db xref: nlx_75303
has db xref: Wikidata: Q784658
synonym: NAAR
synonym: National Alliance for Autism Research
IAO_0000115: Autism Speaks has grown into the nation''s largest autism science and advocacy organization, dedicated to funding research into the causes, prevention, treatments and a cure for autism; increasing awareness of autism spectrum disorders; and advocating for the needs of individuals with autism and their families. We are proud of what we''ve been able to accomplish and look forward to continued successes in the years ahead. In addition to putting money into new and cutting edge research, we also fund resources and programs such as the Autism Speaks Autism Treatment Network, Autism Speaks������?? Autism Genetic Resource Exchange and several other scientific and clinical programs. Autism Speaks was founded in February 2005 by Bob and Suzanne Wright, grandparents of a child with autism. Their longtime friend Bernie Marcus donated $25 million to help financially launch the organization. At Autism Speaks, our goal is to change the future for all who struggle with autism spectrum disorders. We are dedicated to funding global biomedical research into the causes, prevention, treatments, and cure for autism; to raising public awareness about autism and its effects on individuals, families, and society; and to bringing hope to all who deal with the hardships of this disorder. We are committed to raising the funds necessary to support these goals. Autism Speaks aims to bring the autism community together as one strong voice to urge the government and private sector to listen to our concerns and take action to address this urgent global health crisis. It is our firm belief that, working together, we will find the missing pieces of the puzzle.

PubChem Substance
type: Resource
type: NamedIndividual
has db xref: nlx_74645
synonym: NCBI PubChem Substance
synonym: Pcsubstance
synonym: PubChem Substance Database
synonym: PubChem Substances Database
IAO_0000115: As one of three primary databases of PubChem (Pcsubstance, Pccompound, and PCBioAssay), PubChem Substance Database contains descriptions of chemical samples, from a variety of sources, and links to PubMed citations, protein 3D structures, and biological screening results that are available in PubChem BioAssay. If the contents of a chemical sample are known, the description includes links to PubChem Compound. A PubChem FTP is available and new data is accepted into the repository. Pcsubstance contains more than 81 million records (2011).

Accelerated Cure Project for Multiple Sclerosis
type: Organization
type: NamedIndividual
has db xref: grid.468148.7
has db xref: nlx_75004
synonym: Accelerated Cure Project
abbrev: ACP
IAO_0000115: A national nonprofit organization dedicated to accelerating the cure of MS by facilitating research that determines the causes and mechanisms of MS. Our main effort is the creation of a large-scale, multidisciplinary MS Repository of blood samples and data from people with MS and matched controls. We make these samples available to researchers investigating the causes of MS and other demyelinating diseases. In exchange for access to the repository, researchers agree to return the data they generate from the samples so that results from disparate experiments can be combined. We are also developing a Cure Map to establish and document what is known and what is not known about the causes of MS. From the Cure Map, Accelerated Cure Project will facilitate the research most likely to reveal the causes of MS in the shortest time through use of our MS Repository.

National Brain Tumor Society
type: Resource
type: NamedIndividual
has db xref: nlx_143891
abbrev: NBTS
IAO_0000115: National Brain Tumor Society (NBTS) is a nonprofit organization committed to finding a cure for brain tumors. We aggressively drive strategic research, advocate for public policies that meet the critical needs of the brain tumor community, and provide patient information. Headquartered in Watertown, Massachusetts, with offices in San Francisco, California and Wilmington, Delaware, we host activities throughout the United States. Formed in 2008 by the merger of two leading organizations that had served the brain tumor community, the National Brain Tumor Foundation and the Brain Tumor Society, the National Brain Tumor Society is now the largest brain tumor nonprofit organization in the country. Both legacy organizations had been formed in the 1980s by parents and other people who were committed to increasing both research funding and access to resources specific to brain tumors. In 2010, the Kelly Heinz-Grundner Foundation, a Delaware-based organization, joined NBTS as a wholly-owned subsidiary. Founded in 2005, after the death of Kelly Heinz-Grundner to a brain tumor, the group has contributed to NBTS''s efforts to pursue research and public policies that benefit the brain tumor community. NBTS grant programs are effective for academic researchers, inclusive of industry expertise, and promising for the patient community. All funding is open to both the domestic and international research communities. The Innovation Research Grant Program supports catalytic transformative projects that will significantly move the field forward. These may include out-of-the-box projects or research that is critical to move therapies down the pipeline. Research that represents an incremental advance is not considered innovative. NBTS will accept Innovation Letters of Intent throughout the year. Researchers in academic or industry labs and at all stages of their career may be funded through this program.

Integrated Software
type: Resource
type: NamedIndividual
has db xref: nlx_75188
synonym: Integrated Software View
synonym: NIF Integrated Software
synonym: NIF Integrated Software View
synonym: NIF Software
IAO_0000115: A virtual database currently indexing software and tools from the SciCrunch Registry, Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC), Visiome Platform, Cerebellar Platform, Brain Machine Interface Platform, and Genetic Analysis Software (GAS).

Fox Chase Biosample Repository Core Facility
type: Resource
type: NamedIndividual
has db xref: nlx_75230
synonym: FCCC Biosample Repository Core Facility
synonym: Fox Chase BRCF
synonym: Fox Chase Cancer Center Biosample Repository
synonym: Fox Chase Cancer Center Biosample Repository Core Facility
synonym: Fox Chase Tumor Bank
abbrev: FCCC BRCF
IAO_0000115: Fox Chase has developed a facility dedicated to the collection and distribution of human subject biosamples and supporting personal and family cancer history data. In response to announcement (CA-00-025; P30 CA06927S2), the Fox Chase Cancer Center''s Biosample Repository (BR) and Tumor Bank Facility (TBF) is making blood specimens (i.e., whole blood, plasma, platelet-rich plasma, platelet homogenates, red blood cells, leukocytes, lymphoblastoid cell lines, and DNA isolated from leukocytes) and tumor tissues (i.e., multi-tissue microarrays and tumor DNAs) collected by our facilities available for research. Request for blood and tissue will be reviewed by a panel of scientists and ranked. Priority will be given to those investigators with current NIGH/NCI funding, but will be made available as recommended by the internal and external advisory committees. * Blood Inventory: Plasma, Serum, Whole Blood, Lymphocytes, DNA * Tissue Inventory: Tumor and Normal Adjacent Tissue, Fresh-Frozen, Formalin-Fixed Paraffin-Embedded Tissue, OCT Embedded Tissue, Ethanol-fixed Tissue

deStruct
type: Resource
type: NamedIndividual
has db xref: OMICS_00314
synonym: deStruct - Bioinformatics tool for identifying structural variation in tumour genomes
IAO_0000115: A software tool for identifying structural variation in tumour genomes from whole genome illumina sequencing.

Oklahoma Brain Tumor Foundation
type: Resource
type: NamedIndividual
has db xref: nlx_143892
abbrev: OKBTF
IAO_0000115: The Oklahoma Brain Tumor Foundation (OKBTF) is a nonprofit organization that provides education, advocacy and support for Oklahomans with brain tumors and their families to improve their quality of life and help find a cure. Founded by Nancy Thomason after the death of her son Cade Thomason to a brain stem PNET tumor on February 17, 2000, she vowed to fight the disease in honor and memory of her son Cade. OKBTF is dedicated to meeting the needs of Oklahoma families, caregivers and patients affected by primary brain or central nervous system tumors. We work to provide for needs through education, advocacy, research and service. Whatever your needs, whether financial, physical, mental or spiritual, we will work with you to fight the battle. Here you will find many of the services we offer in support of families just like yours, who are confused, hurting and just wanting straight answers. Feel free to browse around, get to know us, see what we are doing to help and send us your comments or questions... We are here for you.

PILGRM
type: Resource
type: NamedIndividual
has db xref: biotools:pilgrm
has db xref: nlx_75372
synonym: Platform for Interactive Learning by Genomics Results Mining
abbrev: PILGRIM
IAO_0000115: PILGRM (the platform for interactive learning by genomics results mining) puts advanced supervised analysis techniques applied to enormous gene expression compendia into the hands of bench biologists. This flexible system empowers its users to answer diverse biological questions that are often outside of the scope of common databases in a data-driven manner. This capability allows domain experts to quickly and easily generate hypotheses about biological processes, tissues or diseases of interest. Specifically PILGRM helps biologists generate these hypotheses by analyzing the expression levels of known relevant genes in large compendia of microarray data. PILGRM is for the biologist with a set of proteins relevant to a disease, biological function or tissue of interest who wants to find additional players in that process. It uses a data driven method that provides added value for literature search results by mining compendia of publicly available gene expression datasets using lists of relevant and irrelevant genes (standards). PILGRM produces publication quality PDFs usable as supplementary material to describe the computational approach, standards and datasets. Each PILGRM analysis starts with an important biological question (e.g. What genes are relevant for breast cancer but not mammary tissue in general?). For PILGRM to discover relevant genes, it needs examples of both genes that you would (positive) and would not (negative) find interesting. Lists of these genes are what we call standards and in PILGRM you can build your own standards or you can use standards from common sources that we pre-load for your convenience. PILGRM lets you build your own literature-documented standards so that processes, disease, and tissues that are not well covered in databases of tissue expression, disease, or function can still be used for an analysis.

MeSH
type: Resource
type: NamedIndividual
has db xref: nlx_75424
synonym: Medical Subject Headings
synonym: MeSH (Medical Subject Headings)
IAO_0000115: A controlled vocabulary thesaurus that consists of sets of terms naming descriptors in a hierarchical structure that permits searching at various levels of specificity. MeSH, in machine-readable form, is provided at no charge via electronic means. MeSH descriptors are arranged in both an alphabetic and a hierarchical structure. At the most general level of the hierarchical structure are very broad headings such as Anatomy or Mental Disorders. More specific headings are found at more narrow levels of the twelve-level hierarchy, such as Ankle and Conduct Disorder. There are 27,149 descriptors in 2014 MeSH. There are also over 218,000 entry terms that assist in finding the most appropriate MeSH Heading, for example, Vitamin C is an entry term to Ascorbic Acid. In addition to these headings, there are more than 219,000 headings called Supplementary Concept Records (formerly Supplementary Chemical Records) within a separate thesaurus. The MeSH thesaurus is used by NLM for indexing articles from 5,400 of the world' '''s leading biomedical journals for the MEDLINE/PubMED database. It is also used for the NLM-produced database that includes cataloging of books, documents, and audiovisuals acquired by the Library. Each bibliographic reference is associated with a set of MeSH terms that describe the content of the item. Similarly, search queries use MeSH vocabulary to find items on a desired topic.

Phymm and PhymmBL
type: Resource
type: NamedIndividual
has db xref: OMICS_01461
abbrev: Phymm
abbrev: PhymmBL
IAO_0000115: Software for Phylogenetic Classification of Metagenomic Data with Interpolated Markov Models to taxonomically classify DNA sequences and accurately classify reads as short as 100 bp. PhymmBL, the hybrid classifier included in this distribution which combines analysis from both Phymm and BLAST, produces even higher accuracy.

LREC Conferences
type: Resource
type: NamedIndividual
has db xref: nlx_75451
synonym: Language Resources Evaluation Conferences
synonym: LREC Conference
IAO_0000115: The LREC conference has become a major event in the field of language engineering, and constitutes a milestone in the life of Human Language Technologies (HLT). The International Conference on Language Resources and Evaluation is organized by ELRA biennially with the support of institutions and organizations involved in HLT, and brings together a large number of people working and interested in HLT.

USeq
type: Resource
type: NamedIndividual
has db xref: biotools:useq
has db xref: OMICS_00499
IAO_0000115: A collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms.

NCI Specimen Resource Locator
type: Resource
type: NamedIndividual
has db xref: nlx_80312
abbrev: Specimen Resource Locator
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. The Specimen Resource Locator is a database to help researchers locate human specimens (tissue, serum, DNA/RNA, other specimens) for cancer research. It includes tissue banks and tissue procurement systems with access to normal, benign, precancerous and cancerous human tissue from a variety of organs. Researchers specify the types of specimens, number of cases, preservation methods and associated data they require. The Locator will then search the database and return a list of tissue resources most likely to meet their requirements. When no match is obtained, the researcher is referred to the NCI Tissue Expediter (tissexp@mail.nih.gov). The Tissue expediter is a scientist who can help researchers identify appropriate resources and/or appropriate collaborators.

Pediatric Brain Tumor Foundation
type: Resource
type: NamedIndividual
has db xref: nlx_143893
abbrev: PBTF
IAO_0000115: The Pediatric Brain Tumor Foundation (PBTF) is a nonprofit organization dedicated to eradicating childhood brain tumors and providing support to families. It is a 501(c)(3) nonprofit charitable organization that seeks to * find the cause of and cure for childhood brain tumors by supporting medical research * increase public awareness about the severity and prevalence of childhood brain tumors * aid in the early detection and treatment of childhood brain tumors * support a national database on all primary brain tumors * provide educational and emotional support for children and families affected by this life-threatening disease. As the world''s largest non-governmental source of funding for childhood brain tumor research, we''re dedicated to not only eradicating this disease, but to providing support to families. Our educational resources deliver comfort and hope to families in need of information, and our college scholarship program gives brain tumor survivors a boost for the future. Through our efforts to raise public awareness, more attention has been focused on this deadly disease. Whether addressing congressional briefings or funding international conferences, the PBTF is an unwavering advocate. Together, we''re making a difference in the lives of children with brain tumors. And with your continued help, we will cure the kids!

Compass of Pleasure
type: Resource
type: NamedIndividual
has db xref: nlx_75617
synonym: The Compass of Pleasure
synonym: The Compass of Pleasure: Vice virtue and the brain''s pleasure circuits
IAO_0000115: A blog written by David J. Linden, Ph.D., professor of Neuroscience at the Johns Hopkins University School of Medicine, focusing on the brain''s pleasure circuits. Topics covered include exercise, pleasure and the brain; and understanding the biology of runners high. The Compass of Pleasure: How Our Brains Make Fatty Foods, Orgasm, Exercise, Marijuana, Generosity, Vodka, Learning, and Gambling Feel So Good is also a book and available for purchase. David J. Linden, Ph.D., is a professor in the Department of Neuroscience at the Johns Hopkins University School of Medicine. His laboratory has worked for many years on the cellular substrates of memory storage in the brain and a few other topics. He has a longstanding interest in scientific communication and serves as the Chief Editor of the Journal of Neurophysiology. He has written two books for a general audience about the biological basis of mental function: The Compass of Pleasure (Viking Press, 2011) and The Accidental Mind (Harvard/Belknap, 2007).

ANTS - Advanced Normalization ToolS
type: Resource
type: NamedIndividual
has db xref: nlx_75959
synonym: Advanced Normalization Tools
abbrev: ANTS
abbrev: ANTsX
IAO_0000115: Software package designed to enable researchers with advanced tools for brain and image mapping. Many of the ANTS registration tools are diffeomorphic*, but deformation (elastic and BSpline) transformations are available. Unique components of ANTS include multivariate similarity metrics, landmark guidance, the ability to use label images to guide the mapping and both greedy and space-time optimal implementations of diffeomorphisms. The symmetric normalization (SyN) strategy is a part of the ANTS toolkit as is directly manipulated free form deformation (DMFFD). *Diffeomorphism: a differentiable map with differentiable inverse. In general, these maps are generated by integrating a time-dependent velocity field. ANTS Applications: * Gray matter morphometry based on the jacobian and/or cortical thickness. * Group and single-subject optimal templates. * Multivariate DT + T1 brain templates and group studies. * Longitudinal brain mapping -- special similarity metric options. * Neonatal and pediatric brain segmentation. * Pediatric brain mapping. * T1 brain mapping guided by tractography and connectivity. * Diffusion tensor registration based on scalar or connectivity data. * Brain mapping in the presence of lesions. * Lung and pulmonary tree registration. * User-guided hippocampus labeling, also of sub-fields. * Group studies and statistical analysis of cortical thickness, white matter volume, diffusion tensor-derived metrics such as fractional anisotropy and mean diffusion.

Pediatric Low Grade Astrocytoma Foundation
type: Resource
type: NamedIndividual
has db xref: nlx_143894
synonym: Fight Juvenile Pilocytic Astrocytoma
abbrev: PLGA Foundation
IAO_0000115: The Pediatric Low Grade Astrocytoma (PLGA) Foundation is the largest, and only, non-profit organization dedicated to providing hope to children, parents, and families fighting Pediatric Low Grade Astrocytomas (PLGAs). We were founded in August 2007, as a 501(c)(3) foundation made up of families and friends dedicated to helping children who are struggling with brain tumors. To date, families associated with the Pediatric Low Grade Astrocytoma (PLGA) Foundation have raised over $6 million for DEDICATED PLGA research and funded over a dozen new research projects targeted specifically at children''s brain tumors or PLGA''s. These funds have supported the launch of the Dana Farber Cancer Institute''s PLGA Research Program as well as numerous grants distributed by the Brain Tumor Society, and other fine institutions. The PLGA Foundation awards 100% of funds to education and research in the search for more effective, less toxic treatment options for this potentially devastating childhood brain tumor. The PLGA Foundation actively promotes partnerships with other non-profit organizations, private individuals and government entities and has collaborated on fund raising, education and grant allocations in order to leverage resources and funds. Our goal at the Pediatric Low Grade Astrocytoma (PLGA) Foundation, also known as Fight Juvenile Pilocytic Astrocytoma (FightJPA.org), is to UNITE families around the country and around the world in the FIGHT for the lives of our children who suffer from PLGAs - childhood brain tumors. We can defeat childhood brain tumors through a united effort on all fronts to increase awareness, education, fundraising and research of pediatric low grade astrocytomas.

XNAT Extras
type: Resource
type: NamedIndividual
has db xref: nlx_156023
IAO_0000115: User software contributions for XNAT - The Extensible Neuroimaging Archive Toolkit, http://www.xnat.org

National Gene Vector Biorepository
type: Resource
type: NamedIndividual
has db xref: nlx_76398
abbrev: NGVB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Archiving services, insertional site analysis, pharmacology and toxicology resources, and reagent repository for academic investigators and others conducting gene therapy research. Databases and educational resources are open to everyone. Other services are limited to gene therapy investigators working in academic or other non-profit organizations. Stores reserve or back-up clinical grade vector and master cell banks. Maintains samples from any gene therapy related Pharmacology or Toxicology study that has been submitted to FDA by U.S. academic investigator that require storage under Good Laboratory Practices. For certain gene therapy clinical trials, FDA has required post-trial monitoring of patients, evaluating clinical samples for evidence of clonal expansion of cells. To help academic investigators comply with this FDA recommendation, the NGVB offers assistance with clonal analysis using LAM-PCR and LM-PCR technology.

Boston Biochem
type: Organization
type: NamedIndividual
has db xref: nlx_152321
synonym: Boston Biochem Inc.
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 17, 2021. An Antibody supplier.

Gerry and Nancy Pencer Brain Trust
type: Resource
type: NamedIndividual
has db xref: nlx_143895
abbrev: Gerry & Nancy Pencer Brain Trust
IAO_0000115: The Gerry & Nancy Pencer Brain Trust is a not-for-profit organization with a mandate to make a difference in the quality of life of people living with brain tumors. This registered charity is the primary source of funding for The Gerry & Nancy Pencer Brain Tumor Centre, and carries out annual fundraising events to support its'' ongoing research and patient care activities. The Gerry & Nancy Pencer Brain Tumor Centre is located in Toronto, Canada at the world-renowned Princess Margaret Hospital. The Centre provides multidisciplinary care, treatment, support, and education for brain tumor patients and their families, and promotes brain tumor research in the hopes of one day finding a cure for brain cancer. All of this is made possible through your very generous donations.

NGVB Toxicology Database
type: Resource
type: NamedIndividual
has db xref: nlx_76547
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 26, 2019, The National Gene Vector Biorepository offers an informational toxicology database as a resource to gene therapy investigators. The database contains information on animal studies that have been con…

Brain Injury Alliance of Kentucky
type: Resource
type: NamedIndividual
has db xref: nlx_143896
abbrev: BIAK
IAO_0000115: At Brain Injury Alliance of Kentucky (BIAK), a 501(c)(3) non-profit agency, our sole mission is to serve Kentucky citizens whose lives have been affected by brain injury. We do this through advocacy, education, prevention, research, service and support. BIAK links survivors of brain injury and their families to support from others with similar experience; provides them with education and information about living and coping with brain injury; assists them in locating resources for financial assistance; and seeks to connect people with sources of emotional support. BIAK began as an outgrowth of a Lexington area support group in the early 1980s. Family members, medical staff and others felt the need to expand the services and support to reach statewide. The state office was moved to Louisville and incorporated in 1986. BIAK now has offices and staff in Louisville and Lexington. BIAK seeks to share its philosophy, experience and skills with survivors, family members, students, caregivers, administrators, health professionals, legislators, the lay community and all those who desire to make a difference in the life of individuals with brain injuries and their families. At BIAK you will find information about brain injury. We define brain injury as any injury to the brain including injury received from a fall, a stroke, trauma, anoxia, infection, and tumors or other illnesses. Each year, a growing number of Kentucky citizens are affected by brain tumors. These may range from benign tumors to aggressive cancers. The Michael Quinlan Brain Tumor program recently joined BIAK to provide service and support to individuals and families who have been affected by brain tumors. There is always help available to you and your family.

NucPosSimulator
type: Resource
type: NamedIndividual
has db xref: OMICS_00512
IAO_0000115: A simulation tool to identify positions of nucleosomes from Next Generation Sequencing data.

National University of Sciences and Technology; Islamabad; Pakistan
type: NamedIndividual
has db xref: nlx_153821
synonym: National University of Sciences & Technology
synonym: National University of Sciences and Technology
abbrev: NUST

Loma Linda University Cancer Center Biospecimen Laboratory
type: Resource
type: NamedIndividual
has db xref: nlx_76868
abbrev: LLU Cancer Center Biospecimen Laboratory
IAO_0000115: The Loma Linda University Cancer Center Biospecimen Laboratory provides specimens for researchers as they search for the causes of cancer, and look for new means of prevention and treatment. The specimens include tissues, blood products (blood cell, plasma and serum) and bone marrow cells. Researchers interested in gaining access to the Biospecimen Laboratory''s samples should email Dr. Saied Mirshahidi, requesting access. The number and types of samples we have available for research can be viewed, http://www.llu.edu/catissuesummary/. Use the Biospecimen Laboratory Tissue Request Form to request specimens for research studies.

Southeastern Brain Tumor Foundation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100003421
has db xref: grid.481206.9
has db xref: ISNI: 0000 0004 5902 7216
has db xref: nlx_143897
abbrev: SBTF
IAO_0000115: Founded in 1995, the Southeastern Brain Tumor Foundation (SBTF), a 501c3 not-for-profit charitable foundation, is devoted to improve the quality of life for brain tumor patients and their families. By offering information, education and support services, we aspire to instill hope, knowledge and comfort to all involved. The Southeastern Brain Tumor Foundation also raises funds for research and medical personnel so that a cure can be found. For over a decade, the SBTF has become a well-known fundraising entity supporting critical, cutting edge brain tumor research at major medical centers in the Southeast. Our annual Race for Research held in Atlanta, Georgia each summer, is our main fundraising event popular throughout Atlanta and the surrounding metropolitan area and has funded over $1.2 million dollars in research grants to leading researchers at major medical centers throughout the Southeast over the past decade. We are proud of our dedicated, all volunteer Board of Directors who meet monthly. Our Board is a diverse group comprised of individuals who''ve been touched by brain tumors in many different ways. Ranging from patients and family members to healthcare professionals; we are all committed to promoting the awareness of brain tumors in the community, communicating with patients and families and raising critical funds for research grants furthering advancements in the treatment of brain tumors. Our monthly support group, lead by a nurse practitioner, welcomes patients and their families to sit side by side with each other, share their experiences, communicate and receive support. As a neurosurgeon-scientist focused on the treatment of patients with brain tumors, I am committed to advancing the mission of SBTF forward in the fight against brain tumors. Our ability to serve the brain tumor community is dependent on each of you. Whether you support us with a financial donation in our fundraising efforts or with your time as a volunteer, each of you are a vital an…

GENEtics Video
type: Resource
type: NamedIndividual
has db xref: nlx_76974
IAO_0000115: GENEticS is arap video about genetics. So let''s talk about genes, and I don''t mean trousers, go the lyrics to this catchy rap video created for The GAMY (Genetics and Merthyr Youth) Project. It is one of the many videos, games, and digital media used by researchers at the University of Glamorgan in the United Kingdom use to engage local teenagers in a conversation about genetics. Video produced by Jon Chase (aka Oort Kuiper).

Pain Genes database
type: Resource
type: NamedIndividual
has db xref: nlx_77039
has db xref: r3d100012129
synonym: PainGenes DB
abbrev: PainGenesdb
IAO_0000115: Database of genes regulated by pain derived from published manuscripts describing results of pain-relevant knockout studies. The database has two levels of exploration: across-gene and within-gene. The across-gene level, the PainGenesdbSelector, is encountered first. All genes in the database can be accessed and sorted by their gene name, protein name, common names and acronyms, or genomic position (by navigating a graphic representation of the mouse genome). The gene and protein names can be selected from an alphabetical list, or by typing a text string into a search box.

NBC
type: Resource
type: NamedIndividual
has db xref: OMICS_01458
synonym: Naive Bayes Classification tool
synonym: Naive Bayesian Classification Tool
synonym: Na����ve Bayesian Classification tool
IAO_0000115: Webserver for taxonomic classification of metagenomic reads.

University of Lausanne; Lausanne; Switzerland
type: NamedIndividual
has db xref: nlx_17468
synonym: Universite de Lausanne
synonym: University of Lausanne
synonym: Université de Lausanne
abbrev: UNIL

Division of cancer treatment
type: Government granting agency
type: NamedIndividual
has db xref: nlx_inv_1005053
abbrev: CM
abbrev: NCI
IAO_0000115: PAsRFAs.htm

Barth Syndrome Biorepository
type: Resource
type: NamedIndividual
has db xref: nlx_77178
synonym: Barth Syndrome Registry and Repository
abbrev: BRR
IAO_0000115: The Barth Syndrome Registry and Repository (BRR) at the University of Florida and Children''s Hospital Boston was created to provide additional information about this rare disorder. By collecting information directly from families and abstracting medical information from patient records, we hope to build a large anonymized database that is useful for answering scientific research questions and that is a source of medical information. Additionally, we are collecting blood samples for DNA isolation and storage and for the development of special cell lines. These tools will allow researchers to better understand the cellular and genetic nature of this disease and how these abnormalities may impact the clinical variability of Barth syndrome patients. Currently available data from the Barth Syndrome Registry and Repository includes self-reported data. This includes basic demographics, age at diagnosis of Barth Syndrome, reason for diagnosis, family history; symptoms, presence or absence of a history of cardiomyopathy, history regarding hospitalizations, cardiac transplant or listing for transplant, presence or absence of a history of neutropenia; history of infections, medical therapy and basic developmental history. We are in the process of abstracting medical data to build a more complete medical database and may be able to provide additional data with a specific request. Currently the DNA bank has data from 65 patients, genomic DNA from 50 patients, lymphoblast lines from 41 patients, fibroblast lines from 3 patients, and myocardium/autopsy from 3 patients. However, this is increasing as new patients enroll in the Registry. Please contact us with questions and specific requests about data or specimens.

Interpore Cross International
type: Resource
type: NamedIndividual
has db xref: nlx_77350
abbrev: Interpore Cross
IAO_0000115: Biomet and Interpore Cross are on the cutting edge of technology in the orthopedic biomaterials market. Our focus is developing and providing truly innovative products, which meet the rapidly expanding needs of orthopedic surgeons both today and in the future. Our Pro Osteon resorbable bone graft material is derived from an abundant non-decorative coral. Pro Osteon is available in a selection of fully resorbable sterile granules and blocks, in a variety of shapes and sizes. Our InterGro DBM products combine the osteoinductivity of DBM with a natural, non-soluble carrier that won''t wash away, delivering a unique bone graft that offers superior handling and performance characteristics. This highly-moldable composite graft can be easily formed to fit any shape fracture or defect.

SVMerge
type: Resource
type: NamedIndividual
has db xref: biotools:svmerge
has db xref: OMICS_00325
synonym: SVMerge - Enhanced structural variant and breakpoint detection
IAO_0000115: Software pipeline to detect structural variants (SVs) by integrating calls from several existing SV callers, which are then validated and the breakpoints refined using local de novo assembly. The output is in BED format allowing for easy downstream analysis or viewing in a genome browser. It is modular and extensible allowing new callers to be incorporated as they become available.

Knut and Alice Wallenberg Foundation
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 501100004063
has db xref: grid.453057.0
has db xref: nlx_77359
synonym: Knut och Alice Wallenbergs Stiftelse
abbrev: Wallenberg Foundation
IAO_0000115: One of the largest financiers of research in Sweden that promotes scientific research, teaching and/or education beneficial to the Kingdom of Sweden. 20-30 percent of the Foundation''s grants relate to high-value research equipment for use within the technical, natural sciences and biomedical fields, and about 50 percent relate to major research projects and substantial scientific networks. Universities, academies and similar research and educational institutions are eligible for grants within the following fields: * Expensive scientific equipment * Fellowship programs initiated by the Foundation * Selected research projects of significant potential * Larger educational research projects Applications may be submitted by individual scientists, or research groups affiliated to a Swedish university or equivalent institution. An application may also be submitted by the management of a university, university college, scientific academy, or national research associations. Applications from private individuals without connection to a scientific institution are not considered.

BrainPod
type: Resource
type: NamedIndividual
has db xref: nlx_77376
synonym: BrainPod Podcast
synonym: Neuropsychopharmacology Podcast
synonym: NPP Podcast
IAO_0000115: BrainPod is the podcast from the journal Neuropsychopharmacology. Join us as we delve into the latest basic and clinical research that advance our understanding of the brain and behavior, featuring highlighted content from a top journal in fields of neuroscience, psychiatry, and pharmacology.

Causal Cognition Group
type: Organization
type: NamedIndividual
has db xref: nlx_143899
synonym: Grupo Investigaci��n Aprendizaje Causal
abbrev: CCG
IAO_0000115: At the Website of the Causal Cognition Group (CCG) of the University of M��laga, you may read information about our group, its members, our research, main activities, and more. Our main interests are cognitive psychology and learning, and more recently cognitive neuroscience, physiological correlates of learning and cognitive control. This site is in constant evolution... though there are things that hardly change: Cognitio rei per causas.

Arnold Arboretum of Harvard University: Weld Hill Molecular Lab
type: Resource
type: NamedIndividual
has db xref: nlx_156118
IAO_0000115: The molecular lab at Weld Hill is well equipped for modern molecular studies, from RNA expression studies to phylogenetic analyses.

PATO
type: Resource
type: NamedIndividual
has db xref: nlx_77534
synonym: PATO - Phenotypic Quality Ontology
synonym: Phenotype and Trait Ontology
synonym: Phenotypic Quality Ontology
IAO_0000115: Ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation. The new PATO differs from the old in that the system of attributes and values has been abandoned in favor of a single hierarchy of qualities. PATO is designed to be used in conjunction with ontologies of quality-bearing entities. An example of such an entity is an insect eye (taken from the fly_anatomy ontology), which could be the bearer of the quality ''red'' (PATO:0000322). This combination is the red eye phenotype. We say that the phenotype term is ''post-coordinated'', as it is formed by coordinating two terms together. This is in contrast to ontologies of pre-coordinated phenotypes, such as the Mammalian Phenotype (MP) ontology. PATO is independent of any exchange format or database schema. One way of expressing phenotype annotation using PATO is pheno-syntax, or pheno-xml. They will also post recommendations for representing phenotypes using OWL. All representations share the same basic formal underpinnings, a combination of quality-bearing entity and a quality (the EQ model).

UAB Traumatic Brain Injury Model System
type: Resource
type: NamedIndividual
has db xref: nlx_143902
synonym: University of Alabama at Birmingham Traumatic Brain Injury Model System
abbrev: UAB-TBIMS
IAO_0000115: This website offers educational materials and information on services of the UAB Traumatic Brain Injury Model System (UAB-TBIMS) along with links to national organizations, government agencies, and educational resources related to traumatic brain injury. The UAB-TBIMS is one of 16 national TBI Model Systems Centers working to maintain and improve a cost-effective, comprehensive service delivery system for people who incur a traumatic brain injury. A Model System must demonstrate outstanding care to individuals with traumatic brain injury, from the emergency medical services, to acute care in the hospital, to rehabilitation. The UAB TBIMS * conducts research, * distributes their research findings to both clinical and consumer audiences * collaborates with other clinical research programs and * participates in the Model Systems Database. This Center, operates within the UAB Department of Physical Medicine and Rehabilitation, which is located at Spain Rehabilitation Center in the UAB Hospital complex. Here it establishes and maintains links with emergency medical service agencies throughout the state, with state vocational rehabilitation and long-term follow-up programs.

mouseMAP
type: Resource
type: NamedIndividual
has db xref: nlx_143914
synonym: mouseMAP: Tissue-specific functional networks for the laboratory mouse
abbrev: MouseMAP
IAO_0000115: In collaboration with several research groups at Jackson Laboratory, we mapped the tissue-specific functional relationship networks in the laboratory mouse by simulating the natural tissue specificity realized by differential protein expression between tissues. MouseMAP is an interface that allows browsing networks of different tissues and the comparison between them. The current version of MouseMAP includes one global network as an extension of mouseNET (http://mousenet.princeton.edu) and 107 tissue-specific networks organized into 15 different major body systems. The interface has the following features (their usage are detailed in Help and FAQ page): 1. Single graph query with one or multiple genes of interests. 2. Expansion/shrinking of query results through edge or node cutoffs. 3. Comparison of local networks between different tissues. 4. Dynamic generation of figure legend to facilitate manuscript writing.

Human Tissue Resource Network
type: Resource
type: NamedIndividual
has db xref: nlx_78270
has db xref: nlx_144405
synonym: Ohio Tissue Procurement Shared Resources
abbrev: HTRN
IAO_0000115: Collect, bank, and distribute human tissue and fluid specimens by uniting tissue-based research resources within the OSU Department of Pathology and promoting collaborative research within the OSU Medical Center and related national human research projects. The HTRN is comprised of the Pathology Core Facility (PCF), Tissue Archive Service (TAS), Tissue Procurement Service (TPS), AIDS and Cancer Specimen Resource (ACSR), the Cancer and Leukemia Group B Pathology Coordinating Office (CALGB - PCO), and an Adenoma Polyp Tissue Bank (APTB).

GeneDB Tbrucei
type: Resource
type: NamedIndividual
has db xref: nlx_78417
synonym: Trypanosoma brucei TREU927 homepage on GeneDB
synonym: Trypanosoma brucei TREU927 on GeneDB
abbrev: GeneDB T. brucei
abbrev: GeneDB_Tbrucei
IAO_0000115: Database of the most recent sequence updates and annotations for the T. brucei genome. New annotations are constantly being added to keep up with published manuscripts and feedback from the Trypanosomatid research community. You may search by Protein Length, Molecular Mass, Gene Type, Date, Location, Protein Targeting, Transmembrane Helices, Product, GO, EC, Pfam ID, Curation and Comments, and Dbxrefs. BLAST and other tools are available. T. brucei possesses a two-unit genome, a nuclear genome and a mitochondrial (kinetoplast) genome with a total estimated size of 35Mb/haploid genome. The nuclear genome is split into three classes of chromosomes according to their size on pulsed-field gel electrophoresis, 11 pairs of megabase chromosomes (0.9-5.7 Mb), intermediate (300-900 kb) and minichromosomes (50-100 kb). The T. brucei genome contains a ~0.5Mb segmental duplication affecting chromosomes 4 and 8, which is responsible for some 75 gene duplicates unique to this species. A comparative chromosome map of the duplicons can be accessed here (PubmedID 18036214). Protozoan parasites within the species Trypanosoma brucei are the etiological agent of human sleeping sickness and Nagana in animals. Infections are limited to patches of sub-Saharan Africa where insects vectors of the Glossina genus are endemic. The most recent estimates indicate between 50,000 - 70,000 human cases currently exist, with 17 000 new cases each year (WHO Factsheet, 2006). In collaboration with GeneDB, the EuPathDB genomic sequence data and annotations are regularly deposited on TriTrypDB where they can be integrated with other datasets and queried using customized queries.

Division of clinical sciences
type: Government granting agency
type: NamedIndividual
has db xref: nlx_inv_1005054
abbrev: NCI
IAO_0000115: dcshome.htm

California Transplant Services
type: Resource
type: NamedIndividual
has db xref: nlx_78575
synonym: California Transplant Services Inc.
abbrev: CTS
IAO_0000115: California Transplant Services (CTS) is a full service eye and tissue bank headquartered in Carlsbad, California. CTS is a California non-profit public benefit corporation qualified by the IRS as a section 501(c)3 public charity, licensed by the California Department of Public Health as a Tissue Bank and registered and inspected by the United States Food and Drug Administration. We were also inspected by the American Association of Tissue Banks in September of 2003 and awarded Accreditation in December 2003. California Transplant Services is a Member of the Eye Bank Association of America. We are registered in California with the Office of Charitable Trusts. Most of CTS California Transplant''s fulltime staff are Certified Tissue Bank Specialists (CTBS) by the AATB or Certified Eye Bank Technicians (CEBT) by the Eye Bank Association of America. CTS staffing includes fulltime and part time tissue procurement specialists. CTS helps tissue banks by providing 24 hour tissue placement services from it''s west coast USA distribution center. CTS has provided cornea and bone tissue placement services nationwide since 1994.

National Cancer Institute Biorepositories
type: Resource
type: NamedIndividual
has db xref: nlx_78616
synonym: National Cancer Institute Biological Testing Branch Services
synonym: NCI BTB Services
abbrev: NCI Biorepositories
IAO_0000115: National Cancer Institute Biorepositories provides information on the tumor repository, animal production program, and access to other NIH Repositories. A catalog of in vitro cell lines, transplantable animal and human tumors and microarrays, including ordering information, is available. In the Animal Production Program, rodents are supplied to Federal Institutions and to grantees/contractors with a current OLAW Assurance on file. Requests from international entities seeking rodent strains solely available from the NCI Animal Production Program must have an OLAW Assurance or current AAALACi accreditation and will be evaluated on a case-by-case basis. In general, the rodents are supplied to the following: * Researchers at NCI-Frederick * NIH on-campus laboratories * NIH/NCI funded research contracts * NIH/NCI funded grantees * Other government agencies To meet the above needs, animal production contracts plus quality control contracts are used. The animal production contracts are used to propagate the NIH sublines of the strains. Many of the strains produced are not available commercially and the NCI program is the sole source of several lines.

OSUCCC-James
type: Resource
type: NamedIndividual
has db xref: nlx_78698
synonym: Ohio State University Comprehensive Cancer Center
synonym: Ohio State University Comprehensive Cancer Center - James Cancer Hospital and Solove Research Institute
synonym: Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Solove Research Institute
synonym: OSUCCC
synonym: OSUCCC - The James Cancer Hospital and Solove Research Institute
synonym: The James
synonym: The James Comprehensive Cancer Center
IAO_0000115: As the Midwest''s first and Ohio''s only fully dedicated cancer hospital and research institute, The Ohio State University Comprehensive Cancer CenterArthur G. James Cancer Hospital and Solove Research Institute (OSUCCC-James) is one of the nation''s premier cancer centers for the prevention, detection and treatment of cancer. The OSUCCC-James is one of only 40 centers in the United States designated by the National Cancer Institute a Comprehensive Cancer Center. In addition, the OSUCCC-James is a founding member of the National Comprehensive Cancer Network (NCCN), an alliance of 21 of the world''s leading cancer centers that develops clinical practice guidelines to improve the quality and effectiveness of care provided to patients with cancer. The Ohio State cancer program is part of The Ohio State University, the largest public university in the nation. We are affiliated with The Ohio State University Medical Center, one of the largest and most diverse academic medical centers in the nation and the only academic medical center in central Ohio. The cancer program at Ohio State encompasses more than 200 comprehensive cancer center members from 13 of the 18 colleges at The Ohio State University and includes physicians from 16 specialties. The OSUCCCJames'' singular focus on cancer has led to multiple accomplishments that have changed the standards of care with respect to prevention, diagnosis and treatment, in a way that substantially improves outcomes for cancer patients.

Boehringer
type: Organization
type: NamedIndividual
has db xref: grid.508568.6
has db xref: nlx_152320
IAO_0000115: An Antibody supplier

MLTreeMap
type: Resource
type: NamedIndividual
has db xref: biotools:mltreemap
has db xref: OMICS_01457
synonym: Phylogenetic analysis of metagenomics sequence data
IAO_0000115: Data analysis service that analyzes DNA sequences and determines their most likely phylogenetic origin. Its main use is in metagenomics projects, where DNA is isolated directly from natural environments and sequenced (the organisms from which the DNA originates are often entirely undescribed). It will search such sequences for suitable marker genes, and will use maximum likelihood analysis to place them in the ' '''Tree of Life' '''. This placement is more reliable than simply assessing the closest relative of a sequence using BLAST. More importantly, MLTreeMap decides not only who is the closest relative of your query sequence, but also how deep in the tree of life it probably branched off. Additionally, MLTreeMap searches the sequences for genes, which are coding for key enzymes of important functional pathways, such as RuBisCo, methane monooxygenase or nitrogenase. In case of a positive hit, MLTreeMap uses maximum likelihood analysis to place them in the respective ' '''gene-family tree' '''.

Surgical Procedures
type: Resource
type: NamedIndividual
has db xref: nlx_79028
synonym: Surgical Procedures (Wikibook)
IAO_0000115: Surgical Procedures is a wikibook on surgical procedures. It is by no means intended to be a guide to at-home surgery. Surgical illness should only be managed by a professional medical expert (e.g Surgeon). Topics include: 1. Abdominoplasty 2. Adenoidectomy 3. Amputation 4. Melanoma 5. Mandibular Fractures 6. General Surgery Guidelines 7. Abdominal Surgery A. Cholecystectomy * Open Cholecystectomy * Lap Cholecystectomy B. Cholecystitis C. Cholecystography D. Cholelithiasis E. Choledocholithiasis 8. General Surgery 9. Acid Base Disorder 10. Plastic Surgery

LifeCenter Organ Donor Network
type: Resource
type: NamedIndividual
has db xref: nlx_79032
abbrev: LifeCenter
IAO_0000115: LifeCenter Organ Donor Network, A Donate Life Organization, encourages and coordinates the donation of human organs and tissues for transplantation. In 1981 LifeCenter began operating as an independent, not-for-profit organ procurement organization (OPO) with a mission to save, enhance and change lives through organ and tissue donation. LifeCenter is accredited by the Association for Organ Procurement Organizations (AOPO) and the American Association of Tissue Banks (AATB), and has been approved and designated by the Centers for Medicare and Medicaid Services (CMS) as the primary OPO serving eight counties in Southwestern Ohio, six counties in Northern Kentucky and two counties in Southeastern Indiana. LifeCenter is an institutional member of the United Network for Organ Sharing (UNOS) and follows all the guidelines for organ sharing. The population of LifeCenter''s service area is approximately two million people. Within this area there are 30 hospitals that LifeCenter works with to facilitate and coordinate organ and tissue donation. The clinical staff provides 24-hour service for referrals, case management, recovery and organ placement. Our education staff provides programs for schools, civic and community groups, religious institutions and healthcare professionals. Additional services offered by LifeCenter include bereavement services for donor families, volunteer opportunities, and donor drives for area businesses and organizations that facilitate the enrollment of donors.

Cardiovascular Gene Ontology Annotation Initiative
type: Resource
type: NamedIndividual
has db xref: nlx_79058
synonym: Cardiovascular Gene Ontology
synonym: Cardiovascular GO Annotation Initiative
abbrev: BHF-UCL
abbrev: CV-GO
IAO_0000115: Full Gene Ontology annotation to genes associated with cardiovascular processes. Every GO annotation made, is attributed to an identified source, such as a publication identifier (PMID), and an indication of the type of evidence which supports the association between the gene product and the GO term. Over 4,000 cardiovascular associated genes have been identified. A variety of tools have been provided to enable cardiovascular scientists to review the annotation of their ' '''favorite' ''' gene and suggest information that may be missing, inaccurate or incomplete in these annotations. Annotation suggestions can be sent through the feedback form or by email. The Gene Ontology (GO) vocabulary is the established standard for the functional annotation of gene products. By using GO to curate scientific literature and by integrating results from high-quality high-throughput experiments they will create an information-rich resource for the cardiovascular-research community, enabling researchers to rapidly evaluate and interpret existing data and generate hypotheses to guide future research.

RIKEN Brain Science Institute
type: Resource
type: NamedIndividual
has db xref: nlx_143907
synonym: Brain Science Institute
synonym: RIKEN BSI
abbrev: BSI
IAO_0000115: RIKEN Brain Science Institute (BSI) has a mission to produce innovative research and technology leading to scientific discoveries of the brain. In addition, BSI aims to develop domestic and international brain researchers by creating an environment that will integrate various intellectual disciplines and from that convergence find solutions that will ultimately benefit society in the realms of medicine, engineering, business, and education. In striving toward this goal, BSI has become a leading international center for brain research with a reputation for discovery, innovation, training, and globalization of the scientific enterprise. Brain science is valuable not only for the advancement of science but also because it can greatly impact our society and economy. To meet these expectations, the Brain Science Institute (BSI) was established in 1997 as part of RIKEN, an independent research institution supported by the Japanese government.

PEDRAW/WPEDRAW
type: Resource
type: NamedIndividual
has db xref: nlx_154527
synonym: Pedigree Drawing/ Window Pedigree Drawing (MS-Window and X-Window version of PEDRAW)
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A pedigree drawing program using LINKAGE data files (entry from Genetic Analysis Software)

Code4Lib Journal WordPress Customizations
type: Resource
type: NamedIndividual
has db xref: nlx_79075
IAO_0000115: WordPress plugins for Anti-Spam, Metadata, Presentation, URLs, and Workflow from the Code4Lib community, a group of computer programmers and library technologists who largely work for and with libraries. Anti-Spam *Akimset - Filters out spam-link comments based on their content *reCAPTCHA - Requires users to copy a distorted word before they can comment Metadata *COinS Quicktags Button - In the non-WYSIWYG editor, can be used to build a basic COinS tag. This has been abandoned in favor of the generator at http://generator.ocoins.info/. *unAPI Server - Provides information about articles. Useful for Zotero users. Presentation *SyntaxHighlighter - Makes code pretty. *C4LJ Custom the_author()- Replaces the text returned by the_author() with the value of the author custom field. Necessary since articles are entered by their editors, but we want author information to appear on the articles and in the syndication feeds. URLs *C4LJ Remove Parents - A customization of http://wordpress.org/extend/plugins/remove-parents/. Prettifies category URLs so that issues appear at http://journal.code4lib.org/issues/issue1 instead of http://journal.code4lib.org/issues/issues/issue1. *FeedBurner FeedSmith - Redirects the main feed and the general comments feed to FeedBurner Workflow *Issue Manager - Enables one-click publishing of new issues, and prevents articles from being published until their associated issue is published. *Role Manager - Allows creation of custom roles and editing of roles' permissions. Used to create the Reviewer role, which can read Private articles, so that authors can see their articles before publication, and to prevent editors from publishing articles on accident.

Dresden University of Technology; Saxony; Germany
type: Organization
type: NamedIndividual
has db xref: Crossref Funder ID 501100002957
has db xref: GRID grid.4488.0
has db xref: ISNI 0000 0001 2111 7257
has db xref: nlx_53167
has db xref: Wikidata Q158158
synonym: Dresden University of Technology
synonym: Technische Universitat Dresden
synonym: Technische Universität Dresden
abbrev: TU Dresden
abbrev: TUD
IAO_0000115: Public research university founded in 1828. One of the largest Universities of Technology in Germany.

Apo and Holo structures DataBase
type: Resource
type: NamedIndividual
has db xref: biotools:ah-db
has db xref: nlx_143908
synonym: Apo-Holo DataBase
abbrev: AH-DB
IAO_0000115: Database of apo and holo structure pairs of proteins before and after binding. Various protein functions have been shown directly associated with conformational transitions triggered by binding other molecules. Tertiary structures determined in the unbound and bound state are usually named apo and holo structures, respectively. AH-DB is the largest database of apo-holo structure pairs and provides a sophisticated interface to search and view the collected data. It contains 746314 apo-holo pairs of 3638 proteins from 702 organisms.

NCBI BioProject
type: Resource
type: NamedIndividual
has db xref: biotools:bioproject
has db xref: nlx_143909
has db xref: r3d100013330
synonym: BioProject
synonym: NCBI BioProject Database
IAO_0000115: Database of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. It is a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. Submissions are supported by a web-based Submission Portal. The database facilitates organization and classification of project data submitted to NCBI, EBI and DDBJ databases that captures descriptive information about research projects that result in high volume submissions to archival databases, ties together related data across multiple archives and serves as a central portal by which to inform users of data availability. BioProject records link to corresponding data stored in archival repositories. The BioProject resource is a redesigned, expanded, replacement of the NCBI Genome Project resource. The redesign adds tracking of several data elements including more precise information about a project' '''s scope, material, and objectives. Genome Project identifiers are retained in the BioProject as the ID value for a record, and an Accession number has been added. Database content is exchanged with other members of the International Nucleotide Sequence Database Collaboration (INSDC). BioProject is accessible via FTP.

Digital Enterprise Research Institute
type: Resource
type: NamedIndividual
has db xref: nlx_79295
synonym: Digital Enterprise Research Institute (DERI)
abbrev: DERI
IAO_0000115: The Digital Enterprise Research Institute is an internationally recognized institute in semantic web research, education and technology transfer. DERI brings together academic and industrial partners to boost innovation in science and technology, which directly contributes to the Irish government''s plan of transforming Ireland into a competitive knowledge economy.

HemaCare Corp.
type: Resource
type: NamedIndividual
has db xref: nlx_80638
synonym: HemaCare Corporation
abbrev: HemaCare
IAO_0000115: Collects, processes, and distributes human blood products to hospitals and research-related organizations. They operate donor centers and mobile donor vehicles to collect transfusable blood products from healthy donors, and offer human-derived blood products to research organizations. HemaCare also provides blood related services, principally therapeutic apheresis procedures, stem cell collection and other blood treatments, to patients and in connection with clinical trials.

SVseq
type: Resource
type: NamedIndividual
has db xref: biotools:svseq
has db xref: OMICS_00327
synonym: SVseq1
synonym: SVseq2
IAO_0000115: Software for accurate and efficient calling of structural variations with low-coverage sequence data. Version 2 uses the BAM files of paired Illumina reads with soft-clip signature as input. It calls both deletions and insertions.

Daniel Mietchens demo wiki: What would scholarly communication look like if it were invented today?
type: Resource
type: NamedIndividual
has db xref: nlx_79345
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 08, 2013. Wiki serving as a demo for integrating wikis with scientific workflows, extending peer review and open access from formal scholarly publishing to the whole research cycle. Just imagine you could browse science as it happens. It is intended to be launched, as a prototype, in early 2011, and any help with it is welcome just create an account and mention here how you would like to get involved. In the initial phase, the platform will primarily be used to simply archive copies of scholarly articles that were formally published under an Open license. This WikiRepository shall provide a unified front-end to search, discover and sort all these Open Access papers, and to annotate, share, bookmark and discuss them. Later on, it is intended to be complemented by a formal publishing platform, WikiJournal. From the start on, emphasis will be placed on updatability of published research, on placing new research in the context of existing knowledge as well as ongoing and even planned research on the matter, and of the communities concerned.

Neuroscientists Talk Shop
type: Resource
type: NamedIndividual
has db xref: nlx_151818
IAO_0000115: The University of Texas at San Antonio''s (UTSA) Neurobiology Podcast, showcasing the current research of internationally renowned guest Neuroscientists. Each episode features a moderated discussion with a cross section of UTSA Neurobiology faculty, highlighting the featured guest''s research, and the state of the art in the field at hand.

OpenFlyData.org
type: Resource
type: NamedIndividual
has db xref: nlx_79461
synonym: open fly data
synonym: OpenFlyData
synonym: openflydata
IAO_0000115: A cross-database search service for Drosophila gene expression data, including microarray data from FlyAtlas and in situ images from BDGP and Fly-TED. The applications provide different ways to search for and compare gene expression data for the fruit fly Drosophila melanogaster. You may Search Gene Expression Data by Gene, Gene Batch, and by Tissue Expression Profile. A number of Web services (SPARQL endpoints) are provided from this site which may be queried programmatically for data.

SEQanswers
type: Resource
type: NamedIndividual
has db xref: nlx_143910
has db xref: OMICS_01710
synonym: SEQanswers: the next generation sequencing community
IAO_0000115: An information resource and user-driven community focused on all aspects of next-generation genomics. They hope to become the central location for next generation sequencing technology discussion and education. The site will always attempt to cater to everyone, regardless of scientific background or knowledge. The High-Throughput Sequencing Map site was conceived by James Hadfield (Cancer Research UK, Cambridge) and built by Nick Loman (University of Birmingham). The database is as only as good as you, the users.

Bio-Mixer
type: Resource
type: NamedIndividual
has db xref: nlx_80071
synonym: BioMixer
IAO_0000115: Bio-Mixer is a web-based environment that supports the flexible exploration of biomedical ontologies. The concepts in the ontologies and their mappings can be explored in different views such as graph views, lists and timeline views. Drag-and-drop interaction can be used to show items and collections in different views, to create filtered views and to synchronize selections. Bio-Mixer enhances drag and drop with a new drop target highlighting and preview approach to make working with multiple collections and views easy. Bio-Mixer also provides support for ontology annotation and workspace sharing between collaborators. For more information, visit code.google.com/p/bio-mixer/

SEQanswers Wiki
type: Resource
type: NamedIndividual
has db xref: nlx_143911
has db xref: OMICS_01743
abbrev: SEQwiki
IAO_0000115: Wiki forum providing an extensive catalogue of manually categorized analysis tools, technologies and information about service providers, maintained by the members of the SEQanswers community. * Minimum Information about a high-throughput Sequencing Experiment * Software Hub: The place to add to, edit or browse the software database on SEQwiki. * Service Providers: Browse or edit the list of NGS service facilities. * How-to Hub: Mini reviews for the most used tools broken down by common tasks. * Developers Hub: The place to discuss the development of the SEQwiki site and its associated data. See also publishing SEQ*. * Publications: Publication about SEQwiki and selected citations.

Human Brain and Spinal Fluid Resource Center
type: Resource
type: NamedIndividual
has db xref: nif-0000-00231
synonym: Human Brain and Spinal Fluid Resource Center (HBSFRC)
synonym: Human Brain Spinal Fluid Resource Center
synonym: The Human Brain and Spinal Fluid Resource Center (HBSFRC)
synonym: UCLA Brain Bank
synonym: UCLA Brainbank
abbrev: HBSFRC
IAO_0000115: A biomaterial supply resource which collects, stores, and distributes donated tissue to research scientists around the world. Collection occurs through the an anatomical donor program which accepts tissue donation from people with neurological/ psychiatric disorders. The Center also provides a continuous boost to biomedical research by providing high quality and quantity of pre- and post-mortem brains, spinal cords, cerebrospinal fluid (CSF), serum, blood cells and urine to use in investigations of neurological and psychiatric diseases. Scientists without a clinical site may use the Center''s readily available, high quality banked specimens.

PRISM - Pair Read Informed Split Mapper
type: Resource
type: NamedIndividual
has db xref: OMICS_02288
synonym: Pair Read Informed Split Mapper
synonym: PRISM (Pair Read Informed Split Mapper)
IAO_0000115: Software for split read (reads which span across a structrual variant -- SV ) mapping and SV calling from the mapping result. It is able to detect small insertions and abitrary size deletions, inversions and tandom duplications with the direction of discordant read pairs. PRISM_CTX is a tool for detecting inter-chromosome trans-location events.

miRNAKey
type: Resource
type: NamedIndividual
has db xref: biotools:mirnakey
has db xref: OMICS_00364
IAO_0000115: A software pipeline for the analysis of microRNA Deep Sequencing data.

MG-RAST
type: Resource
type: NamedIndividual
has db xref: biotools:mg-rast
has db xref: OMICS_01456
synonym: Metagenomics RAST
synonym: MG-RAST - metagenomics analysis server
synonym: The Metagenomics RAST server
abbrev: MG RAST
IAO_0000115: An automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data. The server primarily provides upload, quality control, automated annotation and analysis for prokaryotic metagenomic shotgun samples.

Alaska Brain Injury Network
type: Resource
type: NamedIndividual
has db xref: nlx_143915
synonym: Alaska Brain Injury Network Inc.
synonym: Alaska Traumatic Brain Injury Advisory Board
synonym: ATBIAB
abbrev: ABIN
IAO_0000115: The Alaska Brain Injury Network, Inc (ABIN) is a non-profit organization dedicated to Alaskans whose lives have been changed by brain injury. The ABIN mission is to educate, plan, coordinate, and advocate for services for the survivors of traumatic brain injury and their families. ABIN''s Board of 18 directors represents all regions of Alaska, and at least 50 percent are TBI survivors or family members. ABIN has two primary functions: TBI Advisory Board and TBI Resource Navigation Agency. Advisory Board -Visit both urban and rural communities, and listen to the stories that the public shares about the issues facing Alaskans with brain injuries. -Collaborate with our partner boards to affect changes in policies to improve programs and services. -Advocate for safety legislation, in-state brain injury rehabilitation, and TBI Waiver services. -Bring TBI professional training to Alaska. -Conduct ''needs assessment'' surveys of survivors, family members, and health workers. -Maintain up to date information on emerging issues identified through callers, public testimony, and the media. Resource Navigation (Information and Referral) -Respond to requests for assistance, information, resources, and referral. -Distribute a brain injury resource directory with statewide and local resources and supports available to individuals, families, friends, professionals, caregivers and the general public. -Work to establish a TBI hotline and brain injury support groups. -Distribute educational and informational resources to the public.

NCBI Probe
type: Resource
type: NamedIndividual
has db xref: biotools:ncbi_dbprobe
has db xref: nlx_80513
has db xref: r3d100010780
synonym: dbProbe
synonym: Entrez Probe Database
synonym: NCBI Probe Database
synonym: Probe Database
synonym: ProbeDB
IAO_0000115: Public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications including genotyping, gene expression studies, SNP discovery, genome mapping, and gene silencing. Probe records contain information on reagent distributors, probe effectiveness, and computed sequence similarities. The database is constantly updated, with over 11,000,000 probes available. Users may deposit their data into NCBI Probe Database.

TrackVis
type: Resource
type: NamedIndividual
has db xref: nlx_143916
synonym: TrackVis and Diffusion Toolkit
IAO_0000115: TrackVis is software tool that can visualize and analyze fiber track data from diffusion MR imaging (DTI/DSI/HARDI/Q-Ball) tractography. It does NOT perform actual fiber tracking. Diffusion Toolkit is a set of tools that reconstruct diffusion imaging data and generate fiber track data for TrackVis to visualize. Because these two sets of tools were developed and maintained separately and each has distinguished funtionalities, they decided to distribute them as two separate programs for the ease of maintenance and upgrade. You do need both of them to perform complete diffusion data processing and analysis. Features of TrackVis include: * Cross-platform. Works on Windows, Mac OS X and Linux with native look and feel. * A variety of track filters (track selecting methods) allowing users to explore and locate specific bundles with ease. * Multiple rendering modes with customizable scalar-driven color codes. * Real-time parameter adjustment and 3D render. * Open format of the track data file allowing users to integrate customized scalar data into the track file and visualize and analyze it. Save and restore scenes in XML style scene file. * Statistical scalar analysis of tracks and ROIs. * Synchronized real-time multiple dataset analysis and display allowing time-point and/or subject comparison. Synchronized analysis and display on same dataset can also be performed in real-time remotely over the network. * Upfront in-line parameter adjustment in real-time. No tedious pop-up dialogs. TrackVis works with Track File created by Diffusion Toolkit. Diffusion Toolkit processes raw DICOM, Nifti format and ANALYZE images. TrackVis and Diffusion Toolkit are cross-platform software. They can run on Windows XP, Mac OS X as well as Linux.

BFO
type: Resource
type: NamedIndividual
has db xref: nlx_80606
synonym: Basic Formal Ontology
IAO_0000115: A small, upper level ontology that is designed for use in supporting information retrieval, analysis and integration in scientific and other domains. BFO is a genuine upper integration in scientific and other domains. Thus it does not contain physical, chemical, biological or other terms which would properly fall within the coverage domains of the special sciences.

Mercer University; Georgia; USA
type: Organization
type: NamedIndividual
has db xref: grid.259906.1
has db xref: ISNI:0000 0001 2162 9738
has db xref: nlx_84851
has db xref: Wikidata:Q1798612
synonym: Mercer
IAO_0000115: Private research university with its main campus in Macon, Georgia. Founded in 1833 as Mercer Institute and gaining university status in 1837.

LONI MiND
type: Resource
type: NamedIndividual
has db xref: nlx_143920
synonym: Metadata in NIfTI for DWI
synonym: MiND: Metadata in NIfTI for DWI
abbrev: MiND
IAO_0000115: The MiND: Metadata in NIfTI for DWI framework enables data sharing and software interoperability for diffusion-weighted MRI. This site provides specification details, tools, and examples of the MiND mechanism for representing important metadata for DWI data sets at various stages of post-processing. MiND framework provides a practical solution to the problem of interoperability between DWI analysis tools, and it effectively expands the analysis options available to end users. To assist both users and developers in working with MiND-formatted files, we provide a number of software tools for download. * MiNDHeader A utility for inspecting MiND-extended files. * I/O Libraries Programming libraries to simplify writing and parsing MiND-formatted data. * Sample Files Example files for each MiND schema. * DIRAC LONI''s Diffusion Imaging Reconstruction and Analysis Collection is a DWI processing suite which utilizes the MiND framework.

Fellowship for Interpretation of Genomes
type: Resource
type: NamedIndividual
has db xref: nlx_80790
abbrev: FIG
IAO_0000115: Fonstein, Kogan, Osterman, Overbeek and Vonstein found the non-profit Fellowship for Interpretation of Genomes (FIG) to follow their vision of seeking advances in understanding through comparative analysis of the growing body of genomic data. The team at FIG began a new open source comparative genomics environment, the SEED. The Project to Annotate 1000 Genomes is a central goal of FIG. FIG is a nonprofit organization devoted to providing support for those analyzing genomes. It focuses on organizing the data needed to support interpretation of genomes, providing the infrastructure needed by the world community in its efforts to achieve understanding. FIG offers the key services required to architect and implement a comparative framework for interpreting genomes. In addition, we pick specific, critical problems and attempt to actively participate in the unraveling of the secrets within these amazing entities. It is only by merging the work of building infrastructure with the applications that use it that we will more deeply understand what is needed at each step.

Brain and Body Donation Program
type: Resource
type: NamedIndividual
has db xref: nlx_80798
synonym: Banner Brain and Tissue Bank
synonym: Banner Health Brain and Tissue Bank
synonym: Banner Sun Health Research Institute Brain and Body Donation Program
synonym: Banner Sun Health Research Institute Brain and Tissue Bank
synonym: Brain / Body Donation Program
synonym: Brain/Body Donation Program
abbrev: BBDP
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. An autopsy-based, research-devoted brain bank, biobank and biospecimen bank that derives its human donors from the Arizona Study of Aging and Neurodegenerative Disease (AZSAND), a longitudinal clinicopathological study of the health and diseases of elderly volunteers living in Maricopa county and metropolitan Phoenix, Arizona. Their function is studied during life and their organs and tissue after death. To date, they have concentrated their studies on Alzheimer's disease, Parkinson's disease, heart disease and cancer. They share the banked tissue, biomaterials and biospecimens with qualified researchers worldwide. Registrants with suitable scientific credentials will be allowed access to a database of available tissue linked to relevant clinical information, and will allow tissue requests to be initiated., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Life Extension
type: Resource
type: NamedIndividual
has db xref: nlx_81015
IAO_0000115: Life Extension is a global authority on nutrition, health and wellness as well as a provider of scientific information on anti-aging supplements and therapies. We supply only the highest quality nutritional supplements, including minerals, vitamins, herbs and hormones. Life Extension publishes the very latest information on anti-aging and wellness in its monthly publication, Life Extension Magazine, the Disease Prevention and Treatment book of integrative health protocols, the Life Extension Update e-mail newsletter and the Daily Health Bulletin, and at this website. All to support more informed health choices. In addition to a wealth of information, Life Extension offers 300+ premium-quality vitamins, minerals, hormones, diet and nutritional supplements, and even skin care products, which are often the fruits of research reported on or funded by the Life Extension Foundation.

Triplet-SVM
type: Resource
type: NamedIndividual
has db xref: nlx_82947
IAO_0000115: This program is developed for predicting a query sequence with hairpin structure as a real miRNA precursor or not. The triplet-SVM classifier analyzes the triplet elements of the query and predicts it using a SVM classifier. The SVM classifier is previously trained based on the triplet element features of a set of real miRNA precursors and a set of pseudo-miRNA hairpins. triplet-SVM classifier was written by Chenghai Xue and is free to all users but without any warranty.

University of Freiburg; Baden-Wurttemberg; Germany
type: Organization
type: NamedIndividual
has db xref: nlx_80780
synonym: Albert Ludwig University of Freiburg
abbrev: Uni Freiburg
IAO_0000115: Public research university located in Freiburg im Breisgau, Baden-Württemberg, Germany.

National Yang-Ming University; Taipei; Taiwan
type: NamedIndividual
has db xref: nlx_42821

Kings College London Infectious Diseases BioBank
type: Resource
type: NamedIndividual
has db xref: nlx_81398
synonym: Infectious Diseases BioBank
synonym: King''s College London Infectious Diseases BioBank
abbrev: IDB
IAO_0000115: Centralized specimen archiving and molecular analysis facility that assists researchers wishing to undertake cohort-based projects in areas such HIV/AIDS, HCV infection or MRSA. Its aim is to make medical research easier, more efficient and faster to perform. The IDB collects valuable clinical samples from patients with infections who are attending their partner NHS-Trust clinics. Their core collections include blood samples from patients infected with human immunodeficiency virus (HIV), hepatitis B (HBV) & hepatitis C (HCV) viruses or methicillin resistant Staphylococcus aureus (MRSA). Blood samples are separated so that patients������?? DNA, plasmas (cell-free blood) and lymphocytes (white blood cells) can be frozen into a comprehensive library. Medical researchers can access complete sets of samples to answer important clinical questions, if their research project is approved by the IDB''s Management Committee. For this reason they are actively recruiting ''medically interesting'' patients who are infected with HIV, for example: those who remain well ������?? despite being infected for many years; others who are exposed to HIV but remain uninfected; others who develop AIDS very quickly; and, those who are in the process of sero-converting.

Health++
type: Resource
type: NamedIndividual
has db xref: nlx_81403
synonym: HealthPlusPlus
IAO_0000115: Health++ (HealthPlusPlus) is a wiki about health, also a medical knowledge base, an online medical encyclopedia. We are making this wiki unique with adding relevant videos, links, resources and communities. Please join us in this effort to make this wiki the most useful and comprehensive medical wiki resource site. Some of the initial content on this page may be incorporated in part from copyleft sources in the public domain including wikis such as Wikipedia and AskDrWiki. Drug information for patients came from the The National Library of Medicine. Infectious disease information may have come from the Centers for Disease Control (CDC). * Health care in the United States * List of common health issues * List of RSS feeds on health * List of encyclopedias on medicine * MedlinePlus Health News * List of medical websites * List of medical wikis * List of online medical encyclopedia * List of online medical dictionaries * List of hospitals

Information Hyperlinked Over Proteins
type: Resource
type: NamedIndividual
has db xref: biotools:ihop
has db xref: nif-0000-00232
has db xref: OMICS_01185
synonym: iHOP - Information Hyperlinked over Proteins
abbrev: iHOP
IAO_0000115: Information system that provides a network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. It provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research. Moreover, this literature network can be superimposed on experimental interaction data (e.g., yeast-two hybrid data from Drosophila melanogaster and Caenorhabditis elegans) to make possible a simultaneous analysis of new and existing knowledge. The network contains half a million sentences and 30,000 different genes from humans, mice, D. melanogaster, C. elegans, zebrafish, Arabidopsis thaliana, yeast and Escherichia coli.

ConnectomeDB
type: Resource
type: NamedIndividual
has db xref: nlx_143923
IAO_0000115: Data management platform that houses all data generated by the Human Connectome Project - image data, clinical evaluations, behavioral data and more. ConnectomeDB stores raw image data, as well as results of analysis and processing pipelines. Using the ConnectomeDB infrastructure, research centers will be also able to manage Connectome-like projects, including data upload and entry, quality control, processing pipelines, and data distribution. ConnectomeDB is designed to be a data-mining tool, that allows users to generate and test hypotheses based on groups of subjects. Using the ConnectomeDB interface, users can easily search, browse and filter large amounts of subject data, and download necessary files for many kinds of analysis. ConnectomeDB is designed to work seamlessly with Connectome Workbench, an interactive, multidimensional visualization platform designed specifically for handling connectivity data. De-identified data within ConnectomeDB is publicly accessible. Access to additional data may be available to qualified research investigators. ConnectomeDB is being hosted on a BlueArc storage platform housed at Washington University through the year 2020. This data platform is based on XNAT, an open-source image informatics software toolkit developed by the NRG at Washington University. ConnectomeDB itself is fully open source.

IRIS DMC FDSNWS event Web Service
type: Resource
type: NamedIndividual
has db xref: SciRes_000181
synonym: fdsn-event webservice
synonym: FDSNWS event Web Service
synonym: IRIS FDSNWS Event
abbrev: FDSNWS Event
abbrev: fdsnws-event
abbrev: FDSNWS: event
IAO_0000115: International Federation of Digital Seismograph Networks (FDSN) Web service that returns event (earthquake) information from the catalogs submitted to the Incorporated Research Institutions for Seismology (IRIS) Data Management Center (DMC). Events may be selected based on location, time, catalog, contributor and internal identifiers. By default, events are retrieved from the NEIC PDE catalog for recent events and then the ISC catalog when it becomes available. These default results include only that catalog''s primary origin and primary magnitude for each event, they may optionally include all available origin and magnitude estimates. By default results are returned as XML in QuakeML format but may also be requested in text formats. This service is an implementation of the FDSN web service specification version 1.

Conticabase - European Sarcoma Database and Tumour Bank
type: Resource
type: NamedIndividual
has db xref: nlx_81679
synonym: Conticabase - European Sarcoma Database Tumor Bank
synonym: Conticabase - European Sarcoma Database Tumour Bank
synonym: CONTICANET database and tumor bank
synonym: CONTICANET database and tumour bank
synonym: CONTICANET database tumor bank
synonym: CONTICANET database tumour bank
synonym: CTCN database and tumour bank
abbrev: Conticabase
IAO_0000115: This database contains anonymized information describing the tumor, treatment and follow-up as well as tumor sample availability and molecular biology analyses for mesenchymal tumors except GIST and bone tumors. The query tool allows users to ask questions about the overall content of the database in order to evaluate the feasibility of specific collaborative studies. We hope this database will become an important tool for increasing our knowledge on these rare tumors and for developing joint research programs. The tool can be used as a local center database thanks to its rules for access to patient data and material. Conticabase currently contains the following data from 31 out of the 48 registered centers (Last modification on 28/03/2012): * 11518 Patients * 11562 Tumors * 13897 Samples (13636 Paraffin and 5773 Frozen) Use of conticabase data At anytime, a data manager can export data of patients from his (her) Centre or group according to his (her) level of rights. To obtain data from another Centre, a partner should ask the coordinator of the corresponding Centre for these data. To use data for a cooperative study, a member should write a short text describing the project and send it to partners of interest. Each partner may decide whether to participate or not and therefore, whether to send or not the corresponding data to the project leader. In the event that the data from the conticabase result in a publication, acknowledgement is required. Use of tumour material entered in the ConticaBank To obtain material from another Centre for a cooperative study, a partner should write a short text describing the project and send it to the partners of interest. Each partner may decide whether to participate or not and, therefore, whether to send or not the corresponding material to the project leader. In the event that the material used result in a publication, acknowledgement is required.

BMA Biomedicals
type: Organization
type: NamedIndividual
has db xref: nlx_152319
IAO_0000115: An Antibody supplier

NIF Data Federation
type: Resource
type: NamedIndividual
has db xref: nlx_81822
synonym: Neuroscience Information Framework Data Federation
abbrev: Data Federation
IAO_0000115: Service that partners with the community to expose and simultaneously drill down into individual databases and data sets and return relevant content. This type of content, part of the so called hidden Web, is typically not indexed by existing web search engines. Every record links back to the originating site. In order for NIF to directly query these independently maintained databases and datasets, database providers must register their database or dataset with the NIF Data Federation and specify permissions. Databases are concept mapped for ease of sharing and to allow better understanding of the results. Learn more about registering your resource, http://neuinfo.org/nif_components/disco/interoperation.shtm Search results are displayed under the Data Federation tab and are categorized by data type and nervous system level. In this way, users can easily step through the content of multiple resources, all from the same interface. Each federated resource individually displays their query results with links back to the relevant datasets within the host resource. This allows users to take advantage of additional views on the data and tools that are available through the host database. The NIF site provides tutorials for each resource, indicated by the Professor Icon professor icon showing users how to navigate the results page once directed there through the NIF. Additionally, query results may be exported as an Excel document. Note: NIF is not responsible for the availability or content of these external sites, nor does NIF endorse, warrant or guarantee the products, services or information described or offered at these external sites. Integrated Databases: Theses virtual databases created by NIF and other partners combine related data indexed from multiple databases and combine them into one view for easier browsing. * Integrated Animal View * Integrated Brain Gene Expression View * Integrated Disease View * Integrated Nervous System Connectivity View * Integrated Pod…

Upstate New York Transplant Services
type: Resource
type: NamedIndividual
has db xref: nlx_81901
synonym: UNYTS: Upstate New York Transplant Services
abbrev: UNYTS
IAO_0000115: Leading procurement organization in the United States and one of the only eight centers nationwide to house organ, tissue and eye procurement in one location. With the addition of Community Blood Service, Upstate New York Transplant Services has become the first organization of its kind nationwide. It operates as a non-profit serving the eight counties of Western New York and works to assist donor families, coordinate the donation process and increase knowledge and awareness within the community regarding transplantation. Upstate New York Transplant Services is ranked as one of the top procurement organizations nationwide. In 1997, Upstate New York Transplant Services had just 200 donors; in 2007 the organization surpassed 1,000. In the summer of 2007, Upstate New York Transplant Services added community blood banking services - bringing both a significant savings to area hospitals and assurance to Western New York donors that their blood donations remain local.

Globus Medical, Inc.
type: Organization
type: NamedIndividual
has db xref: grid.459811.0
has db xref: ISNI: 0000 0004 0376 7450
has db xref: nlx_81975
synonym: Globus Medical
abbrev: Globus
IAO_0000115: A privately held spinal company that is driving significant technological advancements across a complete suite of spinal products. Founded in 2003, Globus'' single-minded focus on advancing spinal surgery has made it the fastest growing company in the history of orthopedics. Globus is driven to utilize superior engineering and technology to achieve pain free, active lives for all patients with spinal disorders. The ultimate goal at Globus is to deliver innovation by utilizing superior engineering and technology to help improve patients'' lives. This clinical inspiration is central to every endeavor we undertake. We have developed a Spine Innovation Engine to focus our efforts on delivering industry leading solutions to surgeons and their patients. Our Spine Innovation Engine has developed a portfolio that includes a comprehensive line of technologically-advanced spine products. To date we have released over 50 major products and have over 30 more in various stages of development. Clinical Studies are the foundation for advancing innovative spine care and Globus is committed to a robust investment into prospective and retrospective clinical trials to evaluate the safety and efficacy of our products. Globus is currently conducting several FDA-approved Investigational Device Exemption (IDE) clinical studies.

SciVee
type: Resource
type: NamedIndividual
has db xref: nlx_82223
synonym: SciVee Make Your Research Known
IAO_0000115: A video resource containing short, scientific videos which can be browsed or searched for. The videos are based on published papers, talks or posters. It is free to use and disseminates research findings to the world wide web. SciVee enables researchers to combine video with documentation and data in a media rich format, enhancing journal articles with pubcasts by linking and synchronizing video explanations to their published text. Similarly, video summaries can be associated and synchronized with scientific posters to create postercasts highlighting the key finding of the research.

Donor Services of Indiana
type: Resource
type: NamedIndividual
has db xref: nlx_82227
abbrev: DSI
IAO_0000115: Donor Services of Indiana (DSI) in Fort Wayne is the nonprofit tissue bank established to provide high-quality human tissue and eye tissue for transplant to patients in our region, and for use in medical research. The program depends on contributions made by generous people who have consented to donation after the death of a family member. Bone, tendons, skin grafts and heart valves can significantly improve the quality of life for transplant recipients by preventing amputation, restoring mobility, relieving pain and sometimes saving lives. DSI adheres to the strict guidelines of the American Association of Tissue Banks and is widely recognized for its leadership in tissue banking. Transplant tissue provided by DSI is from regional donors evaluated and procured by our clinical staff, tested under our rigorous protocols, and distributed, tracked and followed by our professionals. DSI provides tissues back to the community from which they came and is equipped to deliver needed tissues on an urgent basis for medical emergencies, surgeries and procedures.

Patent Abstracts
type: Resource
type: NamedIndividual
has db xref: nlx_84408
abbrev: PATABS
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016. Patent Abstracts is a set of biology-related abstracts of patent applications derived from data products of the European Patent Office (EPO). Patent documents from Europe (EP), USA (US) and World (WO) are included. Abstracts are extracted from the ESPACE ACCESS and GlobalPat CD/DVD products according to the International Patent Classification (IPC) classes covering biology topics. The data are transformed to a common XML format and combined into one SRS dataset.

Minnesota Liver Tissue Cell Distribution System
type: Resource
type: NamedIndividual
has db xref: nlx_82318
synonym: Liver Tissue Cell Distribution System
synonym: Liver Tissue Cell Distribution System (LTCDS)
synonym: Liver Tissue Procurement and Distribution System
synonym: LTPADS
synonym: University of Minnesota Liver Tissue Cell Distribution System
abbrev: LTCDS
IAO_0000115: Tissue bank that provides human liver tissue from regional centers for distribution to scientific investigators throughout the United States. These USA regional centers have active liver transplant programs with human subjects approval to provide portions of the resected pathologic liver for which the transplant is performed.

Brain Connectivity Toolbox
type: Resource
type: NamedIndividual
has db xref: nlx_143925
abbrev: BCT
IAO_0000115: A large selection of complex network measures in Matlab that are increasingly used to characterize structural and functional brain connectivity datasets. Several people have contributed to the toolbox, and if you wish to contribute with a new function or set of functions, please contact Olaf Sporns. All efforts have been made to avoid errors, but users are strongly urged to independently verify the accuracy and suitability of toolbox functions for the chosen application. Please report bugs or substantial improvements.

Susan G. Komen for the Cure
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID: 100000869
has db xref: grid.428834.1
has db xref: ISNI: 0000 0001 0241 5320
has db xref: nlx_82488
has db xref: Wikidata: Q246898
synonym: Susan G. Komen
IAO_0000115: Susan G. Komen for the Cure is the global leader of the breast cancer movement, having invested more than $1.9 billion since inception in 1982. As the world''s largest grassroots network of breast cancer survivors and activists, we''re working together to save lives, empower people, ensure quality care for all and energize science to find the cures. Thanks to events like the Susan G. Komen Race for the Cure and the Susan G. Komen 3-Day for the Cure, and generous contributions from our partners, sponsors and fellow supporters, we have become the largest source of nonprofit funds dedicated to the fight against breast cancer in the world.

Research Tissue Repository - University of Connecticut
type: Resource
type: NamedIndividual
has db xref: nlx_82584
synonym: Research Tissue Repository Core Facility
synonym: UConn Health Center Research Biorepository
synonym: University of Connecticut Health Center Research Tissue Repository Core Facility
abbrev: UConn Research Biorepository
IAO_0000115: The UConn Health Center Research Biorepository consists of de-identified tissue and/or blood samples and patient data obtained from consented patients coupled with a database of clinical and laboratory data. Identified samples are available to researchers with IRB approval. Our goal is to develop a comprehensive resource that will procure, characterize and distribute high quality human specimens according to rigid protocols and ethical guidelines. We are sponsored by the Carole and Ray Neag Comprehensive Cancer Center and work closely with clinical and basic science investigators concentrating on translational research. The Biorepository is one of the many core facilities that receives support from the Health Center Research Advisory Committee (HCRAC). Our services include consenting of eligible patients, coordination for specimen collection, storage, data management and specimen distribution. We offer H & E, unstained and frozen sections on slides as well as paraffin and OCT curls. RNA and DNA isolation from specimens are also available, using methods that preserve the integrity of the nucleic acids. Logged in investigators can browse the catalogue for a detailed description of our services and prices on the Research Store and see an inventory of our samples using the link on this page titled ����??Sample Inventory����??. The inventory is updated on a regular basis.

Small Molecule Pathway Database
type: Resource
type: NamedIndividual
has db xref: biotools:smpdb
has db xref: nlx_143926
has db xref: r3d100012753
synonym: Small Molecule Pathway Database (SMPDB)
synonym: SMPDB (The Small Molecule Pathway Database)
abbrev: SMPDB
IAO_0000115: An interactive, visual database containing more than 350 small molecule pathways found in humans. More than 2/3 of these pathways (>280) are not found in any other pathway database. SMPDB is designed specifically to support pathway elucidation and pathway discovery in metabolomics, transcriptomics, proteomics and systems biology. It is able to do so, in part, by providing exquisitely detailed, fully searchable, hyperlinked diagrams of human metabolic pathways, metabolic disease pathways, metabolite signaling pathways and drug-action pathways. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Each small molecule is hyperlinked to detailed descriptions contained in the HMDB or DrugBank and each protein or enzyme complex is hyperlinked to UniProt. All SMPDB pathways are accompanied with detailed descriptions and references, providing an overview of the pathway, condition or processes depicted in each diagram. The database is easily browsed and supports full text, sequence and chemical structure searching. Users may query SMPDB with lists of metabolite names, drug names, genes / protein names, SwissProt IDs, GenBank IDs, Affymetrix IDs or Agilent microarray IDs. These queries will produce lists of matching pathways and highlight the matching molecules on each of the pathway diagrams. Gene, metabolite and protein concentration data can also be visualized through SMPDB''s mapping interface. All of SMPDB''s images, image maps, descriptions and tables are downloadable.

Mount Sinai Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_82806
synonym: Mount Sinai School of Medicine Biobank
IAO_0000115: The Mount Sinai Biobank is a large collection of DNA and plasma samples that are stored in a way that protects patients'' privacy while allowing research to be performed on de-identified clinical information from Mount Sinai''s data warehouse system. The Biobank''s goal is to acquire samples from a total of 100,000 donors over a period of several years. Mount Sinai is one of only a handful of places nationwide establishing biobanks on such a large scale. Funded by the Charles R. Bronfman Institute for Personalized Medicine, the Biobank project is a research project that is approved by the Mount Sinai Institutional Review Board and is continuously reviewed. Biobank Facts: * 17947 donors between 18 and 89 years of age have already participated in Biobank. * 194111 aliquots of DNA and * 212005 aliquots of plasma are available for future research.

PubMed
type: Resource
type: NamedIndividual
has db xref: nlx_82958
has db xref: OMICS_01195
synonym: Pub Med
IAO_0000115: Public bibliographic database that provides access to citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. PubMed citations and abstracts include fields of biomedicine and health, covering portions of life sciences, behavioral sciences, chemical sciences, and bioengineering. Provides access to additional relevant web sites and links to other NCBI molecular biology resources. Publishers of journals can submit their citations to NCBI and then provide access to full-text of articles at journal web sites using LinkOut.

Rocky Mountain Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_83001
abbrev: RMTB
IAO_0000115: The Rocky Mountain Tissue Bank is a Colorado, 501c3 non-profit corporation, established in 1980. It is governed by a Board of Directors and is an independent tissue processing facility with no affiliation with any other tissue bank. It develops and produces irradiated allogenic cancellous bone and marrow for human transplantation. This product stimulates bone regeneration in patients with bone loss due to trauma, disease, or genetic malformation and provides a foundation for dental implants. The primary distribution network is through Periodontists, and Oral Surgeons and clinicians specializing in implant dentistry.

MetaPhyler
type: Resource
type: NamedIndividual
has db xref: biotools:metaphyler
has db xref: OMICS_01455
synonym: MetaPhyler - Estimating Bacterial Composition from Metagenomic Sequences
IAO_0000115: A taxonomic classifier for metagenomic shotgun reads, which uses phylogenetic marker genes as a taxonomic reference. The classifier, based on BLAST, uses different thresholds (automatically learned from the reference database) for each combination of taxonomic rank, reference gene, and sequence length. The reference database includes marker genes from all complete genomes, several draft genomes and the NCBI nr protein database.

FieldTrip
type: Resource
type: NamedIndividual
has db xref: nlx_143928
IAO_0000115: Software toolbox for analysis of MEG, EEG, and other electrophysiological data. Used by experimental neuroscientists.

MARTA
type: Resource
type: NamedIndividual
has db xref: OMICS_01454
synonym: Metagenomic AND rDNA Taxonomic Assignment
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Java-based software that blasts each sequence that you provide it, and then looks for a consensus taxon among the top-hits returned from blast. MARTA uses NCBI''s megablast program to align your sequence(s) against a local installation of blast. Then MARTA uses GenInfo Identifiers from the top-hits to retrieve taxonomic information from NCBI''s taxonomy database. Using your thresholds/cutoffs, MARTA ''votes'' to find a taxonomic assignment by consensus; MARTA might resolve some sequences to species level, and others to kingdom or to no level, depending on the taxonomic information held within your tag or sequence.

AntWeb
type: Resource
type: NamedIndividual
has db xref: nlx_84285
IAO_0000115: Database of images, specimen records, and natural history information on ants including Search Tools, Regional Lists, In Depth Information, Ant Image Comparison Tool, PDF Field Guides, Maps on AntWeb and Google Earth, and Ant Genera of the World Slideshow. It is community driven and open to contribution from anyone with specimen records, natural history comments, or images. As of February of 2013, AntWeb has 97,814 ant images, of 23,272 specimens representing over 10,549 species. AntWeb provides tools for submitting images, specimen records, annotating species pages, and managing regional species lists. AntWeb contains information on the ant faunas of several areas in the Nearctic and Malagasy biogeographic regions, and global coverage of all ant genera. AntWeb provides tools for exploring the diversity and identification of ants (Hymenoptera: Formicidae). These tools have been developed to encourage the study of ants, to facilitate the use of ants in inventory and monitoring programs, and to provide ant taxonomists with access to images of type specimens. AntWeb illustrates the diversity of ants by providing information and high quality color images of many of the approximately 10,000 known species of ants. AntWeb currently focuses on the species of the Nearctic and Malagasy biogeographic regions, and the ant genera of the world. Over time, the site will grow to describe every species of ant known.

Mercer University College of Pharmacy; Georgia; USA
type: Organization
type: NamedIndividual
has db xref: nlx_52664
synonym: Mercer University College of Pharmacy and Health Sciences
IAO_0000115: One of four health sciences units within Mercer Health Sciences Center. Provides the first pharmacy program in the region to offer the Doctor of Pharmacy degree as its sole professional degree. The College offers the Doctor of Pharmacy (Pharm.D.) degree and the Doctor of Philosophy (Ph.D.) degree in pharmaceutical sciences, as well as four combined degree programs – Pharm.D./M.B.A, Pharm.D./M.P.H., Pharm.D./Ph.D. and Pharm.D./M.S. in Health Informatics.

siDirect
type: Resource
type: NamedIndividual
has db xref: nlx_83672
IAO_0000115: siDirect 2.0 provides functional and off-target minimized siRNA design for mammalian RNAi. The previous version of our software designed functional siRNAs by considering the relationship between siRNA sequence and RNAi activity, and provided them along with the enumeration of potential off-target gene candidates by using a fast and sensitive homology search algorithm. In the new version, the siRNA design algorithm is extensively updated to eliminate off-target effects by reflecting our recent finding that the capability of siRNA to induce off-target effect is highly correlated to the thermodynamic stability, or the melting temperature (Tm), of the seed-target duplex, which is formed between the nucleotides positioned at 2-8 from the 5'' end of the siRNA guide strand and its target mRNA. Selection of siRNAs with lower seed-target duplex stabilities (benchmark Tm < 21.5 degrees C) followed by the elimination of unrelated transcripts with nearly perfect match should minimize the off-target effects. siDirect 2.0 provides functional, target-specific siRNA design with the updated algorithm which significantly reduces off-target silencing. When the candidate functional siRNAs could form seed-target duplexes with Tm values below 21.5 degrees C, and their 19-nt regions spanning positions 2-20 of both strands have at least two mismatches to any other non-targeted transcripts, siDirect 2.0 can design at least one qualified siRNA for > 94% of human mRNA sequences in RefSeq. Enter an accession number and retrieve sequence or Paste in a nucleotide sequence.

NCBI BioSample
type: Resource
type: NamedIndividual
has db xref: nlx_143929
has db xref: OMICS_01024
has db xref: r3d100012828
synonym: BioSample Database
synonym: NCBI BioSample Database
abbrev: BioSample
IAO_0000115: Database containing descriptions of biological source materials used in experimental assays. Sources include: GenBank, Sequence Read Archive (SRA), Coriell, ATCC. Submissions are supported by a web-based Submission Portal that guides users through a series of forms for input of rich metadata describing their samples. As the capacity and complexity of biological data sets expands, databases face new challenges in ensuring that the information is adequately organized and described. The NCBI BioSample database is being developed to help address the challenges by providing the means by which data generators can organize and describe a broad range of sample types, and link to corresponding sets of experimental data in archival databases.

MPO
type: Resource
type: NamedIndividual
has db xref: nlx_83784
synonym: Mammalian Phenotype Ontology
abbrev: MP
IAO_0000115: Community ontology to provide standard terms for annotating mammalian phenotypic data. It has a hierarchical structure that permits a range of detail from high-level, broadly descriptive terms to very low-level, highly specific terms. This range is useful for annotating phenotypic data to the level of detail known and for searching for this information using either broad or specific terms as search criteria. Your input is welcome.

BioSample Database at EBI
type: Resource
type: NamedIndividual
has db xref: biotools:biosamples
has db xref: nlx_143930
has db xref: OMICS_01025
has db xref: r3d100012628
synonym: BioSample Database
synonym: BioSample Database at the EBI
synonym: BioSamples
synonym: BioSamples database
synonym: BioSamples Database at EBI
synonym: BioSD - BioSample Database
synonym: BioSD at EBI
synonym: EBI BioSample Database
abbrev: BioSD
IAO_0000115: Database that aggregates sample information for reference samples (e.g. Coriell Cell lines) and samples for which data exist in one of the EBI' '''s assay databases such as ArrayExpress, the European Nucleotide Archive or PRoteomics Identificates DatabasE. It provides links to assays for specific samples, and accepts direct submissions of sample information. The goals of the BioSample Database include: # recording and linking of sample information consistently within EBI databases such as ENA, ArrayExpress and PRIDE; # minimizing data entry efforts for EBI database submitters by enabling submitting sample descriptions once and referencing them later in data submissions to assay databases and # supporting cross database queries by sample characteristics. The database includes a growing set of reference samples, such as cell lines, which are repeatedly used in experiments and can be easily referenced from any database by their accession numbers. Accession numbers for the reference samples will be exchanged with a similar database at NCBI. The samples in the database can be queried by their attributes, such as sample types, disease names or sample providers. A simple tab-delimited format facilitates submissions of sample information to the database, initially via email to biosamples (at) ebi.ac.uk. Current data sources: * European Nucleotide Archive (424,811 samples) * PRIDE (17,001 samples) * ArrayExpress (1,187,884 samples) * ENCODE cell lines (119 samples) * CORIELL cell lines (27,002 samples) * Thousand Genome (2,628 samples) * HapMap (1,417 samples) * IMSR (248,660 samples)

Brodmann Areas in the Human Brain with an Emphasis on Vision and Language
type: Resource
type: NamedIndividual
has db xref: nlx_144391
synonym: Brodmann Areas in the Human Brain with an Emphasis on Vision Language
abbrev: Brodmann Areas in the Human Brain
IAO_0000115: Reference atlas of Brodmann Areas in the Human Brain with an Emphasis on Vision and Language. Other Pages include: Flat Brodmann Maps, Brodmann Area Names (with locational Descriptions), Flat Visual Area Maps, Language Areas, PopUp Gyri Maps

EEG Motor Movement/Imagery Dataset
type: Resource
type: NamedIndividual
has db xref: nlx_84003
synonym: EEG Motor Movement / Imagery Dataset
IAO_0000115: Data set of over 1500 one- and two-minute EEG recordings, obtained from 109 volunteers. Subjects performed different motor/imagery tasks while 64-channel EEG were recorded using the BCI2000 system (http://www.bci2000.org). Each subject performed 14 experimental runs: two one-minute baseline runs (one with eyes open, one with eyes closed), and three two-minute runs of each of the four following tasks: # A target appears on either the left or the right side of the screen. The subject opens and closes the corresponding fist until the target disappears. Then the subject relaxes. # A target appears on either the left or the right side of the screen. The subject imagines opening and closing the corresponding fist until the target disappears. Then the subject relaxes. # A target appears on either the top or the bottom of the screen. The subject opens and closes either both fists (if the target is on top) or both feet (if the target is on the bottom) until the target disappears. Then the subject relaxes. # A target appears on either the top or the bottom of the screen. The subject imagines opening and closing either both fists (if the target is on top) or both feet (if the target is on the bottom) until the target disappears. Then the subject relaxes. The data are provided here in EDF+ format (containing 64 EEG signals, each sampled at 160 samples per second, and an annotation channel).

Stanley Medical Research Institute Online Genomics Database
type: Resource
type: NamedIndividual
has db xref: nlx_143935
synonym: SMRI Online Genomics Database
abbrev: Stanley Online Genomics Database
IAO_0000115: The Stanley Online Genomics Database uses samples from the Stanley Medical Research Institute (SMRI) Brain Bank. These samples were processed and run on gene expression arrays by a variety of researchers in collaboration with the SMRI. These researchers have performed analyses on their respective studies using a range of analytic approaches. All of the genomic data have been aggregated in this online database, and a consistent set of analyses have been applied to each study. Additionally, a comprehensive set of cross-study analyses have been performed. A thorough collection of gene expression summaries are provided, inclusive of patient demographics, disease subclasses, regulated biological pathways, and functional classifications. Raw data is also available to download. The database is derived from two sets of brain samples, the Stanley Array collection and the Stanley Consortium collection. The Stanley Array collection contains 105 patients, and the Stanley Consortium collection contains 60 patients. Multiple genomic studies have been conducted using these brain samples. From these studies, twelve were selected for inclusion in the database on the basis of number of patients studied, genomic platform used, and data quality. The Consortium collection studies have fewer patients but more diversity in brain regions and array platforms, while the Array collection studies are more homogenous. There are tradeoffs, the Consortium results will be more variable, but findings may be more broadly representative. The collections contain brain samples from subjects in four main groups: Bipolar Schizophrenia, Depression, and Controls Brain regions used in the studies include: Broadman Area 6, Broadman Area 8/9, Broadman Area 10, Broadman Area 46, Cerebellum The 12 studies encompass a range of microarray platforms: Affymetrix HG-U95Av2, Affymetrix HG-U133A, Affymetrix HG-U133 2.0+, Codelink Human 20K, Agilent Human I, Custom cDNA Publications based on any of the clinical or geno…

NCBI Nucleotide
type: Resource
type: NamedIndividual
has db xref: nlx_84100
has db xref: r3d100010778
synonym: CoreNucleotide
synonym: Entrez Nucleotide
synonym: Nucleotide
synonym: Nucleotide Database
abbrev: NCBI gi
IAO_0000115: Database of nucleotide sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.

NCBI Structure: Cn3D
type: Resource
type: NamedIndividual
has db xref: biotools:cn3d
has db xref: nlx_84208
synonym: Cn3D
IAO_0000115: Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI''s Entrez retrieval service. Cn3D runs on Windows, Macintosh, and Unix. Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features. Cn3D is a tool for visualization of three-dimensional structures with emphasis on interactive examination of sequence-structure relationships and superposition of geometrically similar structures. Can be used to display MMDB structures, superpositions of VAST related structures, and conserved core motifs identified in conserved domains.

DiScRIBinATE
type: Resource
type: NamedIndividual
has db xref: OMICS_01453
synonym: DiScRIBinATE: Distance Score Ratio for Improved Binning and Taxonomic Estimation
synonym: Distance Score Ratio for Improved Binning and Taxonomic Estimation
IAO_0000115: Software for accurate taxonomic classification of metagenomic sequences using a similarity based binning method. User needs to perform a similarity search of the input metagenomic sequences (reads) against the nr protein database using BLASTx search. The generated blastx output is then taken as the input by the DiScRIBinATE program.

University of Leeds; West Yorkshire; United Kingdom
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100000777
has db xref: grid.9909.9
has db xref: ISNI:0000 0004 1936 8403
has db xref: nlx_34628
has db xref: Wikidata:Q503424
IAO_0000115: Public research university in Leeds, West Yorkshire, England. It was established in 1874 as the Yorkshire College of Science. In 1884 it merged with the Leeds School of Medicine and was renamed Yorkshire College.

PubOnto: Open Biomedical Ontology-Based Medline Exploration
type: Resource
type: NamedIndividual
has db xref: nlx_84394
synonym: PubOnto
IAO_0000115: We developed an ontology-based interactive Medline exploration solution called PubOnto to enable the interactive exploration and filtering of search results through the use of multiple ontologies from the OBO foundry. The PubOnto program is a rich internet application based on the FLEX platform. It contains a number of interactive tools, visualization capabilities, an open service architecture, and a customizable user interface. Effective Medline database exploration is critical for the understanding of high throughput experimental results and the development of novel hypotheses about the mechanisms underlying the targeted biological processes. While existing solutions enhance Medline exploration through different approaches such as document clustering, network presentations of underlying conceptual relationships and the mapping of search results to MeSH and Gene Ontology trees, we believe the use of multiple ontologies from the Open Biomedical Ontology can greatly help researchers to explore literature from different perspectives as well as to quickly locate the most relevant Medline records for further investigation.

VariationHunter
type: Resource
type: NamedIndividual
has db xref: OMICS_00328
synonym: VariationHunter-CommonLaw
IAO_0000115: A software tool for discovery of structural variation in one or more individuals simultaneously using high throughput technologies.

Biomedical Computation Review
type: Resource
type: NamedIndividual
has db xref: nlx_84418
IAO_0000115: Magazine published by Simbios, a National NIH Center for Biomedical Computing, covering the latest research wherever computation, biology, and medicine intersect. In addition to disseminating information about the latest research in biomedical computation, they aim to foster community amongst the wide audience interested in any and all aspects of biomedical computing. Whether you are a long time researcher in this area or new to it, please consider joining those who have already started to participate in Biomedical Computation Review. You are encouraged to: * Write a letter to the editor on any relevant topics * Suggest your favorite topics that should receive more attention * Suggest an idea for a feature article * Propose an idea for an Under the Hood tutorial * Tell us any other way in which we can better serve this community

South Texas Accelerated Research Therapeutics
type: Resource
type: NamedIndividual
has db xref: nlx_143931
abbrev: START
IAO_0000115: South Texas Accelerated Research Therapeutics (START) directs clinical trials of novel anticancer agents using a high quality and innovative information technology infrastructure to ensure accurate and rapid clinical trials in a setting that emphasizes personalized and compassionate clinical care. START''s head office is located in San Antonio, Texas, in the heart of the South Texas Medical Center. With centers located in San Antonio, Texas and Madrid, Spain, START conducts the world''s largest Phase I medical oncology program putting more than 400 patients per year on Phase I trials. Patients travel from all over the world to participate in one or more of our Phase I drug trials. START consists of a team of highly trained physicians and staff with extensive experience in Phase I clinical trials research and are nationally recognized as thought leaders in cancer research and drug development. The mission of START is to accelerate the development of new anticancer drugs that will improve the quality of life and survival for patients with cancer. Our drug development program is not only furthering cancer research, but also offers hope to patients facing the toughest cancer battles.

LifeCenter Northwest
type: Resource
type: NamedIndividual
has db xref: nlx_84499
abbrev: LCNW
IAO_0000115: LifeCenter Northwest is one of 58 federally designated nonprofit organ procurement organizations (OPO) in the United States. LifeCenter Northwest works together with families, medical professionals, and communities in Alaska, Montana, North Idaho, and Washington to save lives through organ and tissue donation. LifeCenter Northwest provides the following services: * Hospital Development ** support of donor families throughout and after the donation process ** development of strong relationships between hospitals and LifeCenter Northwest ** helping hospitals stay compliant with federal and state regulations ** ongoing education of hospital staff on donation laws and programs * Organ Recovery Services ** on-site referral response to hospitals ** evaluation of patient medical suitability for donation ** management of patient care through the allocation and recovery of organs ** placement of organs, working with the United Network for Organ Sharing (UNOS) ** coordination of transplant team transportation and arrival at donor hospitals ** surgical recovery and transportation of organs * Tissue Recovery Services ** telephone referral response to hospitals ** evaluation of patient medical suitability for donation ** surgical recovery and transportation of tissues

PANTHER
type: Resource
type: NamedIndividual
has db xref: nlx_84521
has db xref: SCR_015893
synonym: PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System
synonym: PANTHER Classification System
synonym: Protein ANalysis THrough Evolutionary Relationships
synonym: Protein ANalysis THrough Evolutionary Relationships Classification System
IAO_0000115: System that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in absence of direct experimental evidence. Orthologs view is curated orthology relationships between genes for human, mouse, rat, fish, worm, and fly., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

NCBI BLAST
type: Resource
type: NamedIndividual
has db xref: biotools:blast
has db xref: nlx_84530
has db xref: OMICS_01436
synonym: Basic Local Alignment Search Tool
synonym: BLAST
synonym: NCBI Basic Local Alignment Search Tool
IAO_0000115: Web search tool to find regions of similarity between biological sequences. Program compares nucleotide or protein sequences to sequence databases and calculates statistical significance. Used for identifying homologous sequences.

International Histocompatibility Cell and DNA Bank
type: Resource
type: NamedIndividual
has db xref: nlx_85137
synonym: IHWG Cell DNA Bank
synonym: International Histocompatibility Cell DNA Bank
synonym: International Histocompatibility Working Group Cell and DNA Bank
synonym: International Histocompatibility Working Group Cell DNA Bank
abbrev: IHWG Cell and DNA Bank
IAO_0000115: The IHWG Cell and DNA Bank was established as a shared resource to support the scientific projects of the 13th International Histocompatibility Workshop (IHWS). The Research Cell Bank (RCB), located in Fred Hutchinson Cancer Research Center in Seattle, WA, maintains the IHWG inventory. This comprehensive inventory includes B-Lymphoblastoid Cell Lines (B-LCL) from previous International Workshops, HLA heterozygous and homozygous donors, selected families, and individuals of diverse population groups. The RCB maintains stocks of purified DNA derived from these cell lines, as well as DNA reference panels that provide an extensive array of HLA and HLA-related sequence polymorphisms. The RCB also provides cloned HLA genes and B-LCL transfected with selected HLA genes, which are available on a limited basis.

Regional Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_84845
abbrev: RTB
IAO_0000115: The Regional Tissue Bank (RTB), in Halifax Nova Scotia, is a non-profit service dedicated to providing Canadian health care teams with safe high quality allograft tissue and tissue products in support of optimal patient outcomes. It is accredited with the American Association of Tissue Bank (AATB) for all aspects of screening, procurement, processing, storage and distribution for cardiovascular, bone and skin tissues. The RTB is also in compliance with the Eye Bank Association of America (EBAA) and the draft Canadian Standards for Tissue Donation and Transplantation. It also supports autologous tissue transplantation, the bone marrow transplantation program and provides perfusion and preservation service to the Multi-Organ Transplant Program kidney and liver procurement teams. The mission of the Regional Tissue Bank is to ensure all Nova Scotians are offered the option of tissue donation and to provide safe high quality tissue products to Nova Scotian surgical programs and patients. It has expanded its activities with New Brunswick, in collaboration with Health Care Regions, to support tissue donation and transplantation in New Brunswick. The RTB also provides tissue to centers throughout Canada when requested; under the condition that meeting these requests would not disadvantage Atlantic Canadians.

Mount Desert Island Biological Laboratory
type: Resource
type: NamedIndividual
has db xref: nlx_84848
abbrev: MDIBL
IAO_0000115: Non-profit research institution that studies marine and non-marine organisms to learn about the basic biology of life. Our scientists make critical discoveries about how organisms adapt to their environment and how environment, health, and genetics are related. They study a wide range of organisms such as sharks, skates, and sea urchins to learn about development and regeneration. They investigate the root causes of diseases like cystic fibrosis, and they examine the mechanisms that make living creatures age. Research at MDIBL takes place within three centers: the Center for Regenerative Biology and Medicine, the Martha and Wistar Morris Center for Environmental Health Sciences, and the John W. and Jean C. Boylan Center for Cellular and Molecular Physiology. Scientists at each center include both permanent MDIBL faculty and adjunct faculty who come to MDIBL for a few weeks or an entire season, often year after year. Short courses, symposia, and fellowships provide research experience and training to students and scientists at all levels, from high school and college through medical school and senior investigators. Our education programs are always hands-on and engage students in meaningful research. MDIBL is the lead institution for the Maine IDeA Network for Biomedical Researcha research and education network linking MDIBL with The Jackson Laboratory and ten Maine colleges and universities.

MLA-HLS
type: Resource
type: NamedIndividual
has db xref: nlx_84942
synonym: Hospital Librarians Wiki
synonym: Medical Library Association - Hospital Libraries Section
IAO_0000115: Sponsored by the Hospital Libraries Section of the Medical Library Association, the Hospital Librarians Wiki provides the structure in which we can all share best practices. Everyone is invited to participate and can add content to existing pages by Editing This Page. You do not have to be a member of HLS/MLA. To add a new page, click on Join in the upper left corner, wait for your request to be accepted (generally within 24 hours), then click on New Page in the upper left corner. You may add links to the left Navigation bar.

Northwest Tissue Services
type: Resource
type: NamedIndividual
has db xref: nlx_85064
IAO_0000115: Northwest Tissue Services is the only fully accredited non-profit tissue bank in this region. As a non-profit tissue bank, we provide all allograft and tissue products at the lowest possible cost consistent with high quality. Our accreditation by the American Association of Tissue Banks (AATB) is a testament to the quality and safety of tissue we have provided to hospitals and patients in this region for over twenty years. As the most knowledgeable and experienced tissue resource in the Northwest, we work hard every day to provide high quality tissue products and services.

Washington University Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_85095
synonym: RNA Assessment; WUSTL Tissue Procurement Core Facility and Tumor Bank
synonym: Washington University Tissue Procurement Core Facility and Tumor Bank
synonym: WUSTL Tissue Procurement/Tumor Bank
abbrev: Washington University Tissue Procurement/Tumor Bank
IAO_0000115: The Tissue Procurement Core Facility and Tumor Bank is a collaborative effort between the Siteman Cancer Center and the Department of Pathology and Immunology. This shared resource facility provides the resources, infrastructure, and technologies for biospecimen-based translational pathology research. Services include: Tissue Procurement, Processing, and Storage; Archival Frozen Tissue Bank; and Laser Capture Microdissection. * Tissue Procurement, Processing, and Storage: For investigators initiating new protocols that involve biospecimen collection (e.g. solid tissues, blood, bone marrow), the Core can provide model consent forms and personnel to collect specimens through the Division of Surgical Pathology and other clinical sites on campus. Solid tissues are usually snap frozen in the surgical pathology suite, although investigators may request alternate preservation methods. Blood specimens are generally processed to frozen serum aliquots and peripheral leukocyte cell pellets. Other specimens (e.g. lymph node needle aspirations) that may be obtained in a variety of other patient care areas can be collected and processed immediately by a staff member who is on call at all times to receive specimens. * Archival Frozen Tissue Bank: For investigators desiring immediate access to material for molecular and histological studies, an archive of over 18,000 frozen human biospecimens is available. Specimens include solid tumors, patient-matched non-malignant tissue, serum, and peripheral blood leukocytes. Each specimen is accompanied with basic patient demographic information and pathology diagnostic data. Generally, each frozen tissue specimen is reviewed to confirm that the specimen is representative of the written pathology diagnosis. Investigators may request frozen tissue sections for immunohistochemical analysis, genomic DNA, protein extracts, or cellular RNA derived from any specimen in the archive. * RNA Assessment: Cellular RNA prepared by the Core from banked spe…

University of Genoa; Genoa; Italy
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100004702
has db xref: grid.5606.5
has db xref: ISNI:0000 0001 2151 3065
has db xref: nlx_14821
has db xref: Wikidata:Q593321
synonym: Universita degli Studi di Genova
synonym: Universita di Genova
synonym: University of Genoa
synonym: Universit� degli Studi di Genova
synonym: Universit� di Genova
IAO_0000115: UniGe, is one of the largest universities in Italy. It is located in the city of Genoa and regional Metropolitan City of Genoa, on the Italian Riviera in the Liguria region of northwestern Italy. The original university was founded in 1481.

Capital Biosciences
type: Organization
type: NamedIndividual
has db xref: nlx_85333
synonym: Capital Biosciences Inc.
synonym: Capital Biosciences: innovative solutions for life sciences
IAO_0000115: Biological products including Cell Immortalization Products, Clinically Defined Human Tissue, cDNA ORF Clones, Premade Adenoviruses, Purified Proteins, Viral Expression Systems and others as well as services like Custom Recombinant Adenovirus Production, Custom Recombinant Lentivirus Production, Protein Detection and Quantification and Stable Cell Line Production for academic and governmental research institutes, pharmaceutical and biotechnology industry. Capital Biosciences offers most types of human tissues, normal and diseased, with extensive clinical history and follow up information. Standard specimen format: Snap-frozen(flash-frozen), Formalin fixed and paraffin embedded (FFPE) tissues, Blood and blood products, Bone marrow, Total RNA, Genomic DNA, Total Proteins, Primary cell cultures, Viable frozen tissue. Tumor tissue samples include: Bladder cancer, Glioblastoma, Medulloblastoma, Breast Carcinoma, Cervical Cancer, Colorectal Cancer, Endometrial Cancer, Esophageal Cancer, Head and Neck (H&N) Carcinoma, Hepatocellular Carcinoma (HCC), Hodgkin's lymphoma, Kidney, Renal Cell Carcinoma, Lung Cancer, Non-Small Cell (NCSLC), Lung Cancer, Small Cell (SCLC), Melanoma, Mesothelioma, non-Hodgkin's Lymphoma, Ovarian Adenocarcinoma, Pancreatic Cancer, Prostate Cancer, Stomach Cancer.

NCI-Frederick
type: Resource
type: NamedIndividual
has db xref: grid.418021.e
has db xref: ISNI: 0000 0004 0535 8394
has db xref: nlx_85397
has db xref: nlx_155984
has db xref: Wikidata: Q28405614
synonym: Frederick National Lab
synonym: Frederick National Laboratory for Cancer Research
synonym: NCI Frederick National Laboratory for Cancer Research
abbrev: FNLCR
IAO_0000115: A federally funded research and development center dedicated to biomedical research. NCI-Frederick partners with university, government, and corporate scientists to speed the translation of laboratory research into new diagnostic tests and treatments for cancer and HIV/AIDS. NCI-Frederick is comprised of more than 2,800 government- and contractor-employed biomedical researchers, laboratory technicians, and support staff and several cancer research centers. The FNLCR provides quick response capabilities and meets special long-term research and development needs for NCI that cannot be met as effectively by existing in-house or contractor resources.

Lawson Brain Tumour Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_85555
synonym: Lawson Brain Tumor Tissue Bank
synonym: Lawson Health Research Institute Brain Tumour Bank
synonym: Lawson Health Research Institute Brain Tumour Tissue Bank
abbrev: Lawson Brain Tumour Bank
IAO_0000115: To aid researchers, the Brain Tumour Tissue Bank, located located in London Health Sciences Centre in London, Ontario, Canada has been collecting human brain tumor specimens and matching clinical data for neuro-oncology research in Canada and internationally since its establishment in 1991. A wide variety of primary and secondary brain tumors, spinal tumors, peritumors and normal brain tissues are available for molecular, protein, enzyme and immunohistochemical studies. Interested researchers can review the information provided at the website and can contact the tissue bank for information about what is currently available. In order to complete a request, an application must be completed.

SuperCAT
type: Resource
type: NamedIndividual
has db xref: nif-0000-03509
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11,2023. SuperCAT hosts typing databases for the Bacillus cereus group of bacteria. The databases contain MultiLocus Sequence Typing (MLST), MultiLocus Enzyme Electrophoresis (MLEE), and Amplified Fragment Length Polymorphism (AFLP) phylogenetic data. multilocus, sequence, Bacillus cereus, bacteria, Genomics, non-vertebrate, taxonomy, identification

Organ Procurement and Transplantation Network
type: Resource
type: NamedIndividual
has db xref: nlx_143932
synonym: Organ Procurement Transplantation Network
abbrev: OPTN
IAO_0000115: The only national patient waiting list and an online database system, called UNet, that links all of the professionals involved in the donation and transplantation system for the collection, storage, analysis, and publication of all OPTN data pertaining to the patient waiting list, organ matching, and transplants. The system contains data regarding every organ donation and transplant event occurring in the U.S. since October 1, 1987. UNet is a fail-safe, 24/7, secure Internet-based transplant information database created to enable the nation' '''s organ transplant institutions to: * register patients for transplants * match donated organs to waiting patients * manage the time-sensitive, life-critical data of all patients, before and after their transplants Data reports are available by type: National Data, Regional Data, State Data, Center Data, Build Advanced Report, and Annual Report Data. UNet is being used right now by all of the nation' '''s organ transplant programs, organ procurement organizations, and histocompatibility (tissue typing) laboratories working cooperatively to efficiently share a limited number of donated organs among thousands of patients.

hyfi: software suite for binding site search
type: Resource
type: NamedIndividual
has db xref: biotools:hyfi
has db xref: nlx_85657
synonym: Hyfi
IAO_0000115: This collection of software is designed to rapidly identify identifies primer and microarray probe binding sites for a query sequence in genomic DNA. This software suite has four main programs:1. A program for indexing a sequence file to speed up the binding site search. 2. A program for retrieving the binding sites of a query sequence. 3. A program for identifying sites where PCR primers could co-operate to exponentially amplify a sequence 4. A program for analyzing a set of binding sites to tailor the search for different reaction conditions. This software is implemented in C.

Andalusian Regional Tumour Bank
type: Resource
type: NamedIndividual
has db xref: nlx_85675
synonym: Andalusian Regional Tumor Bank
synonym: Red de Bancos de Tumores de Andalucia
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Located in Spain, the Andalusian Regional Tumour Bank is a regional tumor bank. In the last decades cancer knowledge is growing exponentially due human genome knowledge and technological advantages. However, this disease is the biggest problem of health in Europe, with more than 2,5 million new cases per year. The diagnosis and treatment of cancer is now allowing to identify the characteristics that the disease has on each person. The next step is meant to be a great revolution in the treatment of cancer. This scientific development is dependent on the availability of human tumour samples preserved in demanding conditions. Current technology requires the availability of tissue morphological and molecular conditions similar to those that had the sample before being removed. Tumor banks are responsible for these new quality requirements to foster the development of research and health care of patients.

IBIS: Inferred Biomolecular Interactions Server
type: Resource
type: NamedIndividual
has db xref: biotools:ibis_ncbi
has db xref: nlx_85682
has db xref: OMICS_01917
synonym: Inferred Biomolecular Interactions Server
synonym: NCBI Inferred Biomolecular Interactions Server
abbrev: IBIS
IAO_0000115: A web server and database that organizes, analyzes and predicts interactions between proteins and other biomolecules. For a given protein sequence or structure query, it reports protein-protein, protein-small molecule, protein nucleic acids and protein-ion interactions observed in experimentally-determined structural biological assemblies. It also infers/predicts interacting partners and binding sites by homology, by inspecting the protein complexes formed by close homologs of a given query. To ensure biological relevance of inferred binding sites, the IBIS algorithm clusters binding sites formed by homologs based on binding site sequence and structure conservation.

Neurology Podcast
type: Resource
type: NamedIndividual
has db xref: nlx_85698
synonym: Neurology Podcasts
IAO_0000115: Neurology Podcast is a weekly podcast of content from Neurology, the official journal of the American Academy of Neurology. The Neurology podcast is introduced by Editor-in-Chief Robert A. Gross, MD, PhD, who discusses several highlighted articles in the current issue of the journal. The podcast features an interview with the author of an article in the current issue that summarizes the paper and discusses the main findings and clinical implications for neurologists. It concludes with the Lesson of the Week, a short segment on a topic such as a laboratory technique, statistical methods, or historical neurology.

Anatomy Atlases
type: Resource
type: NamedIndividual
has db xref: nlx_85752
IAO_0000115: An anatomy digital health sciences library to educate patients, healthcare providers, and students in a free and anonymous manner while using current, authoritative, trustworthy health information. Anatomy Atlases addresses the continuum of anatomy education and may be of use primarily to three distinct populations. It is written for and intended primarily for use by Medical Students, Residents, Fellows, or Attending Physicians studying anatomy. Other Health Care Providers studying anatomy should find it useful. Finally, Patients (including patient''s family members or friends) may find it helpful. Anatomy Textbooks and Anatomy Atlases: * Atlas of Human Anatomy * Atlas of Human Anatomy in Cross Section * Illustrated Encyclopedia of Human Anatomic Variation * Atlas of Microscopic Anatomy - A Functional Approach: Companion to Histology and Neuroanatomy: Second Edition * Anatomy of First Aid - A Case Study Approach * Lessons From a Bone Box Lessons From a Bone Box

Swedish National Biobank Program
type: Resource
type: NamedIndividual
has db xref: nlx_85929
abbrev: National Biobank Program
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. The National Biobank Program is a joint national program of two Swedish investments on functional genomics, Swegene and Wallenberg Consortium North. This web-site is intended as an information resource on biobanks in Sweden, where knowledge about the Swedish biobanking system is mediated and the progress of the National Biobanking Program is presented. You will also find a list of individual Swedish biobanks. The main objectives of the National Biobank Program are: * to increase the knowledge of the Swedish biobanking system * to increase the quality of Swedish biobanks * to increase usability and availability of samples stored in Swedish biobanks for use in research, diagnosis and treatment * to increase the safety of the providers of samples by stimulating increased protection of the personal integrity and increased ethical awareness The National Biobank Program works through financing of strategic investments to improve biobanking systems of national interest. The program has a budget of SEK 26.4 million for the period of 2002 to 2003.

EEG / ERP Data Set
type: Resource
type: NamedIndividual
has db xref: nlx_85968
synonym: EEG / ERP data available for free public download
synonym: EEG data available for public download
abbrev: EEG / ERP Data set
IAO_0000115: A collection of 32-channel EEG / ERP data from 14 subjects (7 males, 7 females) acquired using the Neuroscan software (3.6 Gb), made available by the laboratory of Arnaud Delormes, along with electrode files and images presented in the experiment. Subjects are performing a go-nogo categorization task and a go-no recognition task on natural photographs presented very briefly (20 ms). Images are only available for viewing. Each subject responded to a total of 2500 trials. Data is CZ referenced and is sampled at 1000 Hz (total data size is 4Gb). Alternate datasets are also compiled including one from the EEGLAB software tutorial.

NCBI Sequence Read Archive (SRA)
type: Resource
type: NamedIndividual
has db xref: nlx_86174
has db xref: OMICS_01031
has db xref: r3d100010775
synonym: NCBI SRA
synonym: Sequence Read Archive
synonym: SRA
IAO_0000115: Repository of raw sequencing data from next generation of sequencing platforms including including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, Complete Genomics, and Pacific Biosciences SMRT. In addition to raw sequence data, SRA now stores alignment information in form of read placements on reference sequence. Data submissions are welcome. Archive of high throughput sequencing data,part of international partnership of archives (INSDC) at NCBI, European Bioinformatics Institute and DNA Database of Japan. Data submitted to any of this three organizations are shared among them.

Integrated Disease
type: Resource
type: NamedIndividual
has db xref: nlx_86401
synonym: Integrated Disease View
synonym: NIF Integrated Disease
synonym: NIF Integrated Disease View
IAO_0000115: A virtual database currently indexing authoritative information on disease and treatment options from NINDS Disorder List and PubMed Health.

Protein Biotechnologies
type: Resource
type: NamedIndividual
has db xref: nlx_86596
synonym: Protein Biotechnologies Inc.
IAO_0000115: Protein Biotechnologies Inc., a San Diego, California based company, provides global pharmaceutical, biotechnology, government and academic institutions with human clinical specimen derivatives and high-throughput protein and tissue microarrays. With the largest collection of ready-to-use, clinically defined, pathology-validated human specimen derivatives on the market, Protein Biotechnologies facilitates biomedical research and drug discovery efforts for cancer, neurodegenerative diseases, cardiovascular diseases, diabetes / obesity and autoimmune disease research. To facilitate high-throughput screening of human clinical specimens, Protein Biotechnologies provides its tissue lysate library on ready-to-use protein microarrays. And, for protein localization, immunohistochemical and in-situ hybridization studies, Protein Biotechnologies'' tissue microarrays are an ideal method for studying multiple human cancer / normal tissues in a single assay. Key Products & Services: * Reverse Phase Protein Microarrays * Human Clinical Tissue Lysates * Tissue Microarrays * Primary & Secondary Antibodies * Supplemental Research Reagents * Protein, RNA and DNA Isolation and Purification * Peptide Synthesis * Custom Protein and Peptide Microarray Design and Manufacturing * Custom Antibody Production

Brainbow mouse resource at Jackson Labs
type: Resource
type: NamedIndividual
has db xref: nif-0000-00249
abbrev: Brainbow mice
IAO_0000115: These Brainbow 1.0 (founder line L) mice allow labeling of individual neuronal types (specifically hippocampal neuron cell bodies, and including motor neurons, dentate gyrus granule cells, pyramidal neurons of the cortex and CA1 area) with approximately 166 distinguishable color variations in cre recombined cells, and may also be useful in conjunction with other Brainbow strains (Stock No. 007901, Stock No. 007911, Stock No. 007921) for neurobiological studies. These Thy1-Brainbow 1.0 (line L) transgenic mice are viable and fertile. The mice possess multiple fluorescent protein sequences uniquely flanked with pairs of incompatible Lox sites alternated to create mutually exclusive recombination events; allowing stochastic expression of multiple fluorescent proteins from a single transgene. Prior to Cre-mediated recombination, the fluorescent protein immediately adjacent to the promoter, dTomato (RFP), is expressed in peripheral and central neurons. When bred to Cre recombinase expressing mice, the resulting offspring can have one of three expression outcomes for each transgene in each cell of the cre expressing tissue(s): dTomato (RFP) (no recombination), mCerulean (CFP), or mYFP. Integration of tandem transgene copies yields combinatorial fluorescent protein expression in each cell, and thus many possible cell colors, providing a way to distinguish adjacent neurons and visualize other cellular interactions. Of note, the single FRT site inserted in the transgene allows tandem transgene copy number reduction through Flp-mediated recombination if desired. These Brainbow 1.0 (founder line L) mice were found to have multiple transgene copies that allow labeling of individual neuronal types (specifically hippocampal neuron cell bodies, and including motor neurons, dentate gyrus granule cells, pyramidal neurons of the cortex and CA1 area) with approximately 166 distinguishable color variations in cre recombined cells, and may also be useful in conjunction with other Brainb…

RTI Donor Services
type: Resource
type: NamedIndividual
has db xref: nlx_86602
IAO_0000115: RTI Donor Services is a not-for-profit, American Association of Tissue Banks (AATB) accredited organization, working with organ and tissue agencies to provide responsible stewardship of the gift of donation. By working with RTI Donor Services, you will receive the benefit of the science, safety and innovation of RTI Biologics, Inc. (RTI). While RTI Biologics and RTI Donor Services are separate but affiliated organizations, our missions are symbiotic ����?? both are aimed at improving the lives of others with a focus on maximizing the gift of tissue donation, providing safe tissue implants for recipients, and providing education and support programs to donor families and the donation community. Please visit http://www.rtidonorservices.org/about_rti_donor_services for more information.

Database of Genomic Variants Archive (DGVa)
type: Resource
type: NamedIndividual
has db xref: nlx_86626
has db xref: r3d100010814
synonym: Database of Genomic Variants Archive
synonym: DGVa
synonym: DGVarchive
IAO_0000115: Public repository that accepts direct submissions and provides archiving, accessioning and distribution of publicly available genomic structural variants, in all species. Variants are accessioned at the study and sample level, granting stable identifiers that can be used in publications. DGVa data is integrated with other EBI resources, including comprehensive EBI search and Ensembl genome browser. Exchanges data with companion database, dbVar, at National Center for Biotechnology Information.NOTE: since 2019 DGVa doesn't accept submissions. Please send the data for submission to European Variation Archive (EVA).

Wikipedia
type: Resource
type: NamedIndividual
has db xref: nlx_86719
IAO_0000115: Wikipedia is a free, web-based, collaborative, multilingual encyclopedia project supported by the non-profit Wikimedia Foundation. Its 19 million articles (over 3.6 million in English) have been written collaboratively by volunteers around the world, and almost all of its articles can be edited by anyone with access to the site. As of July 2011, there were editions of Wikipedia in 282 languages. Wikipedia was launched in 2001 by Jimmy Wales and Larry Sanger and has become the largest and most popular general reference work on the Internet, ranking around seventh among all websites on Alexa and having 365 million readers. The name Wikipedia was coined by Larry Sanger and is a combination of wiki (a technology for creating collaborative websites, from the Hawaiian word wiki, meaning quick) and encyclopedia. Wikipedia''s departure from the expert-driven style of encyclopedia building and the large presence of unacademic content has been noted several times. Some have noted the importance of Wikipedia not only as an encyclopedic reference but also as a frequently updated news resource because of how quickly articles about recent events appear. Although the policies of Wikipedia strongly espouse verifiability and a neutral point of view, critics of Wikipedia accuse it of systemic bias and inconsistencies (including undue weight given to popular culture), and allege that it favors consensus over credentials in its editorial processes. Its reliability and accuracy are also targeted. A 2005 investigation in Nature showed that the science articles they compared came close to the level of accuracy of Encyclopedia Britannica and had a similar rate of serious errors.

Inflammatory Breast Cancer Research Foundation
type: Resource
type: NamedIndividual
has db xref: nlx_86933
abbrev: IBC Research Foundation
IAO_0000115: The Inflammatory Breast Cancer Research Foundation is a non-profit corporation dedicated to the support of research and public awareness. It is dedicated to researching the cause of Inflammatory Breast Cancer, also known as IBC, an advanced and accelerated form of breast cancer usually not detected by mammograms or ultrasounds. Inflammatory breast cancer requires immediate aggressive treatment with chemotherapy prior to surgery and is treated differently than more common types of breast cancer. Our mission is to assist scientists and researchers in their quest to determine the definitive causes of inflammatory breast cancer. The Inflammatory Breast Cancer Research Foundation seeks to assist them in their work so effective and meaningful detection and diagnosis, prevention and treatment can be pursued and achieved. Our Goals Include: * To ignite interest in the study and research of inflammatory breast cancer at every level. From researchers to physicians, educators and scientists, the IBC Research Foundation seeks to support and inspire those seeking to identify the cause(s) of inflammatory breast cancer. * To support research, the purpose of which is to reach an unambiguous definition of inflammatory breast cancer. The clinical/pathological definition in use since the late 1800s with little change in the 1900s is ambiguous and doesn''t result in a diagnosis of all cases of IBC. By using research methods available in the 21st Century, an unambiguous definition is now possible, assuring with high certainty that all cases of IBC will be correctly diagnosed, and possible sub-types of IBC identified, which may lead to better treatment outcomes. * To increase awareness of IBC for primary care physicians, nursing professionals, and medical technicians in order to minimize the time from presentation of symptoms to correct diagnosis of inflammatory breast cancer. * To increase public awareness in an effort to encourage women to seek medical attention for common inflammatory…

Key Driver Analysis
type: Resource
type: NamedIndividual
has db xref: nlx_86947
synonym: Key Driver Analysis Tool
abbrev: KDA
IAO_0000115: Key Driver Analysis (KDA) is an analysis tool, as both an R package and Cytoscape plugin, for identifying key regulators of a gene regulatory network. It takes as input a gene network N (directed or undirected) and a gene set (module) G. The gene set is any subset of genes from the network N (e.g. pathway, module, ontology), permitting focus on a particular biological context. The KDA archive contains the plugin source, the plugin jar file, and several example datasets. Prerequisites: *Java, 5.0+ (www.javasoft.com) *Cytoscape, 2.6+ (www.cytoscape.org)

University of Leicester; Leicester; United Kingdom
type: Organization
type: NamedIndividual
has db xref: nlx_20502
synonym: The University of Leicester
synonym: University of Leicester
IAO_0000115: Public research university based in Leicester, England. Famous for the discovery of genetic fingerprinting and contributing to the discovery and identification of the remains of King Richard III.

University Andrology Laboratory
type: Resource
type: NamedIndividual
has db xref: nlx_87124
abbrev: UIC Andrology Laboratory
IAO_0000115: The University Andrology Laboratory provides physicians and their patients with all forms of male infertility testing, as well as operating a Patient Sperm Banking Program. This full-service facility is dedicated to the diagnosis and treatment of the infertile male using the highest standard of quality of care. Patients can either visit the main laboratory facility on the University of Illinois at Chicago Medical Center campus or visit our satellite laboratory on North Michigan Avenue. Now available through the University Andrology Laboratory is the OverNiteMale Program. The OverNiteMale Program is particularly convenient for patients who are unable to make a personal visit to one of our laboratories to produce a sample. Patients can now produce a sample in the privacy of their own home from any location in the U.S.A. and send it via Federal Express directly to our laboratory. In-patients can also take advantage of the OverNiteMaleTM Program during their hospital stay. The University Andrology Laboratory was originally introduced at Michael Reese Hospital in Chicago in 1982 and relocated in 1996 to the University of Illinois at Chicago Medical Center, Department of Urology. The laboratory meets the highest standard of quality control and quality assurance. The operation of the University Andrology Laboratory has been under the direction of Gail S. Prins, Ph.D., HCLD, from its inception to the present.

Cancer Control using Population-based Registries and Biobanks
type: Resource
type: NamedIndividual
has db xref: nlx_87258
synonym: Cancer Control using Population-based Registries Biobanks
synonym: CCPRB (Cancer Control using Population-based Registries and Biobanks)
synonym: CCPRB (Cancer Control using Population-based Registries Biobanks)
synonym: CCPRB - Cancer Control using Population-based Registries and Biobanks
abbrev: CCPRB
IAO_0000115: CCPRB (Cancer Control using Population-based Registries and Biobanks) is a Network of Excellence project within the sixth framework programme of the European Union. It is aiming at improved control of cancer by facilitating research linking biobanks and cancer registries. The project involves a systematic quality assurance and continuous development of standards and norms for human sample biobanks in Europe, as well as development of improved integrity-protection standards in the handling of sensitive information in connection with biobank-based research. The samples in the biobanks will be used in large-scale cancer research searching for genetic and infectious causes to cancer, in particular in the areas of breast and colorectal cancer and childhood leukemia. Project objectives: * Provide the study base for uniquely large population-based prospective studies on cancer * Define and implement a generally applicable European Quality Standard for Biobanking that will include improved data and specimen standardization, acquisition and analysis, reliable and standardized statistical analysis as well as improved management and co-ordination of European biobanks. * Define and promote the implementation of integrity-proof methods for biobank-based research involving well defined and secure third party code-keeping systems. * Enable large-scale, population-based research on: ** evaluation of cancer treatment and role of molecular markers in treatment selection ** use over-generation registry linkages applied to large biobank cohorts to identify and evaluate genetic predisposition associated with increased cancer risk as well as interactions with common environmental exposures. ** use over-generation registry linkages applied to large biobank cohorts to explore and evaluate intrauterine exposures associated with increased cancer risk ** exploit the power of large population cohorts for design of optimal strategies for cancer prevention and its evaluation. * Establish a Europ…

NIH Biospecimens Interest Group
type: Resource
type: NamedIndividual
has db xref: nlx_143936
abbrev: Biospecimens Interest Group
IAO_0000115: The mission of the Biospecimens Interest Group is to serve as an educational and tutorial vehicle for disseminating information, best practices, regulations, and ethical/legal information formulated and issued by various NIH offices, federal agencies and other leading biospecimens organizations. Please join our listserv so we can inform you about the date, time and the place for future meetings, speakers, website and other activities --- https://list.nih.gov/cgi-bin/wa?SUBED1=biospecimens&A=1. Meetings and seminars are videocast. Vision: #. To create a place where all stakeholders may exchange scientific data, ideas, and information concerning the creation and use of high quality biospecimens for research, assay validation, technology development and other appropriate uses. #. To promote and facilitate interaction between NIH intramural and extramural stakeholders who are interested in and involved with a variety of clinically-oriented, translational research projects using high quality biospecimens. #. To encourage leading stakeholders to address critical elements in study design and statistical analysis of data to facilitate the production of accurate, optimal, and clinically meaningful results (best outcome). #. To educate stakeholders about the potential barriers and obstacles that may obstruct the sharing and collaboration between stakeholders across different organizations and countries. #. To increase the awareness for the necessity of high quality biospecimens and the harmonization, and when appropriate, standardized procedures (best practices, SOPs) for annotating, collecting, transporting, processing, storing, and sharing biospecimens to ensure optimal reproducibility of outcomes and the privacy of the patients (donors) through adherence to the ethical and legal requirements associated with the use of biospecimens. #. To provide the connectivity to various biorepositories and biospecimens around the world, especially those containing rare and difficult to …

POPDIST
type: Resource
type: NamedIndividual
has db xref: nlx_154542
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Software application that calculates a number of different genetic identities, phylogeny reconstructing measures, and distance reconstructing measures (entry from Genetic Analysis Software)

VMD
type: Resource
type: NamedIndividual
has db xref: nlx_87328
synonym: VBI Microbial Database
synonym: Virginia Bioinformatics Institute Microbial Database
abbrev: PAMGO_VMD
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. Database covering a range of plant pathogenic oomycetes, fungi and bacteria primarily those under study at Virginia Bioinformatics Institute. The data comes from different sources and has genomes of 3 oomycetes pathogens: Phytophthora sojae, Phytophthora ramorum and Hyaloperonospora arabidopsidis. The genome sequences (95 MB for P.sojae and 65 MB for P.ramorum) were annotated with approximately 19,000 and approximately 16,000 gene models, respectively. Two different statistical methods were used to validate these gene models, Fickett' '''s and a log-likelihood method. Functional annotation of the gene models is based on results from BlastX and InterProScan screens. From the InterProScan results, putative functions to 17,694 genes in P.sojae and 14,700 genes in P.ramorum could be assigned. An easy-to-use genome browser was created to view the genome sequence data, which opens to detailed annotation pages for each gene model. A community annotation interface is available for registered community members to add or edit annotations. There are approximately 1600 gene models for P.sojae and approximately 700 models for P.ramorum that have already been manually curated. A toolkit is provided as an additional resource for users to perform a variety of sequence analysis jobs.

UCSD Experimental Neuropath Laboratory
type: Resource
type: NamedIndividual
has db xref: nlx_143937
synonym: Laboratory of Experimental Neuropathology
synonym: UCSD Experimental Neuropathology Laboratory
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 31, 2016. The Laboratory of Experimental Neuropathology is engaged in the study of neurodegenerative disease, including Alzheimer's, Parkinson's, and the dementia of HIV encephalitis. It contains a large bank of materials available to fellow investigators including images, publications, and lab safety. Fellow Investigators and Collaborators may request materials from the brain bank. Technologies employed by the laboratory include immunocytochemistry, neurochemistry, molecular genetics, transgenic models of disease, and imaging by scanning laser confocal microscopy.

BioRep
type: Resource
type: NamedIndividual
has db xref: nlx_87504
IAO_0000115: Offer biorepository services to public and private research institutes, to the highest standards of quality and safety with the aim of contributing to the advancement of medical research and scientific discovery. The BioRep Cell Repository establishes, maintains and distributes cell line cultures as well as DNA derived from these cultures. The scientific and business affiliation between BioRep and Coriell allows access to more than a million types of cell vials, stored in liquid nitrogen. Cells that have been stored for nearly 50 years, are still viable and available for research purposes today. Thanks to an exclusive agreement with the Coriell Institute for Medical Research, the oldest and largest biorepository of the world, BioRep is specialized in cell lines preparation, in nucleic acid extraction and long term storage in liquid nitrose (-196 degrees C) and in refrigerators (-80 degrees C) of any kind of biosamples, using procedures and standards developed by the Coriell in over 50 years of activity. BioRep and Coriell together constitute one of the few Global Biorepository able to serve the pharmaceutical industries for world wide clinical trials. BioRep facility is specifically designed to give the utmost efficiency and security by implementing Coriell procedures and standards. The BioRep Tissue Repository provides safe and secure storage of tissue specimens as required for medical research and scientific investigation. All tissues are preserved with the most current preservation techniques and processes. In addition to the storage service, BioRep provides Cell Biology, Molecular Biology, Microbiology services developed in ISO 9001:2008 certified laboratories.

da Vinci European Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_87590
abbrev: daVEB
IAO_0000115: BioBank that collects, stores, processes and distributes biospecimens and the associated data. The biospecimens are human and non-human genetic materials, proteins, cells, tissues and biofluids. The data are the biological information associated to the samples and, in the case of human samples, the clinical information pertaining to the donor. The da Vinci European BioBank (daVEB) is a multicenter biobank with a centralized IT infrastructure and a main repository located at the Polo Scientifico (Scientific Campus of the University of Florence) in Sesto Fiorentino (Florence, Italy). Hosted by the Magnetic Resonance Center (CERM), an expert center on protein structure and metabolomics, daVEB's aim is to host as rich as possible biological human sample collections, stored accordingly to EU guidelines, in order to offer a powerful tool in the study of complex diseases. At the end of July 2011, the da Vinci European BioBank of the Pharmacogenomics FiorGen Onlus Foundation has been audited and got the quality certification according to UNI EN ISO 9001:2008 for Collection, storage and distribution of biological samples and the associated data for scientific research. Besides the samples stored at da Vinci European BioBank in Sesto Fiorentino (Florence), the daVEB is also the administrative biobank for research sample collections that are stored in the delocalized repositories. All the sample collections must be registered in the biobank: * sample collections taken within the regular health care * samples taken from healthy individuals or other persons out of the regular health care * samples that have been taken in hospitals within research protocols on specific pathologies all transferred to daVEB endowed with a transfer agreement signed by the donor. The Research Units actually afferent to daVEB are delocalized in the Florence, Prato, Pisa and Siena provinces. Delocalized repositories are under construction in Tuscany.

European Language Resources Association
type: Resource
type: NamedIndividual
has db xref: nlx_87637
abbrev: ELRA
IAO_0000115: ELRA is the driving force to make available the language resources for language engineering and to evaluate language engineering technologies. In order to achieve this goal, ELRA is active in identification, distribution, collection, validation, standardization, improvement, in promoting the production of language resources, in supporting the infrastructure to perform evaluation campaigns and in developing a scientific field of language resources and evaluation. ELRA''s missions are to promote language resources for the Human Language Technology (HLT) sector, and to evaluate language engineering technologies. To achieve these two major missions, we offer a range of services, listed below and described in the Services around Language Resources section: - Identification of language resources - Promotion of the production of language resources - Production of language resources - Validation of language resources - Evaluation of systems, products, tools, etc., related to language resources - Distribution of language resources - Standardization The promotion of the production of language resources also includes our support of the infrastructure for evaluation campaigns and our support in developing a scientific field of language resources and evaluation, e.g. via the LREC conference. ELRA also regularly conducts market studies and surveys in the field of HLT, and publishes a quarterly newsletter, distributed not only to its members but also to a large number of people in the HLT community.

Wisconsin Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_91313
abbrev: WTB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 2,2026. A non-profit program providing tissue procurement services to the state of Wisconsin. The Wisconsin Tissue Bank handles organ donation, works with organ donors, provides organ donation information and organ transplantation. The Wisconsin Tissue Bank staff provides service to hospitals, Medical Examiners/Coroners and Funeral Directors throughout the state of Wisconsin for the recovery of bone, related soft tissue, veins, skin, and cardiovascular tissue for donation and transplantation. The Wisconsin Tissue Bank is dedicated to the education of health care professionals and the public to promote organ and tissue donation. The Wisconsin Tissue Bank promotes an environment sensitive to the physical, emotional, spiritual, social and economic needs of both those served and those who provide the service.

U-Compare
type: Resource
type: NamedIndividual
has db xref: nlx_87780
IAO_0000115: An integrated text mining / natural language processing system based on the Unstructured Information Management Architecture (UIMA) Framework. It allows interoperability of text mining tools and allows the creation of text mining workflows, comparison and visualization of tools. U-Compare can be launched straight from the web or downloaded. As the name implies comparison of components and workflows is a central feature of the system. U-Compare allows sets of components to be run in parallel on the same inputs and then automatically generates statistics for all possible combinations of these components. Once a workflow has been created in U-Compare it can be exported and shared with other users or used with other UIMA compatible tools and so in addition to comparison, U-Compare also functions as a general purpose workflow creation tool. It contains a repository of 50+ biomedical text mining components. These components are included in the U-Compare single-click-to-launch package, ready to use by just drag-and-drop. You can also use this repository independent from the U-Compare system. Link with Taverna It has a link with Taverna for scientific workflows, http://bioinformatics.oxfordjournals.org/content/26/19/2486.abstract, where you can use U-Compare and its workflow from within the Taverna workflow. There are two ways, the U-Compare Taverna plugin and the U-Compare command line mode as a Taverna activity. We have recently integrated it with Peter Murray-Rust' '''s OSCAR for Chemistry (see http://www.nactem.ac.uk/cheta/) Web Demo: http://www.nactem.ac.uk/software/cheta/

Indiana Organ Procurement Organization - IOPO
type: Resource
type: NamedIndividual
has db xref: nlx_93492
synonym: Indiana Organ Procurement Organization
synonym: Indiana Organ Procurement Organization Inc.
synonym: IOPO - Indiana Organ Procurement Organization
abbrev: IOPO
IAO_0000115: Indiana Organ Procurement Organization (IOPO) is the non-profit health service dedicated to advancing organ, tissue, and eye donation throughout Indiana. Its mission is to save and enhance the quality of life through organ, tissue and eye donation. IOPO''s vision is to create the most effective and influential donation and transplantation delivery model in health care. IOPO, as a health services organization, is regulated by several agencies of the US government and maintains accreditations and compliance with regulatory requirements by strict adherence to quality.

UCSF Laboratory for Visual Neuroscience
type: Resource
type: NamedIndividual
has db xref: nlx_143941
synonym: University of California San Francisco Laboratory for Visual Neuroscience
abbrev: Laboratory for Visual Neuroscience
IAO_0000115: Devise better ways to prevent and treat vision loss due to amblyopia and strabismus, and to advance medical science by understanding the human visual system. Various Images, Videos and Talks related to the research are available. In the Laboratory for Visual Neuroscience at the University of California, San Francisco, we are seeking to discover how visual perception occurs in the human brain. The function of the visual system is to guide our behavior by providing an efficient means for the rapid assimilation of information from the environment. As we navigate through our surroundings, a continuous stream of light images impinges on our eyes. In the back of each eye a light-sensitive tissue, the retina, converts patterns of light energy into electrical discharges known as action potentials. These signals are conveyed along the axons of retinal ganglion cells to the lateral geniculate body, a relay nucleus in the thalamus. Most of the output of the lateral geniculate body is relayed directly to the primary visual cortex (striate cortex, V1), and then to surrounding visual association areas. To understand the function of the visual pathways, our research is focused on 5 major themes: * Organization of Primary Visual Cortex * Mapping of Extrastriate Visual Cortex * Amblyopia and Visual Development * Strabismus and Visual Suppression * The Human Visual Cortex

Wall Street Journal Health Blog
type: Resource
type: NamedIndividual
has db xref: nlx_143942
synonym: Health Blog
abbrev: WSJ Health Blog
IAO_0000115: Health Blog offers news and analysis on health and the business of health. The blog is written by Katherine Hobson and includes contributions from staffers at The Wall Street Journal, WSJ.com and Dow Jones Newswires. A searchable interface allows the user to find topics of interest. Katherine Hobson has been writing about health and business for more than 15 years, including stints covering cancer, nutrition, exercise science, the U.S. economy and the U.K. beer industry.

MetaPhlAn
type: Resource
type: NamedIndividual
has db xref: OMICS_02286
synonym: Metagenomic Phylogenetic Analysis
synonym: MetaPhlAn - Metagenomic Phylogenetic Analysis
synonym: MetaPhlAn v2
synonym: MetaPhlAn version 2
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. It relies on unique clade-specific marker genes identified from reference genomes.

Quebec Leukemia Cell Bank
type: Resource
type: NamedIndividual
has db xref: nlx_88275
synonym: Banque de Cellules Leuc��������miques du Qu��������bec
abbrev: BCLQ
IAO_0000115: The primary objective of the Quebec Leukemia Cell Bank is to support basic and clinical blood cancer research. It also serves to provide an infrastructure and services aimed at facilitating the work of researchers in various fields, such as oncology, hematology and immunology in particular. Several researchers have already benefited from this infrastructure in the course of their work. The main missions of the Quebec Leukemia Cell Bank are : * To set up a bank of well-characterized human blood tumor cells. The constitutional DNA is also stored for the majority of samples. A computerized databank includes all laboratory tests performed on these specimens, as well as the corresponding clinical data. Before this bank was created, the absence of access to adequate blood tumor specimens severely hampered our researchers'' efforts to competitively pursue their work. Also, the availability of these specimens now makes it possible to establish an essential link between the basic and clinical research communities. * Provide chromosomal analysis by conventional cytogenetics and spectral karyotyping (SKY) for human and mouse cells. * Contribute to the training of specialized staff and students. The Quebec Leukemia Cell Bank is a provincial program that groups together hematologists, researchers and clinical scientists from four Quebec universities (Universit�������� Laval, McGill, Sherbrooke, Montr��������al) and Quebec research centers. The cell bank has been in operation since 2001. The purpose of this website is to raise awareness about our cell bank so we can continue to help an increasing number of researchers.

MyOpenArchive
type: Resource
type: NamedIndividual
has db xref: nlx_91662
synonym: My Open Archive
abbrev: MyOA
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 26, 2019.An international Non-Profit Organization that advocates Open Access for never-before-published research papers on the web and provides Self-Archiving platform to enable better knowledge sharing in a way that''s easy to publish. They collect scientific material (not only publications), e.g., Journal Articles, Theses or Dissertations, Departmental Bulletin Papers, Conference Papers, Presentations, Books, Technical Reports, Research Papers, Articles, Preprints, Learning Materials, Others. If you have such a paper and would like to add a Creative Commons license to your work, or if your working organization has no Institutional Repository (IR), Open your archives to spread them to the world. How to use: 1. Sign in with Twitter 2. Select PDF and add a Creative Commons license 3. Publish and Share on Social Media Video tutorial: http://myopenarchive.org/whatsmyoa

LifeBanc
type: Resource
type: NamedIndividual
has db xref: nlx_88315
IAO_0000115: Lifebanc is the nonprofit organ and tissue recovery organization for Northeast Ohio. As one of the original seven independent organ procurement organizations in the United States, Lifebanc serves nearly four million people and works with 80 hospitals in 20 counties. We are a member of the Organ Procurement and Transplantation Network (OPTN), which has been managed by the United Network for Organ Sharing (UNOS) since 1986. We also work closely with local partners, as well as the other Organ Procurement Organizations in the state of Ohio to educate the public and healthcare professionals about the benefits of and need for organ, tissue and eye donations. These organizations include Lifeline of Ohio; LifeCenter and Life Connection of Ohio. Along with serving the public, professional community and donor hospitals, Lifebanc provides life-saving organs to two transplant centers: The Cleveland Clinic and University Hospital Case Medical Center. Recovered tissue is transplanted countless times in hospitals throughout the region. Last year, Lifebanc helped to heal and save more than 25,000 lives. Additionally, it was instrumental in helping to perform the nation''s first near-total face transplant and establishing the world-record for lungs transplanted in a year.

HMP Data Analysis and Coordination Center
type: Resource
type: NamedIndividual
has db xref: nlx_88368
synonym: Data Analysis and Coordination Center for the Human Microbiome Project
synonym: HMPDACC
synonym: Human Microbiome Project Data Analysis and Coordination Center
abbrev: HMP DACC
IAO_0000115: Common repository for diverse human microbiome datsets and minimum reporting standards for Common Fund Human Microbiome Project.

BioMarkers for SMA Data Portal
type: Resource
type: NamedIndividual
has db xref: nlx_88529
synonym: BforSMA Data Portal
synonym: Biomarkers for SMA
synonym: Biomarkers for Spinal Muscular Atrophy
synonym: Biomarkers for Spinal Muscular Atrophy Data Portal
abbrev: BforSMA
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A publicly available tool that contains data from the BforSMA clinical study ( ClinicalTrials.gov, NCT00756821 ), a pilot study to identify candidate biomarkers in blood or urine from a wide range of Spinal Muscular Atrophy (SMA) patients that associate with disease severity. It is hoped that the identification of candidate biomarkers will lead to clinical efficacy and longitudinal natural history studies to verify these markers and enable their use as validated pharmacodynamic markers, longitudinal progression markers, or surrogate endpoint measures in clinical trials.

NIMH Chemical Synthesis and Drug Supply Program
type: Resource
type: NamedIndividual
has db xref: nif-0000-00234
synonym: NIMH Chemical Synthesis Drug Supply Program
abbrev: CSDSP
abbrev: NIMH CSDSP
IAO_0000115: A program that synthesizes, purifies, and distributes otherwise unavailable essential compounds to stimulate basic and clinical research in psychopharmacology relevant to mental health in areas such as the molecular pharmacology and signaling of CNS receptors, longitudinal studies to evaluate the molecular, biochemical, and behavioral actions of psychoactive compounds, and functional brain imaging in both primates and humans. WHAT IS AVAILABLE: * Ligands for CNS receptors, radiolabeled compounds for autoradiography and neuroimaging, biochemical markers, drug analogs and metabolites, and reference standards * Synthesis (including GMP) of promising compounds for mental health research, including preclinical toxicology and safety studies, especially compounds for PET neuroimaging * A listing of currently available NIMH CSDSP compounds is available online at www.nimh-repository.rti.org. RTI International scientists can provide investigators with technical assistance and additional information about the compounds on request. Data sheets containing purity, storage, and handling information are supplied with all NIMH CSDSP compounds. WHO IS ELIGIBLE: Investigators involved in basic or clinical research relevant to mental health are eligible to submit requests. To learn more about current NIMH research areas, please visit the NIMH website at www.nimh.nih.gov. NIMH CSDSP compounds are free to qualified academic investigators, but payment may be required from nonacademic requestors. Investigators interested in obtaining radiolabeled compounds but uncertain about what type of label or specific activity would work best for them may obtain help by communicating with the technical contacts listed on the website.

Cliniques Universitaires Saint-Luc Cancer Centre
type: Resource
type: NamedIndividual
has db xref: nlx_143961
synonym: Centre du Cancer Cliniques Universitaires St-Luc
synonym: Cliniques Universitaires Saint-Luc Cancer Center
IAO_0000115: An essential reference center in Europe and a leader in French-speaking Belgium that treats all types of adult and childhood cancer. They fight against cancer while giving patients comprehensive and humane care. Their quest for excellence is in three main academic fields: clinical care, research and teaching.

LONI Inspector
type: Resource
type: NamedIndividual
has db xref: nlx_155785
IAO_0000115: A Java application for reading, displaying, searching, comparing, and exporting metadata from medical image files: AFNI, ANALYZE, DICOM, ECAT, GE, Interfile, MINC, and NIFTI.

Alzheimer's and Dementia Resource Center
type: Resource
type: NamedIndividual
has db xref: nlx_143948
synonym: alzheimer's disease
synonym: brain
synonym: brain bank
synonym: caregiver
synonym: dementia
synonym: educational resource
synonym: patient support
synonym: tissue
abbrev: ADRC
IAO_0000115: The Alzheimer's and Dementia Resource Center (ADRC) facilitates tissue donations for the Brain Bank Research Program in order to help find better treatments, more diagnostic tools and a cure for Alzheimer's disease and dementia. The Brain Bank Program is administered by Mount Sinai Medical Center in Miami Beach and under contract with the Florida Department of Elder Affairs. ADRC also provides caregivers with the educational resources, spiritual comfort and emotional support. The ADRC facilitates training for professional caregivers that meets requirements for the Florida Department of Elder Affairs.

NeuroDevNet
type: Organization
type: NamedIndividual
has db xref: grid.429756.b
has db xref: nlx_88813
IAO_0000115: NeuroDevNet, a Canadian Network of Centres of Excellence (NCE), is dedicated to helping children overcome neurodevelopmental disorders. Network investigators seek to understand the causes of neurological deficits, and to transfer this knowledge to health care professionals, policy makers, and communities of interest. NeuroDevNet works with its partners in academia, the community, not-for-profit sector, industry, and government, and across traditional disciplinary boundaries and sectors, to ensure generated knowledge is translated into tangible diagnostic, preventative, therapeutic, social, economic, and health benefits for all. NeuroDevNet supports transformative research, provides training to build a new generation of Canadian researchers, strengthens communities with the right tools and information, and translates research findings into early diagnostic, preventative, and therapeutic strategies for children with neurological disorders to live healthier lives. Currently, the network''s research focuses on autism spectrum disorder, cerebral palsy, and fetal alcohol spectrum disorder. These demonstration projects are supported by NeuroDevNet''s central infrastructure and cores, including Neuroethics, Neuroinformatics, and Knowledge Translation.

Stanford Research Institute International
type: Organization
type: NamedIndividual
has db xref: nif-0000-00235
synonym: SRI International
synonym: Stanford Research Institute
abbrev: SRI
IAO_0000115: Independent, nonprofit research institute conducting client sponsored research and development for government agencies, commercial businesses, foundations, and other organizations. SRI also brings its innovations to the marketplace by licensing its intellectual property and creating new ventures. SRI was founded as Stanford Research Institute in 1946 by a group of West Coast industrialists and Stanford University. SRI formally separated from the University in 1970, and we changed our name to SRI International in 1977.

Tayside Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_89099
synonym: Tayside Tissue Bank - Dundee
abbrev: TTB
IAO_0000115: Tayside Tissue Bank is a secure bio-repository which holds small samples of surplus tissue and other specimens generously donated by patients who have undergone surgery or other more minor medical procedures during the course of their investigations and treatment. Such samples are vital for medical researchers seeking to improve the detection and treatment of many different diseases as well as advance our understanding of how and why they arise. This website is for both patients who wish to know more about how their tissue is used and for researchers who wish to explore the possibility of utilising the donations kindly made by patients to advance medical research. It also explains some of the additional services the Tissue Bank provides to assist researchers with their investigations including: embedding and cutting sections, standard histological staining, immunohistochemistry (IHC), nucleic acid extraction, protein extraction, and generation of Tissue Microarrays. Donations made to the Bank are held within ultra-low temperature (ULT) freezers within the University of Dundee Medical School at Ninewells Hospital, Dundee. The freezers are alarmed and their temperature continuously monitored. The Bank''s location adjacent to the Pathology Department means it is ideally situated for prompt processing and storage of tissue samples after they have been examined by a pathologist. In addition to collecting, logging and storing tissue samples the bank also holds blood specimens and other materials collected as part of national trials. It also plays a role in administering access to the Tayside Type II diabetes cohort. The Bank contains in the region of 30,000 fresh frozen tissue samples from around 6000 different patients. There are also in excess of 5000 blood samples. Storage of the samples is split between separate, continuously monitored freezers. In addition the Bank has access to the Pathology Department''s Histopathology Archive (30,000 new specimens annually).

MethodBox
type: Resource
type: NamedIndividual
has db xref: nlx_89127
IAO_0000115: Collaboration environment for sharing variable sets and statistical methods for analysis across social science survey data. MethodBox enables you to browse and download datasets, share methods and scripts, find fellow researchers with similar interests and share your knowledge. MethodBox source available on Google code. Finding the variables you need to support a particular research question can be time consuming. Wading through hundreds of pages of PDF documents, codebooks and metadata and then trying to find the exact column in a huge spreadsheet can be very frustrating. MethodBox gets you to the variables faster and lets you download only the data you need. You can also share your scripts with others to allow them to adopt best practice quicker than before.

Classifier for Metagenomic Sequences
type: Resource
type: NamedIndividual
has db xref: nlx_144629
has db xref: OMICS_01452
abbrev: ClaMS
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 2nd, 2023. Sequence composition based classifier for metagenomic sequences. It works by capturing signatures of each sequence based on the sequence composition. Each sequence is modeled as a walk in a de Bruijn graph with underlying Markov chain properties. ClaMS captures stationary parameters of the underlying Markov chain as well as structural parameters of the underlying de Bruijn graph to form this signature. In practice, for each sequence to binned, such a signature is computed and matched to similar signatures computed for the training sets. The best match that also qualifies the normalized distance cut-off wins. In the case that the best match does not qualify this cut-off, the sequence remains un-binned.

NIH Neuroscience Microarray Consortium
type: Resource
type: NamedIndividual
has db xref: nif-0000-00074
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 24, 2012. (no longer being funded) The NIH Microarray Consortium provides for-fee services to a community of NIH grantees, together with a more limited set of services to the public. The primary goal of this consortium is to move basic and translational research forward through acquisition and dissemination of high quality genomic data. This site includes a repository of microarray data sets and offers one-click links to public projects. These datasets were generated by various researchers on these platforms: Affymetrix, Agilent, Ambion, cDNA, Illumina, and Operon. The species currently covered are: Arabidopsis, Bovine, chicken, C. Elegans, Drosophila, Human, Macaca mulatta (Rhesus macaque), Mouse, Rat, Songbird, Xenopus, Yeast, and zebra finch. Basic search functions allows users to choose multiple options for finding the projects that interest them, and raw data files can also be downloaded after user registration. Web-based data analysis tools are also available. Scientists can analyze microarray data from the consortium repository or investigators can upload outside data for analysis.

Open University; Milton Keynes; United Kingdom
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100008509
has db xref: grid.10837.3d
has db xref: ISNI:96069301
has db xref: nlx_19814
has db xref: Wikidata:Q2413375
synonym: Open University
synonym: The Open University
abbrev: OU
IAO_0000115: Public research university and the largest university in the UK for undergraduate education. The majority of the OU's undergraduate students are based in the United Kingdom and principally study off-campus; many of its courses can also be studied anywhere in the world.

ScienceOnline2012
type: Resource
type: NamedIndividual
has db xref: nlx_143949
synonym: Science Online 2012
IAO_0000115: ScienceOnline2012 is the sixth annual international meeting on science and the Web. The agenda includes more than 70 discussion sessions and workshops over three full days, and additional demonstrations, science lab tours, a museum reception & a dose of comedy. ScienceOnline2012 #scio12 across social media will take place January 19-21, 2012 on the campus of NC State University in the spacious McKimmon Center, with some 450 participants. Every January since 2007, the Research Triangle area of North Carolina has hosted scientists, students, educators, physicians, journalists, librarians, bloggers, programmers and others interested in the way the World Wide Web is changing the way science is communicated, taught and done. As in all the previous years, the meeting will be held in an ''unconference'' style the program is built beforehand with the help of participants on the planning wiki, and the sessions are designed to foster conversations and discussions among everyone in the room rather than a traditional one-before-many lecture approach. Help us continue the success of past conferences by familiarizing yourself with the plans for ScienceOnline2012, volunteering to help, offering your organization''s or company''s sponsorship or in-kind support, and, above all, engaging with the online science community before, during and after the conference.

SGN
type: Resource
type: NamedIndividual
has db xref: biotools:sol_genomics_network
has db xref: nlx_89764
has db xref: r3d100012078
synonym: SGN ref
synonym: Sol Genomics Network
IAO_0000115: A clade oriented, community curated database containing genomic, genetic, phenotypic and taxonomic information for plant genomes. Genomic information is presented in a comparative format and tied to important plant model species such as Arabidopsis. SGN provides tools such as: BLAST searches, the SolCyc biochemical pathways database, a CAPS experiment designer, an intron detection tool, an advanced Alignment Analyzer, and a browser for phylogenetic trees. The SGN code and database are developed as an open source project, and is based on database schemas developed by the GMOD project and SGN-specific extensions.

Forsyth Institute
type: Organization
type: NamedIndividual
has db xref: nlx_89852
synonym: The Forsyth Institute
abbrev: Forsyth
IAO_0000115: Affiliated with Harvard School of Dental Medicine and Harvard Medical School and has collaborations with university and research organizations around the world. Dedicated to advancing human health and wellbeing through scientific discovery and education. Independent non-profit organization.

Biobank Suisse
type: Resource
type: NamedIndividual
has db xref: nlx_89853
synonym: Foundation biobank suisse
synonym: Foundation biobank-suisse
abbrev: BBS
IAO_0000115: The foundation biobank-suisse (BBS) is a collaborative network of existing and future research biobanks in Switzerland. The primary goals are: 1. to provide researchers a quick overview of available human biospecimens (by using the web query interface) and up to date person related data; and 2. to provide biobankers with services to further improve the quality of biobanks in Switzerland (e.g. information about up-to-date IT and database software for biobanking; solutions for ethical, legal, and social issues; develop common platform for biobankers; etc.). We maintain a database with data about patients and biospecimens. The database can be queried from our web-site. Once the researcher has found suitable biospecimens we will bring him in contact with the biobanks, which have collected the biospecimen. The researcher and the biobank manager will then discuss the next step without further participation of the foundation biobank-suisse. We provide advice and support to biobank manager, who are in the process to start a biobanking activity for material from humans. Well established biobanks can benefit from our help in realizing specific projects to improve their operations. BBS was founded in December 2005 as an initiative of Oncosuisse and SWISS BRIDGE with the goal to build a collaborative network of existing and future biobanks for research in Switzerland. BBS has currently information from about 60 000 biospecimens and 10 000 patients. This information is provided by the biobanks shown under the Partner biobank menu item and include: * Institut de Pathologie, Centre hospitalier universitaire vaudois (CHUV) * Institut f��r Pathologie Universit��tsspital Basel * Institut f��r Pathologie der Universit��t Bern BBS has entered in a closed collaboration with SAKK''s (Swiss Working Group on Clinical Cancer Research) IT department. BBS''s server is run by SAKK and technical support is provided by the SAKK IT department. BBS is an active member of ISBER (International Socie…

Florida Brain Bank
type: Resource
type: NamedIndividual
has db xref: nlx_143950
synonym: Florida Alzheimer's Disease Brain Bank
synonym: State of Florida Brain Bank
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A service and research oriented network of statewide regional brain bank sites. The intent of the brain bank program is to study brains of persons clinically diagnosed with dementia and provide tissue for research after their deaths. Mt. Sinai Medical Center contracts annually with the State of Florida to operate the primary brain bank. Coordinators at regional brain bank sites in Orlando, Tampa and Pensacola assist in recruiting participants and act as liaisons between the brain bank and participant families. Alzheimer's disease respite care program providers, memory disorder clinics, and model day care programs also recruit brain bank participants. The Florida Brain Bank supports collaborative research programs related to Alzheimer's disease and other degenerative disorders of the brain.

Protocol Online - Your labs reference book
type: Resource
type: NamedIndividual
has db xref: nlx_90492
synonym: Protocol Online Your lab''s reference book
synonym: Protocol-Online
abbrev: Protocol Online
IAO_0000115: Database of research protocols in a variety of life science fields, it contains protocols contributed by worldwide researchers as well as links to web protocols hosted by worldwide research labs, biotech companies, personal web sites. The data is stored in a MySql relational database. Protocol Online also hosts discipline specific discussion forums (BioForum), and provides a free PubMed search and alerting service (PubAlert).

MapAl
type: Resource
type: NamedIndividual
has db xref: OMICS_01261
IAO_0000115: A software tool for RNA-Seq expression profiling that builds on the established programs Bowtie and Cufflinks. Allowing an incorporation of ''gene models'' already at the alignment stage almost doubles the number of transcripts that can be measured reliably.

Saskatoon Arabidopsis T-DNA mutant population SK Collection
type: Resource
type: NamedIndividual
has db xref: nlx_91019
synonym: SK population
abbrev: SK-FST
IAO_0000115: Population of almost 50,000 activation tagged Arabidopsis thaliana lines that have been archived as individual lines to the T3 generation. The population is an excellent tool for both reverse and forward genetic screens and has been used successfully to identify a number of novel mutants. Flanking sequence tags (FST) have been generated and mapped for 15,507 lines to enable further application of the population, while providing a clear distribution of T-DNA insertions across the genome. The population is being screened for a number of biochemical and developmental phenotypes. The population provides an additional tool for plant researcher's to assist with determining gene function for the many as yet uncharacterized genes annotated within the Arabidopsis genome sequence. The presence of enhancer elements on the inserted T-DNA element (pSKI015) allows both knock-out and dominant activation phenotypes to be identified for traits of interest.

Florida Alzheimer's Disease Research Center
type: Resource
type: NamedIndividual
has db xref: nlx_143954
synonym: Florida ADRC
abbrev: FADRC
IAO_0000115: A statewide consortium dedicated to Alzheimer's disease research to better understand the disease and related memory disorders. It includes Alzheimer's researchers and clinicians from institutions across Florida such as USF Health, Mayo Clinic Jacksonville, and Mount Sinai Medical Center. The purpose of the ADRC is to assist institutions in developing an infrastructure (cores) that can be used for various research projects with the goal of better understanding Alzheimer's disease and related disorders. The Florida ADRC is comprised of six cores, three projects and three pilot projects among other collaborations that utilize these cores.

Pennsylvania State University Huck Institutes of the Life Sciences Neuroscience Graduate Program
type: Resource
type: NamedIndividual
has db xref: nlx_91092
synonym: Huck Institutes Neuroscience Graduate Program
IAO_0000115: Program provides preparation for students seeking careers in academia, education and industry. Students are usually admitted with the intent of obtaining a PhD degree in Neuroscience but the MS degree may be sought as part of the doctoral program.

State of Florida Alzheimer's Disease Initiative
type: Resource
type: NamedIndividual
has db xref: nlx_143955
synonym: Florida ADI
synonym: Florida Alzheimer's Disease Initiative
IAO_0000115: A program that provides services to meet the needs of individuals with Alzheimer's disease, and similar memory disorders, and their families. The Alzheimer's Disease Initiative (ADI) of Florida provides caregiver respite services and support which include in-home, facility-based, emergency, and extended care for caregivers who serve patients with memory disorders. Additionally, the ADI includes services provided by Memory Disorder Clinics (MDCs).

TDTASP
type: Resource
type: NamedIndividual
has db xref: nlx_154675
synonym: Power and Sample-Size Calculations for the TDT and ASP Tests
IAO_0000115: Software application for power and sample-size calculations for the TDT and ASP tests under a wide variety of ascertainment schemes. Uses the flexible genetic model of McGinnis. Most calculations are exact rather than asymptotic. (entry from Genetic Analysis Software)

European Genome phenome Archive
type: Resource
type: NamedIndividual
has db xref: BioTools:ega
has db xref: biotools:ega
has db xref: nlx_91316
has db xref: OMICS_01028
has db xref: r3d100011242
synonym: EGA
synonym: The European Genome-phenome Archive
synonym: The European Genome-phenome Archive (EGA)
IAO_0000115: Web service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The repository allows you to explore datasets from numerous genotype experiments, supplied by a range of data providers. The EGA''s role is to provide secure access to the data that otherwise could not be distributed to the research community. The EGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the EGA project. As an example, only members of the EGA team are allowed to process data in a secure computing facility. Once processed, all data are encrypted for dissemination and the encryption keys are delivered offline. The EGA also supports data access only for the consortium members prior to publication.

Erasmus MC Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_91504
synonym: Erasmus MC Virtual Tissue Bank
synonym: Erasmus Medical Center Tissue Bank
IAO_0000115: The Erasmus MC Virtual Tissue Bank is embedded in the department of Pathology. The collection is meant for medical research purposes only. This concerns a typical clinical based pathology biobank. Tissue samples left over from surgical resection specimen are stored under liquid nitrogen and can be requested by Erasmus MC scientists for medical scientific experiments. An application has been developed to enable scientists to search the collection on-line and request tissue samples over the Erasmus MC Intranet. Every request shall be judged according to procedures determined by the Erasmus MC Tissue Bank. A growing need is anticipated for large collections of well-diagnosed fresh frozen tumor tissue and, if available, corresponding pre-malignant and normal tissue samples. Scientific research on patient residual material has to comply with strict rules and regulations. Equipment The Erasmus MC Tissue bank manages the PALM microdissection laser for the center for Biomics, which is available through the center for Biomics ONLY after having followed an introduction course. Additionally, a complete TMA (Tissue Micro Array) platform, fully funded by the Josephine Nefkens Stichting, consisting of a Beecher Automated Tissue Arrayer ATA 27 and a Virtual Microscope or Nanozoomer from Hamamatsu and Medical Solutions with TMA analyses software strongly supports translational research on tissue samples. Complete histologic Images from the Virtual Microscope are available within the Erasmus MC Intranet or available on the Internet either by overview or a direct example.

UniSave
type: Resource
type: NamedIndividual
has db xref: nlx_91568
has db xref: r3d100011244
synonym: UniProtKB Sequence/Annotation Version Archive
IAO_0000115: The UniProtKB Sequence/Annotation Version Archive (UniSave) is a repository of UniProtKB/Swiss-Prot and UniProtKB/TrEMBL entry versions. Entries can be retrieved by entering a primary accession number or an entry name and pressing the Go! button. The result of the query is a list of entry versions with the UniProtKB database name, entry status, primary accession number, entry name, entry version, sequence version, release number and the release date, ordered by the release date, the latest version first. The entry version status can be ' '''incorporated' ''', ' '''active' ''', ' '''changed' ''', ' '''replaced' ''' or ' '''deleted' '''. An incorporated entry version is the first entry version added into UniProtKB, an active entry version is part of the latest public release, a changed entry version has been superseded by a newer entry version, a replaced entry has become secondary to another entry, and a deleted entry has been removed from the UniProtKB without becoming secondary to any other entry. For replaced entry versions, the status ' '''Replaced' ''' can be clicked to return all entries, which have the given entry as a secondary entry. If a date is provided as part of the query then only the version of the entry that was current at that date is displayed. Entries can be viewed by clicking ' '''View' ''' in the query results table. The ' '''<< Earlier' ''' and ' '''Later >>' ''' links can be used to access the earlier and later entry versions. The ' '''Back to List' ''' link returns the user to the query results table. Selecting ' '''UniProtKB' ''' or ' '''Fasta' ''' and pressing ' '''Save' ''' downloads the entry in flat file or fasta format. Comparison between entry versions is straightforward: selecting two entries and clicking the ' '''Compare Selected' ''' button will show the differences between the two entries. Whenever comparisons are made a Smith-Waterman sequence alignment is computed using SSEARCH, and displayed at the bottom of the entry. The actual…

ArchSchema
type: Resource
type: NamedIndividual
has db xref: nlx_91580
synonym: ArchSchema - graphs of related Pfam domain architectures
IAO_0000115: ArchSchema is a java webstart application that generates dynamic plots of related Pfam domain architectures. The protein sequences having each architecture can be displayed on the plot and separately listed. Where there is 3D structural information in the PDB, the relevant PDB codes can be shown on the plot. Sequences can be be filtered by organism, or the output can be limited to just those protein sequences for which there is structural information in the PDB. Search by UniProt sequence id, or by Pfam domain id. Red underlines indicate the extent to which 3D structures of the domains and architectures are available in the PDB. Left-clicking on a node shows a panel containing information about the constituent domains, the protein sequences having the given architecture, and any sequences that have whole or partial structures in the PDB. You can display protein sequence (or, alternatively, the protein structures) associated with each architecture. You can download ArchSchema to run locally from your own machine. Note, however, you only download the code and not the data. Thus you will need to be connected to the Internet whenever you perform a search from within ArchSchema. The search initiates a call to the EBI which returns the data to ArchSchema for graphing.

Integrated Podcasts
type: Resource
type: NamedIndividual
has db xref: nlx_91615
synonym: Integrated Podcasts View
synonym: NIF Integrated Podcasts
IAO_0000115: A virtual database currently indexing multiple podcast resources including: The Brain Science Podcast, Nature Podcast, NeuroPod, Science Podcast, The American Journal of Psychiatry Podcast, 60-Second Mind, and Science Talk.

Tufts University Graduate School of Biomedical Sciences Graduate Programs
type: Resource
type: NamedIndividual
has db xref: nif-0000-02120
IAO_0000115: Graduate school provides training of highly educated biomedical scientists through collaborative and interdisciplinary research. Provides degree programs in Cell, Molecular and Developmental Biology; Genetics; Immunology; Molecular Microbiology; Neuroscience; Clinical and Translational Science; Pharmacology and Drug Development.

MycoBank
type: Resource
type: NamedIndividual
has db xref: nlx_91803
has db xref: r3d100011222
IAO_0000115: Database documenting mycological nomenclatural novelties (new names and combinations) and associated data, for example descriptions and illustrations. The nomenclatural novelties will each be allocated a unique MycoBank number that can be cited in the publication where the nomenclatural novelty is introduced. These numbers will also be used by the nomenclatural database Index Fungorum, with which MycoBank is associated and will also serve as Life Science Identifiers (LSIDs). Nomenclatural experts will be available to check the validity, legitimacy and linguistic correctness of the proposed names in order to avoid nomenclatural errors; however, no censorship whatsoever, (nomenclatural or taxonomic) will be exerted by MycoBank. Deposited names will remain -when desired- strictly confidential until after publication, and will then be accessible through MycoBank, Index Fungorum, GBIF and other international biodiversity initiatives, where they will further be linked to other databases to realize a species bank that eventually will link all databases of life. MycoBank will (when applicable) provide onward links to other databases containing, for example, living cultures, DNA data, reference specimens and pleomorphic names linked to the same holomorph. Authors intending to publish nomenclatural novelties are encouraged to contribute to this new initiative. For the moment 2 search engines are available from the MycoBank website. The first one permits to search for fungal names (at any rank level), the authority or the MycoBank unique number. The second is dedicated to bibliographic queries related to fungal name' '''s publications. MycoBank users willing to deposit their data will have to register so that they willbe able to contact the depositor for specific information (e.g. MycoBank number, possible points of attention regarding the name, actual publication, etc), and to avoid fake entries.

BrainLiner
type: Resource
type: NamedIndividual
has db xref: nlx_91840
synonym: BrainLiner.jp
IAO_0000115: Portal and tools for sharing and editing neurophysiological and behavioral data for brain-machine interface research. Users can search for existing data or login with their Google, Facebook, or Twitter account and upload new data. Their main focus is on supporting brain-machine interface research, so we encourage users to not just provide recordings of brain activity data, but also information about stimuli, etc., so that statistical relationships can be found between stimuli and/or subject behavior and brain activity. The Matlab tools are for writing, reading, and converting Neuroshare files, the common file format. A free, open source desktop tool for editing neurophysiological data for brain-machine interface research is also available: https://github.com/ATR-DNI/BrainLiner Since data formats aren' '''t standardized between programs and researchers, data and analysis programs for data cannot be easily shared. Neuroshare was selected as the common file format. Neuroshare can contain several types of neurophysiological data because of its high flexibility, including analog time-series data and neuronal spike timing. Some applications have plug-ins or libraries available that can read Neuroshare format files, thus making Neuroshare somewhat readily usable. Neuroshare can contain several types of neurophysiological data, but there were no easy tools to convert data into the Neuroshare format, so they made and are providing a Neuroshare Converter Library and Simple Converter using the library. In future work they will make and provide many more useful tools for data sharing. Shared experiments include: EMG signal, Takemiya Exp, Reconstruct (Visual image reconstruction from human brain activity using a combination of multi-scale local image decoders), SPIKE data, Speech Imagery Dataset (Single-trial classification of vowel speech imagery using common spatial patterns), Functional Multineuron Calcium Imaging (fMCI), Rock-paper-scissors (The data was obtained from subjec…

Pythia
type: Resource
type: NamedIndividual
has db xref: nlx_91969
IAO_0000115: Pythia is an open source thermodynamically oriented primer design python module. Pythia can be used in two ways. 1. Executable binaries only: under windows with cygwin and python 2.5 (built with mingw, that comes with the cygwin release). These executables allow the user to index DNA files for primer specificity search, design one primer pair per region, and tile regions with PCR amplicons. 2. A python module: under windows with cygwin, python2.5, numpy, swig, and mingw, or under linux with python2.4 or later, numpy, and swig (everything but numpy should be pre-installed on a normal linux system). The module gets you everything that the binaries get you, in a more pythonic framework. This package also includes modules for computing DNA binding and folding energies using the partition function approach with publicly available thermodynamic data. Usage documentation is in the downloads.

HSSP
type: Resource
type: NamedIndividual
has db xref: biotools:hssp
has db xref: nlx_91976
synonym: Homology derived Secondary Structure of Proteins
synonym: Homology-derived Secondary Structure of Proteins
synonym: homology-derived structures of proteins
synonym: HSSP - Homology derived Secondary Structure of Proteins
synonym: HSSP - Homology-derived Secondary Structure of Proteins
synonym: HSSP database
IAO_0000115: HSSP (homology-derived structures of proteins) is a derived database merging structural (2-D and 3-D) and sequence information (1-D). For each protein of known 3D structure from the Protein Data Bank, the database has a file with all sequence homologues, properly aligned to the PDB protein. Homologues are very likely to have the same 3D structure as the PDB protein to which they have been aligned. As a result, the database is not only a database of sequence aligned sequence families, but it is also a database of implied secondary and tertiary structures. Likely secondary structure are carried over from the PDB protein to each homologous protein. Tertiary structure models can be built by fitting the sequence of the homologue as aligned into the 3D template of the protein of known structure. Special software is needed to construct 3D models by homology, such WHATIF by Gert Vriend or MaxSprout by Liisa Holm and Chris Sander. The command rsync can be used to obtain a local copy of the HSSP. We appreciate receiving an Email from people who do so, but there are no strings attached. Everybody can freely download the files, academia and industry alike. If your institute''s firewall doesn''t allow you to use the (preferred) rsync way of obtaining HSSP files, feel free to work with FTP. The files are in that case available from: ftp://ftp.cmbi.ru.nl//pub/molbio/data/hssp/

University of Georgia; Georgia; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100007699
has db xref: grid.213876.9
has db xref: ISNI:0000 0004 1936 738X
has db xref: nlx_44218
has db xref: Wikidata:Q761534
synonym: University of Georgia
abbrev: UGA
IAO_0000115: Public research university with its main campus in Athens, Georgia. Founded in 1785, it is one of the oldest public universities in the United States.

Cover Pages
type: Resource
type: NamedIndividual
has db xref: nlx_143963
IAO_0000115: Public reference database supporting the XML family of markup language standards, XML vocabularies, and related structured information standards. It promotes and enables the use of open, interoperable, standards-based solutions which protect digital information and enhance the quality of data processing. The Cover Pages web site provides reference material on enabling technologies compatible with SGML/XML descriptive markup language standards and applications: object modeling, semantic nets, ontologies, authority lists, document production systems, and conceptual modeling. It also supplies references for social aspects of distributed and public sector concerns: privacy, open standards, patented technology embedded in standards, etc. NB. This statement and the resource itself are works in progress, subject to continuous revision.

Hackensack University Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_92521
synonym: HUMC Tissue Bank
synonym: John Theurer Cancer Center Tissue Bank
abbrev: JTCC Tissue Bank
IAO_0000115: The Tissue Bank stores tissue, blood, and bone marrow samples that have been taken from patients who have given their consent after they have undergone biopsies, surgery, or other procedures for cancer at the John Theurer Cancer Center. Our scientists use these samples to analyze and study multiple types of human cancer, with a goal toward learning more about how cancer develops, developing innovative new treatments, and determining how well a treatment is working. Our Tissue Bank is overseen by our program and medical director, Andre Goy, M.D., M.S., who is also deputy director of the Cancer Center and chief of the Division of Lymphoma; and our scientific director, K. Stephen Suh, Ph.D. Currently, 30 percent of our Tissue Bank team members work in our clinics, and 70 percent of our team works ����?��������??behind the scenes,����?��������?? conducting important scientific research without meeting patients.

Wellness Wiki
type: Resource
type: NamedIndividual
has db xref: nlx_92572
synonym: Understanding and Curing the Healthcare Crisis: A Wise Way to Better Outcomes and Lower Costs
IAO_0000115: Wellness Wiki is offered to help clarify the complex problems plaguing the U.S. healthcare system and develop sustainable ways to improve the health and well-being of all people. This virtual encyclopedia of the healthcare crisis and potential remedies welcomes your comments! The Wellness Wiki Book (Understanding & Curing American Healthcare: A Wise Way to Better Outcomes and Lower Costs) is available for purchase as a softcover book or pdf download. Table of contents: *Introduction & Executive Summary *Defining the Problem *Examining Three Proposed Solutions *Introducing a New Solution - Overview and Benefits, Wellness-Plus Solution Tactics, Barriers and Drivers to Implementing the Wellness-Plus Solution *Conclusion & Epilogue *Appendix *Wellness Model Technology Blueprint

World BioBank
type: Resource
type: NamedIndividual
has db xref: nlx_92664
IAO_0000115: Founded by the physician partners of ACORN, Inc. (Accelerated Community Oncology Research Network), World BioBank embraces forward-thinking technology and a strong commitment to the advancement of bioscience. The World BioBank collects cancer samples, normal samples, and other non-neoplastic diseases. Data available include sample-specific data, patient-specific data, and study-related data. * SOLID TISSUES (snap frozen and matched formalin-fixed paraffin embedded diseased and normal internal controls) from: Surgical resections, Image-guided biopsies, Bone marrow biopsies, Endoscopic biopsies * LIQUID TISSUES: Peripheral blood, Genomic DNA (from buffy coat), Plasma, Serum World BioBank is committed to marrying samples to a wealth of longitudinal medical data and tissue-specific data.

University of Zurich SCRM - Cell-and Tissue Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_143985
has db xref: OMICS_07231
synonym: SCRM - Cell- Tissue Biobank
synonym: SCRM - Cell-and Tissue Biobank (CTBB)
synonym: SCRM Biobank
synonym: University of Zurich SCRM - Cell and Tissue Biobank
synonym: University of Zurich SCRM - Cell Tissue Biobank
synonym: University of Zurich Swiss Center for Regenerative Medicine Cell-and Tissue Biobank
synonym: UZH SCRM - Cell-and Tissue Biobank
synonym: UZH SCRM-CTBB
synonym: UZH Swiss Center for Regenerative Medicine Cell-and Tissue Biobank
abbrev: SCRM-CTBB
IAO_0000115: The SCRM-CTBB offers state-of-the-art infrastructure and technologies (e.g. cryogenic work bench, semiautomatic cryogenic storage system, uninterrupted cooling chain) and is structured into two areas, including research and a GMP/GCP regulated therapeutic applications. Research: For pre-clinical studies, the SCRM-CTBB provides researchers guidance regarding cell and tissue cryo-preservation, comprising registration, handling, storage and distribution. In order to ensure complete traceability on samples and belonging information all processes are controlled by a Laboratory Information Management System (LIMS) and Quality Assurance (QA) system. The SCRM Biobank is designed to create database that allows connection with other biobanks nationally and internationally. This meta-data file will enable a unique scientific resource for interdisciplinary research. For every new study a contract is established describing the study and the disposition rights. Assistance in writing Biobank Agreements (BAs) and Material Transfer Agreements (MTAs) is provided. Therapeutical applications: As a new feature, apart from research, the SCRM Biobank enables the asservation and preservation of cells and tissues under GMP conditions for later therapeutic use. A special focus will be on a conceptional combination of private and public umbilical cord blood banking (hybrid banking), which allows autologous and/or allogeneic cell applications.

University of Leipzig; Saxony; Germany
type: NamedIndividual
has db xref: nlx_149130
synonym: Universitat Leipzig
synonym: University of Leipzig
synonym: Universität Leipzig

XP-CLR
type: Resource
type: NamedIndividual
has db xref: nlx_94751
synonym: XP-CLR Software
IAO_0000115: XP-CLR (Chen et al. 2010) uses allele frequency differentiation at linked loci to detect selective sweeps. Source code and documentation are available.

Tumorbank Basel Foundation
type: Resource
type: NamedIndividual
has db xref: nlx_143986
synonym: Stiftung Tumorbank Basel
IAO_0000115: Since 1995 the Tumorbank Basel Foundation (German: Stiftung Tumorbank Basel) is a non-for-profit foundation acting in cancer translation research. The purpose of the Tumorbank Basel Foundation is to support in promoting optimization of decision making process for the management of solid cancer personalized treatment modalities to the benefit of the patient. Our Aims: * Acquisition and storage of biological material and clinical data of patients suffering of solid cancer diseases in particular breast and prostate cancer. * Promoting and supporting cancer research using the acquired material and data for clinical studies and translational research. * The development of molecular tumor analyses / tools for cancer patients and the performance of the resulting diagnostic services for personalized treatment modalities. The Tumorbank Basel Foundation has acquired * Data about more than 10''000 breast cancer patients * Data comprise clinical and pathological (histology & IHC) characteristics and biochemical (continuous quantified protein expression levels) features, which are available for almost all samples as well as clinical follow-ups now available for more than 2''000 patients * The RNA expression level of 65 genes has been assessed in >800 samples by Real-Time PCR (317 retrospectively in cases with follow-up, the remaining on a routine basis, prospectively since 2004) The Tumorbank Basel Foundation is storing in Freezers at - 80 degrees C * Ca. 6''000 fresh frozen tissue samples of breast cancer patients * Ca. 9''000 particulate fractions (cytosol / membrane) of all samples analyzed * Ca. 1''000 paired non-malignant adjacent tissue material samples * More than 1''000 extracted RNA samples of good quality * Serum and plasma collection from patients has been started since 2005 All data are stored in a relational SQL data bank using an application. The Tumorbank Basel Foundation is collaborating with several pathology institutes allowing to perform studies correlating re…

D2R Server - Publishing Relational Databases on the Semantic Web
type: Resource
type: NamedIndividual
has db xref: nlx_92812
abbrev: D2R Server
IAO_0000115: D2R Server is a tool for publishing relational databases on the Semantic Web. It enables RDF and HTML browsers to navigate the content of the database, and allows applications to query the database using the SPARQL query language. Data on the Semantic Web is modeled and represented in RDF. D2R Server uses a customizable D2RQ mapping to map database content into this format, and allows the RDF data to be browsed and searched the two main access paradigms to the Semantic Web. D2R Server''s Linked Data interface makes RDF descriptions of individual resources available over the HTTP protocol. An RDF description can be retrieved simply by accessing the resource''s URI over the Web. Using a Semantic Web browser like Tabulator (slides) or Disco, you can follow links from one resource to the next, surfing the Web of Data. The SPARQL interface enables applications to search and query the database using the SPARQL query language over the SPARQL protocol. Requests from the Web are rewritten into SQL queries via the mapping. This on-the-fly translation allows publishing of RDF from large live databases and eliminates the need for replicating the data into a dedicated RDF triple store. The latest source code is available from the project''s CVS repository and can be browsed online.

PR
type: Resource
type: NamedIndividual
has db xref: nlx_92849
synonym: PRO
synonym: Protein Ontology
IAO_0000115: An ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms, orthologous isoforms, and protein complexes) ranging from the taxon-neutral to the taxon-specific. The ontology has a meta-structure encompassing three areas: proteins based on evolutionary relatedness (ProEvo); protein forms produced from a given gene locus (ProForm); and protein-containing complexes (ProComp). NOTICE: The PRO ID format has changed from PRO: to PR: (e.g. PRO:000000563 is now PR:000000563).

Eigensoft
type: Resource
type: NamedIndividual
has db xref: nlx_93059
has db xref: OMICS_07868
synonym: EIGENSOFT Software
abbrev: EIGENSOFT
IAO_0000115: EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker''s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. Source code, documentation and executables for using EIGENSOFT 3.0 on a Linux platform can be downloaded. New features of EIGENSOFT 3.0 include supporting either 32-bit or 64-bit Linux machines, a utility to merge different data sets, a utility to identify related samples (accounting for population structure), and supporting multiple file formats for EIGENSTRAT stratification correction.

Chicken Gene Nomenclature Consortium
type: Resource
type: NamedIndividual
has db xref: nlx_93177
abbrev: CGNC
IAO_0000115: International group of researchers interested in providing standardized gene nomenclature for chicken genes. A Chicken Gene Annotation Tool is available from CGNC-UK which assigns chicken nomenclature based on predicted orthology to human genes. The CGNC-US database includes CGNC-UK information and adds manually biocurated from biocurators and interested contributors. A Human Chicken Ortholog Predictions Search is available. Both resources are part of a united CGNC effort and nomenclature data is shared and co-ordinated between these two resources. They strongly encourage researchers with domain knowledge to participate in this nomenclature effort by requesting a login and providing gene nomenclature for their genes of interest. Please contact them for further information or assistance. The AGNC works in conjunction with public resources such as NCBI and Ensembl and in consultation with existing nomenclature committees, including the Chicken Gene Nomenclature Committee (CGNC). The Avian and Chicken nomenclature efforts are co-ordinated and chicken data is shared between these two groups.

LifeLink Foundation
type: Resource
type: NamedIndividual
has db xref: nlx_96590
IAO_0000115: LifeLink Foundation is a non-profit community service organization dedicated to the recovery of life-saving and life-enhancing organs and tissue for transplantation therapy. The Foundation works in a sensitive, diligent, and compassionate manner to facilitate the donation of desperately needed organs and tissues for waiting patients, support research efforts to enhance the available supply of organs and tissue for transplant patients, improve clinical outcomes of patients post transplantation and works closely with the United Network For Organ Sharing (UNOS) to support its goals. We are committed to inspiring the public to save lives through organ donation. To make organ transplant a reality, LifeLink Foundation focuses its attention in a number of areas: Immunology Laboratory, Public Education, Fundraising, Organ Recovery.

Gift of Hope Organ and Tissue Donor Network
type: Organization
type: NamedIndividual
has db xref: grid.477192.e
has db xref: ISNI: 0000 0004 0628 5713
has db xref: nlx_93206
synonym: Gift of Hope Organ & Tissue Donor Network
abbrev: Gift of Hope
IAO_0000115: Gift of Hope Organ & Tissue Donor Network is proud to serve as the federally designated not-for-profit agency that coordinates organ and tissue donation and supports families of donors in the northern three-quarters of Illinois and northwest Indiana. Since our inception in 1986, we have coordinated donations that have saved the lives of 17,000 organ transplant recipients and helped hundreds of thousands of other patients receive needed tissue transplants. As one of 58 organ procurement organizations (OPOs) that make up the nation''s organ donation system, we work with 179 hospitals in our donation service area. In managing the recovery, care and transportation of donated organs to transplant patients, we work closely with Illinois'' nine transplant centers, which operate 32 transplant programs. We also work with other transplant centers and other OPOs through the United Network for Organ Sharing (UNOS) to provide lifesaving organs for patients awaiting them. UNOS is the federally mandated registration center for organ transplant candidates in the United States. UNOS'' computer-based system matches donated organs with patients in need, in accordance with strict federal guidelines intended to ensure equitable distribution.

Spatially unbiased atlas template of the cerebellum and brainstem
type: Resource
type: NamedIndividual
has db xref: nlx_144300
synonym: A spatially unbiased atlas template of the cerebellum and brainstem
synonym: A spatially unbiased atlas template of the cerebellum and brainstem (SUIT)
synonym: A spatially unbiased atlas template of the cerebellum brainstem
synonym: A spatially unbiased atlas template of the cerebellum brainstem (SUIT)
synonym: Spatially unbiased atlas template of the cerebellum brainstem
abbrev: SUIT
IAO_0000115: High-resolution atlas template of the human cerebellum and brainstem, based on the anatomy of 20 young healthy individuals. The atlas is spatially unbiased, i.e. the location of each structure is equal to the expected location of that structure across individuals in MNI space. At the same time, the new template preserves the anatomical detail of cerebellar structures through a nonlinear atlas-generation algorithm. By using automated nonlinear normalization methods, a more accurate intersubject-alignment than current whole-brain methods can be achieved. The toolbox allows you to: * Automatically isolate cerebellar structures from the cerebral cortex based on an anatomical image * Achieve accurate anatomical normalization of cerebellar structures * Normalize functional imaging data for fMRI group analysis * Normalize focal cerebellar lesions for lesion-symptom mapping * Use Voxel-based morphometry (VBM) to determine patterns of cerebellar degeneration or growth * Use a probabilisitc atlas in SUIT space to assign locations to different cerebellar lobuli in an unbiased and informed way * Automatically define ROIs for specific cerebellar lobuli and summarize function and anatomical data * Improve normalization of the deep cerebellar nuclei using an ROI-driven normalization. The suit-toolbox requires Matlab (Version 6.5 and higher) and SPM. The newest version only supports SPM8, although it likely runs under SPM2 or 5 as well. A standalone version for the suit-toolbox is not planned. Usage of the isolation or normalization functions, however, does not require that the analysis is conducted under SPM.

Peer Review Radio
type: Resource
type: NamedIndividual
has db xref: nlx_93325
synonym: PRR
IAO_0000115: Peer Review Radio is a weekly radio show and podcast that portions the tastiest science and prepares it for public consumption. The end goal of this program is to provide an outlet where anyone and everyone can understand current scientific issues and generate their own informed opinions. In addition, Peer Review Radio promotes careers in research and science and serves as a training ground for future scientists to acquire invaluable communication skills. Peer Review Radio was established by a group of motivated graduate students with a desire to spread their love of science. By breaking down complicated concepts into bite-sized morcels, the ''Peers'' hope to spark the curiosity of their listeners with relevant, reliable information. Our producers determine content and coordinate the activities of the journalists. To ensure variety of content, graduate students are enlisted to act as advisers in their fields of expertise and direct literature research for necessary episode scripts. Then, we get together with professors, industrial scientists, post doctoral fellows and graduate students to talk about issues in science. Also, we supplement each episode with ''what if''-type questions, critiquing of science in film, profiles of alternative careers in science, book reviews and more! Our weekly radio show will air on CHUO 89.1 FM in Ottawa, Ontario, Canada starting this Fall 2010, and with each episode we hope to address another hot topic in science without frying your frontal cortex.

St. Gallen Lung Biopsy Biobank
type: Resource
type: NamedIndividual
has db xref: nlx_143987
synonym: St. Gallen Lung Biopsy Biobank - An interdisciplinary collaboration in pulmonary medicine
abbrev: SGLBB
IAO_0000115: St. Gallen Lung Biopsy Biobank is a tissue and blood sample collation (biobank) of all patients willing to give informed consent, who are undergoing bronchoscopy and/or surgical lung resection in their diagnostic pathway for any pulmonary disease. The special feature of the proposed biobank is the collection of endobronchial biopsies, blood, and molecularly defined cell populations from tumor tissue in a quality suitable for mRNA and other protein expression techniques, which is not possible by standard biobanks.

UniRef at the EBI
type: Resource
type: NamedIndividual
has db xref: nlx_93434
synonym: UniProt Non-redundant Reference
synonym: UniProt Non-redundant Reference database
synonym: UniProt NREF
synonym: UniProt Reference Clusters
synonym: UniProt Reference Clusters database
IAO_0000115: Various non-redundant databases with different sequence identity cut-offs created by clustering closely similar sequences to yield a representative subset of sequences. In the UniRef90 and UniRef50 databases no pair of sequences in the representative set has >90% or >50% mutual sequence identity. The UniRef100 database presents identical sequences and sub-fragments as a single entry with protein IDs, sequences, bibliography, and links to protein databases. The two major objectives of UniRef are: (i) to facilitate sequence merging in UniProt, and (ii) to allow faster and more informative sequence similarity searches. Although the UniProt Knowledgebase is much less redundant than UniParc, it still contains a certain level of redundancy because it is not possible to use fully automatic merging without risking merging of similar sequences from different proteins. However, such automatic procedures are extremely useful in compiling the UniRef databases to obtain complete coverage of sequence space while hiding redundant sequences (but not their descriptions) from view. A high level of redundancy results in several problems, including slow database searches and long lists of similar or identical alignments that can obscure novel matches in the output. Thus, a more even sampling of sequence space is advantageous. You may access NREF via the FTP server.

University of Lincoln; Lincoln; United Kingdom
type: Organization
type: NamedIndividual
has db xref: grid.36511.30
has db xref: ISNI:0000 0004 0420 4262
has db xref: nlx_62325
has db xref: Wikidata:Q2738646
IAO_0000115: Public research university in Lincoln, England. The University has origins that trace back to 1861, and obtained university status in 1992 and its present name and structure in 2001.

Fox Chase Cancer Center
type: Resource
type: NamedIndividual
has db xref: nlx_93591
abbrev: Fox Chase
IAO_0000115: Fox Chase Cancer Center is the region''s only hospital devoted entirely to cancer treatment, research and prevention. Our 100-bed hospital, located in Philadelphia, is consistently ranked by U.S. News and World Report among the top cancer centers in the nation. Our nationally and internationally recognized staff provides consultations and treatment recommendations for all types of adult cancer. Fox Chase Cancer Center is an independent, nonprofit institution formed in 1974 by the union of American Oncologic Hospital (one the the nation''s first cancer hospitals, established in 1904) and the Institute for Cancer Research (founded in 1927). Fox Chase was also among the first institutions to be designated a National Cancer Institute Comprehensive Cancer Center in 1974. In September 2000, the Hospital of Fox Chase Cancer Center became the nation''s first comprehensive cancer center and Pennsylvania''s first hospital to receive Magnet status for nursing excellence from the American Nurses Credentialing Center, which renewed this honor in 2004 and again in 2009, making it the first hospital in Pennsylvania to have achieved two successful Magnet renewals. The Women''s Cancer Center builds on Fox Chase''s world-renowned expertise in breast and gynecologic cancers. The Center offers women a place where they can receive coordinated, state-of-the-art care, support services, and education all under one roof.

University of Malaga; Andalusia; Spain
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100009473
has db xref: grid.10215.37
has db xref: ISNI:0000 0001 2298 7828
has db xref: nlx_20299
has db xref: Wikidata:Q958650
synonym: Universidad de M�laga
synonym: University of M�laga
abbrev: UMA
IAO_0000115: Public university ranked established in 1972. Courses taught entirely in English, related to the world of business, engineering, culture, art and Spanish society.

UNOS - United Network for Organ Sharing
type: Resource
type: NamedIndividual
has db xref: nlx_93605
synonym: United Network for Organ Sharing
abbrev: UNOS
IAO_0000115: United Network for Organ Sharing (UNOS) is the private, non-profit organization that manages the nation''s organ transplant system under contract with the federal government. UNOS is involved in many aspects of the organ transplant and donation process: * Managing the national transplant waiting list, matching donors to recipients 24 hours a day, 365 days a year. * Maintaining the database that contains all organ transplant data for every transplant event that occurs in the U.S. * Bring together members to develop policies that make the best use of the limited supply of organs and give all patients a fair chance at receiving the organ they need, regardless of age, sex, ethnicity, religion, lifestyle or financial/social status. * Monitoring every organ match to ensure organ allocation policies are followed. * Provides assistance to patients, family members and friends. * Educates transplant professionals about their important role in the donation and transplant processes. * Educating the public about the importance of organ donation. UNOS was first awarded the national Organ Procurement and Transplantation Network (OPTN) contract in 1986 by the U.S. Department of Health and Human Services. UNOS continues as the only organization ever to operate the OPTN. As part of the OPTN contract, UNOS has: * established an organ sharing system that maximizes the efficient use of deceased organs through equitable and timely allocation * established a system to collect, store, analyze and publish data pertaining to the patient waiting list, organ matching, and transplants * informed, consulted and guided persons and organizations concerned with human organ transplantation in order to increase the number of organs available for transplantation

DermAtlas.
type: Resource
type: NamedIndividual
has db xref: nlx_93671
synonym: Dermatology Image Atlas
abbrev: DermAtlas
IAO_0000115: Database of dermatology cases and browsable by diagnosis, category or body site with 12,176 images, 583 contributors and dermatology links. You may retrieve images using any diagnosis, disease category, body site, pigmentation, image contributor, patient age, image name, and/or key words. You are welcome submit images or to download images for lectures and other teaching purposes - or with permission for other uses. Additionally, you may search DermAtlas from your website. Add YOUR Link On the DermAtlas' ''' Add a Link Page you can associate your link with as many diagnoses as you like. Case submission If you have a high quality image that you would like to submit to DermAtlas, submit the requested information, and upload the image. The data and image will automatically be sent to the editors for review. You will be notified within one week of submission of images. In order for an image to be considered for inclusion into this collection, consent must be obtained from the patient or his/her legal guardian. Contributors are solely responsible for obtaining consent.

WikiDoc The Living Textbook of Medicine
type: Resource
type: NamedIndividual
has db xref: nlx_93889
synonym: WikiDoc
IAO_0000115: WikiDoc is the Original Medical Wiki / Encyclopedia. 71,700 Textbook Chapters and News Articles in English are available and anyone may edit this medical news service and textbook of medicine. Major sections include WikiDoc News: Today in Medicine, Co-Author The World''s Largest Textbook of Medicine, Community, and Care. WikiDoc is available in other languages including Espa��ol, Fran��ais, Polski, , Rom��n, , and T��rk��e.

Competence Network Heart Failure
type: Resource
type: NamedIndividual
has db xref: nlx_143991
synonym: German Competence Network Heart Failure
abbrev: CNHF
IAO_0000115: Association of physicians, scientists, academics, research institutes and self-help groups that provides and nurtures interdisciplinary cooperation between research and primary, secondary and tertiary health care. Many internationally renowned heart failure researchers and working groups live and work in Germany. Nevertheless, there is insufficient cooperation of the respective working groups and research projects in this area. In order to remain internationally competitive in the heart failure research community, excellent implementation of large scale clinical and genetic trials is indispensable. Further, deficits in the effective presentation and transfer of research findings into clinical practice need to be addressed. An adequate translation of guidelines into practical, tangible instructions can facilitate clinical practice both in primary and tertiary care fundamentally. The need for action to address the research-practice-gap is obvious.

TemplateFilter
type: Resource
type: NamedIndividual
has db xref: OMICS_00514
IAO_0000115: A software pipeline for analyzing deep sequencing maps of chromatin structure.

UCSF AIDS Specimen Bank
type: Resource
type: NamedIndividual
has db xref: nlx_93960
synonym: AIDS Specimen Bank
synonym: UCSF Specimen Bank Core
synonym: UCSF-GIVI CFAR Specimen Bank Core
abbrev: ABS
IAO_0000115: The AIDS Specimen Bank (ASB) provides repository services to cohort studies such as the Women''s Interagency HIV Study (WIHS), Primary HIV Infection Study, Staying Well Study, clinical trials performed at UCSF, and others. The majority of ASB clients are HIV investigators, but the bank also processes and stores specimens collected from some non-HIV studies. The ASB is also the Specimen Bank Core for the UCSF/GIVI Center for AIDS Research. The mission of the AIDS Specimen Bank is to provide the following: * Processing and handling of specimens * Short-term or long-term storage (includes ultra-low temperatures and liquid nitrogen) * Data management * Well-characterized specimens to qualified investigators for translational research * Consultation to investigators inquiring about specimen collection and storage * International resource for HIV research * Networking tool within the research community All body fluids����??sera, plasma, saliva, vaginal lavage, etc.����??are stored as 1-milliliter aliquots in ultra-low freezers (-70��������C). PBMCs are processed and stored in liquid nitrogen. All equipment involved with the processing of specimens (centrifuges and Coulter counter) is calibrated by trained technicians. The ASB is a participant in the Adult AIDS Clinical Trials Group PBMC Cryopreservation and Viability Panel, in which sets of processed and frozen PBMCs are sent to the Immunology Quality Assessment Program (IQA) testing lab for viability and cell counts. Our laboratory has participated in the IQA program for three years, and all samples have proven to be acceptable to their standards. The ASB is compliant with Good Laboratory Practices guidelines.

Anthony Nolan
type: Organization
type: NamedIndividual
has db xref: grid.426412.7
has db xref: ISNI: 0000 0004 0623 6380
has db xref: nlx_97115
has db xref: Wikidata: Q4773196
synonym: Anthony Nolan Trust
synonym: Anthony Nolan UK blood cancer charity
IAO_0000115: Stem cell and bone marrow register in the United Kingdom, managing and recruiting donors internationally for patients who require stem cell transplants. A database of tissue-typing results of all prospective donors is maintained. A national cord blood program consisting of both a cord blood bank and a research institute provides donated umbilical cord blood for use in clinical transplants and research. Research is conducted in immunogenetics, immunotherapy, bioinformatics (curating the World Health Organisation HLA Nomenclature database, ensuring that all new tissue types are consistently documented), and immune reconstitution.

MD Anderson Pancreas Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_94016
synonym: MD Anderson Pancreatic Cancer Study Group Human Tumor Bank and Database
synonym: MD Anderson PTB
abbrev: PTB
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented September 2, 2016. A clinical database and PTB were created in 1990 and 2000, respectively, to collect clinical information and biospecimens from patients with suspected or confirmed pancreatic cancer, other pancreatic diseases, and tumors of the duodenum, ampulla of Vater, and distal bile duct. Standard procedures for biospecimen collection and data entry were developed. The use of human tissue for research is an invaluable tool to understand the basic mechanisms of tumor biology, which will hopefully lead to the development of new therapeutic approaches to pancreatic cancer treatment. The cornerstone of any large translational research program is the development of an accurate and comprehensive tumor bank. All tumors removed in the operating room are sampled for careful pathologic study and the remainder of the tumor is promptly stored in our Pancreas Tissue Bank (PTB) to be used for research. Other samples, including blood, pancreatic juice and biopsy material, can also be utilized to identify early markers for pancreatic cancer. The molecular profile of tumors in the PTB can be linked to information in our clinical database to provide insight on the relationship between molecular events and clinical outcome. Patients may contribute to the tissue banking effort by choosing to participate in select research protocols. Protecting patient privacy is of great importance and thus, to maintain the confidentiality of health information, the PTB complies with all federal and institutional regulations governing research with human participants.

Fred Hutchinson Cancer Center
type: Organization
type: NamedIndividual
has db xref: Crossref Funder ID 100005895
has db xref: GRID grid.270240.3
has db xref: ISNI 0000 0001 2180 1622
has db xref: nlx_94018
has db xref: Wikidata Q1452369
abbrev: Fred Hutch Cancer Research Center
IAO_0000115: Fred Hutchinson Cancer Research Center and Seattle Cancer Care Alliance (SCCA) have merged to form Fred Hutchinson Cancer Center, unified adult cancer research and care center. Independent, nonprofit organization is clinically integrated part of UW Medicine and is UW Medicine’s cancer program.

The Nervous System in Action
type: Resource
type: NamedIndividual
has db xref: nlx_143992
abbrev: Nervous System in Action
IAO_0000115: The Nervous System In Action by Michael D. Mann, Ph.D. is a textbook on nervous system physiology. Available here is the web accessible version of of this textbook. An Adobe Acrobat (PDF) version is also supplied for better printing. You will need Acrobat Reader to see and print it. The textbook consists of the following: Preface (1) Neurophysiology, An Overview (2) Human Behavior (3) 1. Diffusion and Transport (4) 2. Control Systems and Homeostasis (5) 3a. Properties of Excitable Membranes: The Membrane Potential (6) 3b. Properties of Excitable Membranes: The Spike (7) 4a. Receptor Properties: Receptor Potentials and Coding (8) 4b. Sensory Receptors II (9) 5. Somesthesia--Peripheral Mechanisms (0) 6. Somesthesia--Central Mechanisms (a) 7. Vision (b) 8. Audition (c) 9. The Vestibular System (d) 10.Gustatory and Olfactory Senses (e) 11. Muscle Receptors (f) 12. Peripheral Nerves (g) 13. Synapses (h) 14. Muscle Contraction (i) 15. Reflexes (j) 16. Initiation and Control of Movement (k) 17. Activities Involving the Cerebral Hemispheres (l) 18. The Clinical Implications of Neurophysiological Concepts (m) 19. Learning and Memory Appendix: Common abbreviations (n) Glossary (o) Index (p)

Minia
type: Resource
type: NamedIndividual
has db xref: biotools:minia
has db xref: OMICS_00022
IAO_0000115: A short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.

SMD
type: Resource
type: NamedIndividual
has db xref: nlx_94141
has db xref: OMICS_00870
has db xref: r3d100010555
synonym: Stanford Microarray Database
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 17, 2021. Database to store, annotate, view, analyze and share microarray data. It provides registered users access to their own data, provides users access to public data, and tools with which to analyze those data, to any public user anywhere in the world. The GenePattern software package has been incorporated directly into SMD, providing access to many new analysis tools, as well as a plug-in architecture that allows users to directly integrate and share additional tools through SMD. This extension is available with the SMD source code that is fully and freely available to others under an Open Source license, enabling other groups to create a local installation of SMD with an enriched data analysis capability. SMD search options allow the user to Search By Experiments, Search By Datasets, or Search By Gene Names. Web services are provided using common standards, such as Simple Object Access Protocol (SOAP). This enables both local and remote researchers to connect to an installation of the database and retrieve data using pre-defined methods, without needing to resort to use of a web browser.

Brain Research Institute
type: Resource
type: NamedIndividual
has db xref: nlx_143995
synonym: Brain Research Institute UCLA
abbrev: BRI
IAO_0000115: Portal touching on all aspects of neuroscience from molecules to the mind, from the laboratory bench to the patient's bedside. Members study the normal structure and workings of the nervous system, its development, its cognitive functions, its derangement by disease and injury, and the means of its repair and protection. Projects span traditional disciplinary boundaries, as do graduate and postdoctoral training programs. Its major achievement has been to foster and improve multidisciplinary collaborations which has increasingly permitted the identification of pathogenic mechanisms and the formulation of new therapeutic approaches.

MiTCR
type: Resource
type: NamedIndividual
has db xref: OMICS_00003
synonym: MiTCR - T-cell receptor repertoire analysis software
IAO_0000115: An open source software package aimed at extraction of information on repertoire of T-cell clones from Next Generation Sequencing (NGS) data. It is designed with the knowledge of the critical challenges arising in everyday processing of immunological data.

Kentucky Organ Donor Affiliates (KODA)
type: Resource
type: NamedIndividual
has db xref: nlx_94502
synonym: Kentucky Organ Donor Affiliates
synonym: KODA - Kentucky Organ Donor Affiliates
abbrev: KODA
IAO_0000115: Kentucky Organ Donor Affiliates (KODA) is dedicated to saving lives through organ and tissue donation and transplantation. An independent, non-profit organ and tissue procurement agency, KODA was formed to establish a statewide educational and procurement network. Its services include evaluation of organ/tissue donor suitability; coordination of organ recovery; organ placement; tissue recovery; family support and aftercare; hospital staff education; public education. Like all OPOs, KODA is federally designated by the U.S. Department of Health and Human Services (HHS). As a licensed tissue bank, KODA Tissue Operations is regulated by the Food & Drug Administration (FDA). KODA is a member of the United Network of Organ Sharing (UNOS), a government-chartered nationwide network operating the Organ Procurement and Transplantation Network (OPTN) under federal contract with the U.S. Department of Health and Human Services (HHS). Founded in 1987 (Originated as a combination of existing organ and tissue procurement programs at the University of Kentucky and the University of Louisville), it now serves 114 counties in Kentucky, 4 counties in southern Indianan and 2 counties in western West Virginia. (Six northern Kentucky counties are served by LifeCenter in Cincinnati). Its major clients are 112 hospitals, 3 transplant centers and a multicultural population of 4 million people.

German Biobank Registry
type: Resource
type: NamedIndividual
has db xref: nlx_143997
IAO_0000115: German biobank registry containing names, addresses of the contact persons, web links and basic information of the biobanks. The Registry is available in German and English and is organized by content and by region. The goal is to create public awareness and understanding of the objectives and functions of biobanks, and to arrange collaborations between scientists. The registry cooperates with the European initiative Biobanking and Biomolecular Resources Research Infrastructure (BBMRI). Currently the first phase is implemented as an open access registry. A further expansion is planned with the possibility of online data entry and correction. The German Biobank Registry should help scientists and researchers, but also the interested public as an information gateway to serve. The functions of the registry are: * providing a publicly available registry of the medically relevant biobanks in Germany * improving the national and international visibility of German biobanks; * provision of partners for cooperation; * networking among biobanks; * promoting the exchange of information and of samples between research groups and institutions (hospitals, research institutes and pharmaceutical and biotech companies) operating biobanks; * improved use of existing resources; * promotion of transparency and understanding of the objectives and functions of biobanks in the general public; * Establishing a community to develop common solutions for legal and regulatory issues and thus avoiding redundant expenses for the individual researcher; * provide a planning basis for selective and efficient investments in new biobanks and the expansion of the existing infrastructure. The TMF is cooperating with the European BBMRI project to improve the biobank infrastructure in Europe. Data collection for the national registry is consistent with the survey of BBMRI project. You have to sample the data of your biobank only once and your biobank will be visible nationally and internationally. On the…

Tennessee Donor Services
type: Resource
type: NamedIndividual
has db xref: nlx_95112
abbrev: TDS
IAO_0000115: Tennessee Donor Services (TDS) is a nonprofit, independent organization authorized by the Federal Government to accept anatomical gifts for transplantation and research. Its mission is to support families in our communities who have sustained the loss of a loved one by providing an opportunity for organ, eye and tissue donation and by facilitating the recovery and transplantation of these gifts to help others in need. In our area (TN & VA), over 4,600 people now wait for an organ transplant, (heart, liver, lungs, kidneys, intestine or pancreas). Annually, our service area has approximately 300 people who donate one or more organs upon death and over 900 who donate corneas and/or tissues annually. The need for transplants far exceeds the number of donations in the area covered by TDS, and across the nation. Currently, in the United States, more than 108,000 people wait for an organ transplant. One third of them will die waiting for a transplant. TDS'' designated service area includes 84 counties in Tennessee, 10 counties in Virginia, 3 counties in Georgia and 1 county in Kentucky.

TMF
type: Resource
type: NamedIndividual
has db xref: nlx_143998
synonym: Technology Methods and Infrastructure for Networked Medical Research
synonym: Technology Methods Infrastructure for Networked Medical Research
synonym: TMF - Technology Methods and Infrastructure for Networked Medical Research
IAO_0000115: As an umbrella organization for medical research networks, the TMF is responsible for improving the organization and infrastructure of medical research in networked structures. It supports researchers at the various locations in jointly identifying and solving problems of an organizational, legal and technical nature that are often not associated with the particular clinical problem or research focus. The network not only focuses on legal and ethical frameworks for networked medical research but also on the development of IT infrastructure, quality management activities for science-initiated trials and questions on the intermeshing of research and patient care. Under the umbrella organization of the TMF, expert opinions, studies, concepts, requirements specifications, services and tools are created. The products of the cooperation within the TMF are available to the research community. The aims of joint work in the TMF are: * Improvement of medical research in terms of quality, organization and cooperation * Solution of questions spanning networked medical research, e.g. on the collection, processing and exchange of research data * Clarification of the legal and ethical foundations for performing medical research * Issues of quality assurance and quality management * Development and extension of efficient IT infrastructures and their implementation in cross-institutional networked structures * Realization of cross-location solutions * Contributions to sustainable and efficient health research by means of the improved transfer of research findings to patient care

BBMRI Wiki
type: Resource
type: NamedIndividual
has db xref: nlx_143999
synonym: BBMRI Wiki: For a global biomedical research
synonym: Biobanking and Biomolecular Resources Research Infrastructure Wiki
synonym: Biobanking Biomolecular Resources Research Infrastructure Wiki
IAO_0000115: The BBMRI Wiki is intended to help establish a standard vocabulary within the European BBMRI (Biobanking and Biomolecular Resources Research Infrastructure) project. This Wiki also facilitates the definition and updating of new terms as well as the Minimum Information About BIobank data Sharing: MIABIS. MIABIS represents the minimum information required to enable the exchange of biological samples and data between biobanks.

M-pick
type: Resource
type: NamedIndividual
has db xref: OMICS_01447
synonym: M-pick: a modularity-based clustering method for OTU picking
IAO_0000115: A modularity-based clustering software for Operational Taxonomic Unit (OTU) picking of 16S rRNA sequences. The algorithm does not require a predetermined cut-off level, and our simulation studies suggest that it is superior to existing methods that require specified distance or variance levels to define OTUs.

University of Manchester; Manchester; United Kingdom
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:501100000770
has db xref: grid.5379.8
has db xref: ISNI:121662407
has db xref: nlx_74265
has db xref: Wikidata:Q230899
synonym: University of Manchester
IAO_0000115: Public research university in Manchester, England, formed in 2004 by merger of University of Manchester Institute of Science and Technology and Victoria University of Manchester. Second largest university in United Kingdom by enrollment.

Bio X Cell
type: Organization
type: NamedIndividual
has db xref: nlx_152318
has db xref: SCR_019248
IAO_0000115: Commercial supplier and developer of in vivo antibodies. Provides antibodies and antibody production services.

UC Davis Center for Childrens Environmental Health
type: Resource
type: NamedIndividual
has db xref: nif-0000-02124
synonym: Center for Children''s Environmental Health
synonym: Center for Children''s Environmental Health and Disease Prevention
synonym: UC Davis School of Vet Med: Center for Children''s Environmental Health
abbrev: CCEH
IAO_0000115: The Center for Children''s Environmental Health and Disease Prevention is a multi-disciplinary collaborative research organization established to examine how toxic chemicals may influence the development of autism in children. The Center''s goal is to contribute knowledge about autism that will lead to new strategies for the prevention and treatment of this mysterious condition. Parents and health professionals have raised concerns about how environmental factors such as pesticides, a variety of chemicals, or even some ingredients included in vaccines may effect the development of the disorder. We are the first center to examine the roles of a wide range of toxic chemicals, genetic predisposition, and the interplay between these two in altering brain development during early life and leading to abnormal social behavior in children. Scientists in the CCEH study the effects of the environment on children''s health, with a particular focus on autism. Researchers come from all fields including molecular biology, medicine, nutrition, psychology, animal behavior, and genetics. The Center''s research is guided by an Advisory Board with representatives including parents, activists, non-profits, government agencies, and concerned citizens. This Center is one of several children''s centers throughout the nation funded by the U.S. EPA and NIEHS.

CARMA
type: Resource
type: NamedIndividual
has db xref: OMICS_01451
synonym: CARMA - Characterizing Short Read Metagenomes
IAO_0000115: A software pipeline for characterizing the taxonomic composition and genetic diversity of short-read metagenomes. The software was originally designed for the analysis of environmental metagenomes obtained by the ultra-fast 454 pyrosequencing system.

UC Davis Biorepository
type: Resource
type: NamedIndividual
has db xref: nlx_95804
synonym: UC Davis Cancer Center Biorespository
abbrev: UC Davis Biorespository
IAO_0000115: The mission of the Cancer Center Biorespository is to provide high quality, well-characterized cancer-related human tissue specimens and biological materials to collaborators. The specific objectives of the shared resource are: * The procurement, preparation, and preservation of malignant, benign, and normal human specimens in a centralized repository * To provide high quality annotated data (pathological and clinical) using a secure and interactive database system * To facilitate compliance with all mandated regulatory processes (IRB, HIPAA, SRC) thereby promoting ethical research by UC Davis researchers * To provide pathologic consultation to investigators using human specimens for scientific correlation * To efficiently prioritize, disperse, and track specimens via a rapid and standardized approval and monitoring process * To provide TMA consultation and services for cancer center investigators and their collaborators

splitneuron
type: Resource
type: NamedIndividual
has db xref: nlx_95900
synonym: splitneuron library
IAO_0000115: A database-based neuron simulation tool. An innovative approach to large-scale, biologically plausible, neural-network simulation library. Based on data structures and methods directly coded into database, information flow implying separation of data representing neurons, conceived to share load on multiple machines and calibrating operational load on each machine.

Onco Wiki
type: Resource
type: NamedIndividual
has db xref: nlx_95941
synonym: OncoWiki
IAO_0000115: A free repository for oncology information, chemotherapy protocols, and cancer treatment regimens. It is meant for Healthcare providers working in the field of Oncology.

SLIQ
type: Resource
type: NamedIndividual
has db xref: biotools:sliq
has db xref: OMICS_00048
synonym: Simple linear inequalities
synonym: SLiQ: Simple linear inequalities based Mate-Pair reads filtering and scaffolding
IAO_0000115: Software for simple linear inequalities based Mate-Pair reads filtering and scaffolding. A set of simple linear inequalities (SLIQ) derived from the geometry of contigs on the line that can be used to predict the relative positions and orientations of contigs from individual mate pair reads and thus produce a contig digraph. The SLIQ inequalities can also filter out unreliable mate pairs and can be used as a pre-processing step for any scaffolding algorithm. This tool filters mate pairs and then produces a Directed Contig Graph (contig diGraph). Also provided is a Naive scaffolder that can then produce scaffolds out of the contig diGraph.

MD Anderson Gynecologic Cancer Tissue Bank
type: Resource
type: NamedIndividual
has db xref: nlx_96124
synonym: MD Anderson Cancer Center Gynecologic Cancer Tissue Bank
synonym: MD Anderson Cancer Center Gynecologic Cancer Translational Research Tissue Bank
synonym: Multidisciplinary Gynecologic Cancer Translational Research Tissue Bank
IAO_0000115: The purpose of the Multidisciplinary Gynecologic Cancer Translational Research Tissue Bank is to provide investigators with primary human tissue for research projects relating to gynecologic cancer. Priority for samples is given to the MD Anderson scientific community. This tissue bank handles the consent, collection, processing, storage and distribution of primary gynecologic tumor samples as well as ascites, blood and urine of gynecologic cancer patients.

Alamo Tissue Service, Ltd.
type: Resource
type: NamedIndividual
has db xref: nlx_96261
synonym: Alamo Tissue Service
abbrev: ATS
IAO_0000115: Alamo Tissue Service, headquartered in San Antonio, Texas, is a distributor of high quality tissue allografts to physicians, hospitals, surgical clinics and tissue banks. We are a licensed tissue bank and our quality assurance program meets both the Federal Food & Drug Administration (FDA) regulations and American Association of Tissue Bank (AATB) Standards. A list of allografts processed from donated human tissue include: * Fresh frozen ligaments, tendons, and traditional grafts. * Freeze-dried (lyophilized) tissue, cancellous, cortical, femoral shaft, cloward dowel, tricortical block, tibial shaft, unicortical block, fibula section, femoral ring, patella tricortical, radius section, costal cartilage, fascia, femoral head. Alamo Tissue Service is dedicated to providing the highest quality tissue available and our ability to network with the finest accredited Tissue Banks in the United States allows us to help you with those hard to find specialty grafts. Alamo Tissue is available 24 hours a day through our toll-free or local telephone numbers. We look forward to working with you and your facility. Alamo Tissue Service would like to thank all donor families during their time of grief for remembering the needs of others.

DNAPlotter
type: Resource
type: NamedIndividual
has db xref: nlx_96278
has db xref: OMICS_00906
synonym: DNAPlotter: circular and linear interactive genome visualization
IAO_0000115: Software application used to generate images of circular and linear DNA maps to display regions and features of interest. The images can be inserted into a document or printed out directly. As this uses Artemis it can read in the common file formats EMBL, GenBank and GFF3.

Medical University of Vienna; Vienna; Austria
type: NamedIndividual
has db xref: nlx_144016
synonym: Medical University of Vienna
synonym: Medical University Vienna
synonym: Medizinische Universitat Wien
synonym: Medizinische Universität Wien
abbrev: MedUni Vienna

Wikiversity School of Medicine
type: Resource
type: NamedIndividual
has db xref: nlx_96772
synonym: Wikiversity - School:Medicine
IAO_0000115: The Wikiversity School of Medicine is a free online educational resource for the study of medicine. It is a member of the Faculty of Life Sciences and aims to maximize collaboration with other schools within the faculty and elsewhere. Prospective students may study medicine at Wikiversity by registering with the site and joining the school. Students may study via the proposed curriculum pathway, by picking and choosing modules or lessons from the different departments or by joining the school in creating lessons. The school''s medical course is currently divided into pre-clinical and clinical sets of modules. Access to these modules is via the school curriculum. This resource is available in other languages including Deutsch, Espa��ol, Fran��ais, Italiano, Portugu��s, and .

AmphoraNet
type: Resource
type: NamedIndividual
has db xref: biotools:amphoranet
has db xref: OMICS_01450
IAO_0000115: Webserver implementation of the AMPHORA2 workflow for phylogenetic analysis of metagenomic shotgun sequencing data. It is capable of assigning a probability-weighted taxonomic group for each phylogenetic marker gene found in the input metagenomic sample.

University of Ioannina; Ioannina; Greece
type: Organization
type: NamedIndividual
has db xref: grid.9594.1
has db xref: ISNI:0000 0001 2108 7481
has db xref: nlx_158516
has db xref: Wikidata:Q1229924
synonym: Panepistimio Ioanninon
synonym: University of Ioannina
abbrev: UOI
IAO_0000115: University was founded in 1964, as a charter of the Aristotle University of Thessaloniki and became an independent university in 1970.

University of Iowa; Iowa; USA
type: Organization
type: NamedIndividual
has db xref: Crossref funder ID:100008893
has db xref: grid.214572.7
has db xref: ISNI:0000 0004 1936 8294
has db xref: nlx_52860
has db xref: Wikidata:Q45133494
synonym: University of Iowa
abbrev: UI
IAO_0000115: Public research university in Iowa City, Iowa. Founded in 1847, it is the oldest and the second-largest university in the state.

Gene Expression Omnibus (GEO)
type: Resource
type: NamedIndividual
has db xref: nif-0000-00142
has db xref: nlx_96903
has db xref: OMICS_01030
has db xref: r3d100010283
has db xref: SCR_007303
synonym: Entrez GEO DataSets
synonym: Gene Expression Data Sets
synonym: Gene Expression Omnibus
synonym: Gene Expression Omnibus DataSets
synonym: GEO
synonym: GEO DataSets
synonym: NCBI GEO DataSets
IAO_0000115: Functional genomics data repository supporting MIAME-compliant data submissions. Includes microarray-based experiments measuring the abundance of mRNA, genomic DNA, and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. Array- and sequence-based data are accepted. Collection of curated gene expression DataSets, as well as original Series and Platform records. The database can be searched using keywords, organism, DataSet type and authors. DataSet records contain additional resources including cluster tools and differential expression queries.

Competence Network on Parkinson's Disease
type: Resource
type: NamedIndividual
has db xref: nlx_144005
synonym: Kompetenznetz Parkinson
IAO_0000115: A medical network comprised of university clinics, special clinics, and special practices working together to collect data, gene samples, and execute clinical trials in order to bring about diagnoses and therapy methods. Research projects are done in cure research, diagnostic and therapeutic research. The care network includes university clinics, town clinics, special clinics for Parkinson's disease, specialists, and general practitioners.

NeuroBiobank Munich
type: Resource
type: NamedIndividual
has db xref: nlx_144006
synonym: ZNP Biobank
abbrev: NBM
IAO_0000115: A brain bank which collects brain tissue from patients who died from various neurological and psychiatric diseases. These tissues are available for biochemical, molecular biological, and other work groups with the aim of supporting research on the pathogenesis, diagnosis, and therapy of these diseases. Collected brains are clinically and neuropathologically well-characterized. The collection and distribution of brain tissue samples is an ongoing process. NeuroBiobank Munich offers help with the organization and implementation of autopsies as well as with the neuropathologic diagnostics. The thematic emphasis of the NeuroBiobank Munich is Parkinson's disease and demential degenerative disorders such as Alzheimer's disease or Creutzfeldt-Jakob disease. NeuroBiobank Munich coordinates the German national brain tissue bank (BrainNet) and the European brain tissue bank (BrainNet Europe).

Neurodegeneration Research Wiki
type: Resource
type: NamedIndividual
has db xref: nlx_98402
IAO_0000115: A wiki which provides information on neurodegenerative diseases to caregivers, students, and researchers.

Short Time-series Expression Miner (STEM)
type: Resource
type: NamedIndividual
has db xref: nlx_97053
synonym: Short Time-series Expression Miner
abbrev: STEM
IAO_0000115: The Short Time-series Expression Miner (STEM) is a Java program for clustering, comparing, and visualizing short time series gene expression data from microarray experiments (~8 time points or fewer). STEM allows researchers to identify significant temporal expression profiles and the genes associated with these profiles and to compare the behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology (GO) database supporting GO category gene enrichment analyses for sets of genes having the same temporal expression pattern. STEM also supports the ability to easily determine and visualize the behavior of genes belonging to a given GO category or user defined gene set, identifying which temporal expression profiles were enriched for these genes. (Note: While STEM is designed primarily to analyze data from short time course experiments it can be used to analyze data from any small set of experiments which can naturally be ordered sequentially including dose response experiments.) Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Brain-Net
type: Resource
type: NamedIndividual
has db xref: nlx_144007
synonym: BrainNet
synonym: BrainNet Germany
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 28,2022. A network of several university centers in Germany that classifies neurological and psychiatric disorders neuropathologically and collects and provides brain tissue for research. The aim and task of the Brain-Net are: the collection of clinically and neuropathologically well-characterized brain tissue samples; the standardization of neuropathological diagnoses according to internationally accepted criteria; and providing a basis for future research projects using genetic, epidemiological, biometric and other issues to neurological and psychiatric disorders.

Living Bank
type: Resource
type: NamedIndividual
has db xref: nlx_144008
synonym: The Living Bank
IAO_0000115: Nationwide organ and tissue donor registry that is a private, non-profit organization dedicated to the enhancement of organ and tissue donation. They educate the community about the urgent need for donors so no one dies or suffers for lack of donation, honor donors and support organ recipients, living donors and their families. They are cognizant of the many challenges ahead before the day comes when no one will die because a donor organ was not available at the time of need. The Board and Staff of The Living Bank dedicate their efforts to increase the number of registered-informed donors. The programs and services of The Living Bank are: # The Living Donor Bank Program advocates and supports living donors before, during and after the donation process. # Travel Stipend/Donor Support Program assists living donors in arranging transportation and provides stipends if they must travel to donate. # Donor Education Program educates the public regarding the donation and use of organs and tissues and provide donor cards.

Neurologic AIDS Research Consortium
type: Resource
type: NamedIndividual
has db xref: nlx_144010
abbrev: NARC
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. The Neurologic AIDS Research Consortium (NARC) is supported by the National Institutes of Health to design and carry out clinical trials to improve the therapy for HIV induced neurologic disease, and neurologic conditions associated with the AIDS virus. This consortium was established in 1993 when the NARC grant submitted by David B. Clifford, M.D. of Washington University School of Medicine was funded by the National Institute of Neurologic Disorders and Stroke (NINDS) to establish the consortium. Since that time the grant has supported studies of the natural history of neurologic performance in advanced AIDS, treatment of HIV associated peripheral neuropathy, progressive multifocal leukoencephalopathy, and cytomegalovirus.

UPARSE
type: Resource
type: NamedIndividual
has db xref: OMICS_01449
IAO_0000115: An Operational Taxonomic Unit (OTU) clustering software for 16S and other marker genes. Highly accurate OTU sequences and improved diversity measures.

TDTPOWER
type: Resource
type: NamedIndividual
has db xref: nlx_154678
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5th,2023. Software application that calculates the sample size required for obtaining a prescribed power against a specified alternative for TDT. (entry from Genetic Analysis Software)

Duke University Kathleen Price Bryan Brain Bank
type: Resource
type: NamedIndividual
has db xref: nlx_144011
synonym: Bryan Brain Bank
synonym: DU Brain Bank
synonym: Kathleen Price Bryan Brain Bank
IAO_0000115: A research repository of human brains with neurological disorders and normal controls, recruited through the Autopsy and Brain Donation Program coordinator. The Kathleen Price Bryan Brain Bank contains brains from patients with Alzheimer's disease, Parkinson's disease, Amyotrophic Lateral Sclerosis, Huntington's disease, Muscular Dystrophy, and other neurological and dementing disorders. The brain tissue is subjected to a detailed neuropathological evaluation and then stored as fixed and frozen hemispheres, paraffin blocks and histological slides. After receipt of an IRB approved request, tissue is supplied to investigators at Duke University, major medical centers and pharmaceutical companies across the United States and worldwide.

Fairfax Cryobank
type: Resource
type: NamedIndividual
has db xref: nlx_97877
abbrev: Fairfax
IAO_0000115: For over 20 years Fairfax Cryobank has provided the highest quality donor sperm that has led to the creation of many happy healthy families. We provide the caring and sensitive support you need, the high quality donor sperm you require, and are accredited by the AATB (American Association of Tissue Banks) and fully compliant with FDA regulations governing reproductive tissue banks. Fairfax Cryobank offers a large selection of high quality donors; only 1 in 200 applicants make it through our rigorous screening process to become donors. We perform the most extensive genetic and infectious disease testing of all sperm banks. Fairfax Cryobank is dedicated to supplying updated verified and accurate medical and personal information on our donors. We have a caring, sensitive and knowledgeable Client Services Team ready to assist you in your choices. Fairfax Cryobank provides a variety of services that will support your process of selecting your perfect donor match including photo matching and a clear and user friendly donor search. We appreciate the importance of finding the right match, the total package, and so we offer incentives and specials that allow you to purchase donor sperm and accompanying products at reduced cost. We have a long-standing reputation of excellence with over two decades of satisfied physicians and patients. Trust, credibility, and quality are the basis of our success.

Neurogrid
type: Resource
type: NamedIndividual
has db xref: nlx_97879
IAO_0000115: A specialized hardware platform that will perform cortex-scale emulations while offering software-like flexibility. With sixteen 12x14 sq-mm chips (Neurocores) assembled on a 6.5x7.5 sq-in circuit board that can model a slab of cortex with up to 16x256x256 neurons - over a million! The chips are interconnected in a binary tree by 80M spike/sec links. An on-chip RAM (in each Neurocore) and an off-chip RAM (on a daughterboard, not shown) softwire vertical and horizontcal cortical connections, respectively. It provides an affordable option for brain simulations that uses analog computation to emulate ion-channel activity and uses digital communication to softwire synaptic connections. These technologies impose different constraints, because they operate in parallel and in serial, respectively. Analog computation constrains the number of distinct ion-channel populations that can be simulatedunlike digital computation, which simply takes longer to run bigger simulations. Digital communication constrains the number of synaptic connections that can be activated per secondunlike analog communication, which simply sums additional inputs onto the same wire. Working within these constraints, Neurogrid achieves its goal of simulating multiple cortical areas in real-time by making judicious choices.

Joseph and Kathleen Bryan Alzheimer's Disease Research Center
type: Resource
type: NamedIndividual
has db xref: nlx_144012
synonym: Bryan ADRC
synonym: Bryan Alzheimer's Disease Research Center
synonym: Joseph & Kathleen Bryan Alzheimer's Disease Research Center
IAO_0000115: An Alzheimer's disease center (ADC) that offers support services for families caring for persons with memory disorders, community outreach and education programs, in addition to its clinical and basic research activities. Information on current scientific and clinical findings is offered to the general public, medical and scientific community. An important emphasis of the Bryan ADRC is to advance basic medical discovery concerning AD and related dementias. This basic science mission is facilitated through the DNA cell repository located in the Institute of Genome Sciences and Policy (IGSP) and the Bryan ADRC brain donation program of the Kathleen Price Bryan Brain Bank. These affiliated Bryan ADRC programs provide a source of fresh brain tissue.

SMART
type: Resource
type: NamedIndividual
has db xref: biotools:smart
has db xref: nif-0000-03471
synonym: Simple Modular Architecture Research Tool
IAO_0000115: Software tool for identification and annotation of genetically mobile domains and analysis of domain architectures.

Lifeline of Ohio
type: Resource
type: NamedIndividual
has db xref: nlx_98017
abbrev: LOOP
IAO_0000115: An independent, non-profit organization, Lifeline of Ohio (LOOP), promotes and coordinates the donation of human organs and tissue for transplantation. Its mission is to educate and empower central and southeastern Ohioans about organ and tissue donation while also facilitating the donation process. Lifeline of Ohio, a Donate Life Organization, has been approved by the Centers for Medicare and Medicaid Services (CMS) as the designated organ procurement organization (OPO) serving 37 Ohio counties along with Wood and Hancock counties in West Virginia. Accredited by both the Association of Organ Procurement Organizations (AOPO) and the American Association of Tissue Banks (AATB), Lifeline of Ohio provides services to 70 hospitals and the communities they serve through its procurement and tissue coordinators, and other professional staff.

University of Pittsburgh Brain Tissue Donation Program
type: Resource
type: NamedIndividual
has db xref: nlx_144013
synonym: Conte Center Brain Tissue Donation Program
synonym: Conte Center for the Neuroscience of Mental Disorders Brain Tissue Donation Program
synonym: University of Pittsburgh Medical Center Brain Tissue Donation Program
synonym: UPMC Center for the Neuroscience of Mental Disorders and Translational Neuroscience Program Brain Tissue Donation Program
synonym: UPMC TNP Brain Tissue Donation Program
abbrev: CCNMD Brain Tissue Donation Program
abbrev: UPMC Brain Tissue Donation Program
IAO_0000115: THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 19,2024. Brain tissue donation is a valuable contribution to mental health research. It enables scientists to investigate how the normal brain works, and how the brain is disturbed when it is affected by schizophrenia, depression, bipolar (manic depressive) disease or other related disorders. The Department of Psychiatry at the University of Pittsburgh has established a brain tissue bank to which brain tissue can be donated at no expense. The gift of brain tissue enables scientists to conduct research designed to understand causes, to develop new treatments, and ultimately to find cures for diseases that affect the brain. Brain tissue donation is a gift that makes it possible for researchers to study various types of mental disorders. Donations of brain tissue from individuals without these disorders are also needed to establish comparisons with brain samples from individuals who have these disorders. Any legally competent adult or guardian may indicate during life their interest in donating brain tissue after death. Next-of-kin either of healthy individuals or of those with psychiatric disorders may give consent to donate brain tissue following the death of a loved one. Brain tissue is removed during autopsy at a morgue or hospital and is transported to the University of Pittsburgh Medical Center for examination and study.

Medical University of Vienna Institute of Neurology
type: Organization
type: NamedIndividual
has db xref: nlx_144015
synonym: Vienna Brain Bank
synonym: Vienna Institute of Neurology
abbrev: MedUni Vienna IN
IAO_0000115: The (Clinical) Institute of Neurology (IN) of the Medical University Vienna was founded in 1882 by Heinrich Obersteiner. It is the oldest institution embracing the multidisciplinarity of neurosciences and has served as model for the establishment of similarly designed institutions in many countries. The original location of the then Neurological Institute in Vienna was at Schwarzspanierstrasse. Since 1993, IN is located in the Vienna General Hospital in top-class laboratory facilities. IN is committed to its proud tradition as Obersteiner Institute and to a promising future of a nationally and internationally leading institution in the clinical neurosciences. Our work aims to translate the understanding of nervous diseases to the development of novel therapeutics and diagnostics. IN' '''s tasks include diagnostic patient service, research and graduate / postgraduate teaching in neuropathology, neurochemistry, and neuro-molecular biology in an integrated way. Neuropathology is a recognized medical specialty in Austria. It analyzes structural changes of nervous tissues in disease. Diagnostic neuropathology makes use of most modern morphological techniques applied to diseased central, peripheral and vegetative nervous tissues and fluids, and muscle. Neuropathological diagnoses are a basis for disease classification and rational therapies. Neurodegenerative disorders, in particular prion diseases, virus diseases affecting the nervous system, and brain tumors (neuro-oncology) are research priorities. In the highly publicized area of prion diseases, IN has developed into a national and international center of excellence and expertise that leads several European, EU-funded networks in prion research. As an indispensable asset, the IN possesses a large brain bank that has systematically collected neuropathological specimens since 1948. Most samples are fixed and paraffin-embedded tissue only, but in a part of neurosurgical, nerve and muscle biopsies and autopsies, also fres…

OpenNeuro
type: Resource
type: NamedIndividual
has db xref: DOI:10.17616/R33047
has db xref: DOI:10.18112
has db xref: DOI:10.25504/FAIRsharing.s1r9bw
has db xref: nlx_144048
has db xref: r3d100010924
synonym: Open fMRI
synonym: OpenfMRI
IAO_0000115: Open platform for analyzing and sharing neuroimaging data from human brain imaging research studies. Brain Imaging Data Structure ( BIDS) compliant database. Formerly known as OpenfMRI. Data archives to hold magnetic resonance imaging data. Platform for sharing MRI, MEG, EEG, iEEG, and ECoG data.

FlyAtlas: the Drosophila gene expression atlas
type: Resource
type: NamedIndividual
has db xref: nlx_98284
abbrev: FlyAtlas
IAO_0000115: FlyAtlas gives you a quick answer to the question: where is my gene of interest expressed/enriched in the adult fly? For each gene and tissue, you''re given the mRNA SIGNAL (how abundant the mRNA is), the mRNA ENRICHMENT (compared to whole flies), and the Affymetrix PRESENT CALL (out of 4 arrays, how many times it was detectably expressed). The dataset so far comprises 44 Affymetrix Dros2 expression arrays, each mapping the expression of 18770 transcripts - corresponding to the vast majority of known Drosophila genes. The dataset thus contains over 822800 separate datapoints. This website is intended to make the data easily accessible and comprehensible to mere mortals. FlyAtlas provides the most comprehensive view yet of expression in multiple tissues of Drosophila melanogaster. Meta-analysis of the data shows that a significant fraction of the genome is expressed with great tissue specificity in the adult, demonstrating the need for the functional genomic community to embrace a wide range of functional phenotypes. Well-known developmental genes are often reused in surprising tissues in the adult, suggesting new functions. The homologs of many human genetic disease loci show selective expression in the Drosophila tissues analogous to the affected human tissues, providing a useful filter for potential candidate genes. Additionally, the contributions of each tissue to the whole-fly array signal can be calculated, demonstrating the limitations of whole-organism approaches to functional genomics and allowing modeling of a simple tissue fractionation procedure that should improve detection of weak or tissue-specific signals.